New or Seldom Used Terms

This page is a collection of terminology that is new, seldom used, or of current interest in the life sciences, medicine, information technology, and other technical disciplines. It is maintained by Dr. Feistner, a scientist, professional English <> German translator, and sole proprietor of ALSC. At the same time, this page also reflects, in part, Dr. Feistner's scientific interests.

New entries will be made as the workload and other commitments allow. Although links are validated each time a new entry is made, it is impossible to guarantee that they will work in the future because Internet files are frequently moved (in which case you might want to try the server's search function) or deleted. However, enough context is always given that this page should remain useful even without external links. Happy browsing!

If you have any questions or comments, including broken links, please don't hesitate to contact me.

Copyright 2000-2002 Gottfried Feistner - Please do not plagiarize.

B. Hao et al.: A New UAG-Encoded Residue in the Structure of a Methanogen Methyltransferase Science 296: 1462 - 1466 (2002)
"Genes encoding methanogenic methylamine methyltransferases all contain an in-frame amber (UAG) codon that is read through during translation. We have identified the UAG-encoded residue in a 1.55 angstrom resolution structure of the Methanosarcina barkeri monomethylamine methyltransferase (MtmB). This structure reveals a homohexamer comprised of individual subunits with a TIM barrel fold. The electron density for the UAG-encoded residue is distinct from any of the 21 natural amino acids. Instead it appears consistent with a lysine in amide-linkage to (4R,5R)-4-substituted-pyrroline-5-carboxylate. We suggest that this amino acid be named L-pyrrolysine."

The Dictionary of Cell and Molecular Biology:
"One of the three termination codons. Its sequence is UAG. See also ochre codon, opal codon."

Where does the name come from? The following acount was found on the web site of the Biology Learning Center at the University of Arizona:
"The work of the ribosome ends when it reaches one of the three stop codons that are used: UAG, UAA or UGA. The stop codons were originally identified by mutations in bacteriophage T4. The first one identified was UAG and was called the amber codon.
I like to maintain the history of the amber codon. Here's the story. In Benzer's lab at Caltech the search was on for a mutation that would allow a certain kind of phage mutant to grow. Seymour said that whoever identified the mutation, he would name it after him (in some versions of the story, it would be named after the discoverer's mother). The graduate student who isolated the mutation was a young man named Harris Bernstein. The name "Bernstein" in German means "amber". And so the UAG codon, known as a nonsense codon (later known as a stop codon), was named the amber codon. Later, the other two stop codons were called ochre (UAA) and opal (UGA) (sometimes called, "umber") to maintain the color metaphor."

Julie Clayton: Dengue strains vaccine development. 10th International Congress on Infectious Diseases, March 13, 2002
"Chow's team are now placing their bets for the best vaccine candidate on a more conserved protein of the virus, the protease known as NS3, which normally splices the virus's initial polyprotein chain. They are now testing this as a construct in a DNA vaccine, together with a second target, NS1, for its ability to protect mice against viral challenge.
His concern is that the tetravalent vaccines currently in clinical trials will be inadequate. 'A vaccine that works against certain strains may not be useful against new strains that may emerge in the future. From the molecular work they are emerging very quickly,' he said. In addition, the team has conducted an epidemiological study on healthy student volunteers attending the National University of Singapore.
They found that as many as 40% of the group have antibodies to dengue viruses, suggesting some past exposure to the virus. The students were unaware of ever having been infected. But in only half of these cases were the antibodies detected by ELISA tests able to neutralize serotype 2 virus.
This means that even after natural exposure, many people are still vulnerable to a second infection. Furthermore, those with non-neutralizing antibodies face the risk of even worse disease, through a phenomenon known as antibody enhancement in which antibodies bind to the virus, and enhance its uptake into monocytes through Fc receptors.
'We need a tetravalent vaccine, given early in life. But the bad news is that there is not going to be a vaccine anytime soon,' concluded Chow."

Seth Schiesel and Simon Romero: WorldCom: Out of Obscurity to Under Inquiry. The New York Times, March 13, 2002
"With the S.E.C. adopting its usual no-comment stance and WorldCom executives saying they have nothing to hide, it was left for analysts yesterday to infer the reasons for the inquiry. People who have had experience with S.E.C. practice said yesterday that despite the sweep of the S.E.C.'s request, the specificity indicated that it was relatively certain of what it expected to find.
'They're looking into some very precise areas,' said John P. Gavin, president of SEC Insight, a company that specializes in retrieving documents from the S.E.C. 'They seem to know just what they're after.'
Carr Conway, a former S.E.C. enforcement official, agreed. 'They are not kitchen-sinking this,' said Mr. Conway, who is now senior forensic accountant at the Dickerson Financial Investigation Group in Denver."

Emily Nussbaum: Inside the Love Lab. Lingua Franca, Volume 10, No. 2 - March 2000
"A bald man with a handlebar mustache slumps in his chair, looking a bit like a pinned butterfly. Across from him, his wife--her chest encased by a plastic tube that measures the depth of her breathing--ticks off a list of complaints: He's willing to act goofy but won't behave like a real dad; he's irresponsible; he lacks follow-through. Visibly uncomfortable and upset, Handlebar wriggles, breathes in, blinks, darts his eyes around.
'Take a look at this,' says Dr. Sybil CarŽrre, the coordinator of the Family Research Laboratory at the University of Washington, pointing to the video monitor. 'She's kitchen-sinking - throwing in every complaint at once.'"

The Application Essay Tutorial gives the following advice:
"[Kitchen sinking] is a common practice. Applicants hope to "hit" on a secret trigger topic that the admissions people are looking for - those special buzz words that will throw open the gates of Stanford.
There is no such thing as a trigger topic, and by throwing in everything but the kitchen sink, you dilute the force of your essay. Rather than a well focused discourse that addresses two or possibly three important themes, the kitchen sinker produces a rambling laundry list of unrelated issues that make no lasting impression on the reader."

The following example was found at the web site of Barr Laboratories:
"To the extent that any statements made in this website contain information that is not historical, these statements are essentially forward-looking. These statements are subject to risks and uncertainties that cannot be predicted or quantified and, consequently, actual results may differ materially from those expressed or implied by such forward-looking statements. Such risks and uncertainties include: the timing and outcome of legal proceedings; the difficulty of predicting the timing of U.S. Food and Drug Administration ("FDA") approvals; the difficulty in predicting the timing and outcome of FDA decisions on patent challenges; market and customer acceptance and demand for new pharmaceutical products; ability to market proprietary products; the impact of competitive products and pricing; timing and success of product development and launch; availability of raw materials; the regulatory environment; fluctuations in operating results; and, other risks detailed from time-to-time in the Company's filings with the Securities and Exchange Commission. Forward-looking statements can be identified by their use of words such as "expects," "plans," "will," "believes," "estimates," "intends," "may" and other words of similar meaning. Should known or unknown risks or uncertainties materialize, or should our assumptions prove inaccurate, actual results could vary materially from those anticipated. The Company undertakes no obligation to publicly update any forward-looking statements."

Another Safe Harbor Statement by Worthington Industries explains:
"The company wishes to take advantage of the Safe Harbor provisions included in the Private Securities Litigation Reform Act of 1995 ("the Act") ..."

While investorwords.com explains the Private Securities Litigation Reform Act of 1995 (PSLRA) as follows:
"Passed in 1995, this legislation made significant changes to securities fraud litigation, introduced proportionate liability, and created new responsibilities for auditors to detect and report illegal activities."

The text of the Law itself can be found at lectlaw.com. The following is only an excerpt:
SAFE HARBOR- '(1) IN GENERAL- Except as provided in subsection (b), in any private action arising under this title that is based on an untrue statement of a material fact or omission of a material fact necessary to make the statement not misleading, a person referred to in subsection (a) shall not be liable with respect to any forward-looking statement, whether written or oral, if and to the extent that--
'(A) the forward-looking statement is--
'(i) identified as a forward-looking statement, and is accompanied by meaningful cautionary statements identifying important factors that could cause actual results to differ materially from those in the forward-looking statement; or
'(ii) immaterial; or
'(B) the plaintiff fails to prove that the forward-looking statement--
'(i) if made by a natural person, was made with actual knowledge by that person that the statement was false or misleading; or
'(ii) if made by a business entity; was--
'(I) made by or with the approval of an executive officer of that entity, and
'(II) made or approved by such officer with actual knowledge by that officer that the statement was false or misleading."

Paul Molyneaux: The Fish-Eye View. The New York Times, March 10, 2002
"For most of his career, McLeod searched for scallops with little more information about the sea floor than his ancestors had gleaned through the use of lead lines. 'We found them almost by feel,' he said. 'And we tore up a lot of places we didn't have to. But those days are over.'
Multibeam data sets developed by Canada's Seabed Resource Mapping Program gave McLeod an almost photographic image of the bottom, with resolution to one meter. A computer in McLeod's wheelhouse displayed a multicolored topographical chart that was created through the fusion of multibeam sonar, backscatter imagery and high-speed computer programs...
... in the United States, the development of multibeam charts has been a patchwork effort conducted by different agencies with different objectives.
Page Valentine, of the United States Geological Survey, oversaw the multibeam mapping of the Stellwagen Bank National Marine Sanctuary off northeastern Massachusetts. 'It's a proven technology with obvious benefits for fishermen and management,' he said. Valentine would like to see a multibeam mapping program for the entire continental shelf of the United States. 'There just hasn't been enough call in the right circles,' he said.
Commercial fishermen from the United States also see the value of the charts, but lack the resources to equip a vessel and pay for the mapping. 'It costs a million dollars to outfit a vessel, and Pittman told us this would cost around $1,000 a square mile,' said Jim Kendall of the New Bedford Seafood Coalition. 'We're not like the Canadians. There's no cohesive group that's going to pay for it.'"

Neal Gabler: The Face of Botox Economics. Los Angeles Times, March 10, 2002
"Despite the ridicule he has endured, what Skilling and his fellow Enron conspirators are articulating is a new and, it turns out, widely practiced economic theory--one that has less to do with finance than with a larger cultural phenomenon. Call their theory Botox economics, after the faddish treatment for wrinkles, because, like that treatment, it is predicated on the idea that the only thing that really matters in America is how something looks. In Botox therapy, muscle tissue is injected with a form of botulinum toxin that paralyzes the surrounding tissues, weakening facial muscles and thus temporarily eradicating wrinkles. The only hitch is that one may also lose a degree of facial control--the little crinkle of the eye, the turn of the lip, the furrow of the brow--that enables us to express emotion. Personality is sacrificed for appearance.
In the same way, Botox economics eradicates some of the nastier financial wrinkles by presenting a neat set of books, but the appearance comes at the expense of substance.
In arriving at their theory, what Skilling, his predecessor Kenneth L. Lay, Chief Financial Officer Andrew S. Fastow and the rest of the Enron gang discovered--and they certainly weren't the first--is that business is no different from anything else in modern American life. Perception is everything. The Enron boys had only to look around them to see a nation obsessed with image--in the clothes one wore, the car one drove, the neighborhood one lived in, the schools one's children attended, the books one read, and, yes, the Botox one injected into one's face. Everyone was performing for everyone else. Or, in historian Daniel Boorstin's words, Americans had learned to live within their illusions. Enron simply adapted this cultural phenomenon to business. The trick wasn't making a sound company, which was a difficult thing to do and which depended on too many variables. The trick was making a company that seemed to be sound, which was much easier and much more American."

Constance Holden: Primate Parthenotes Yield Stem Cells Science 295: 779-780 (2002)
"A reproductive quirk of some reptiles, insects, and other species may help stem cell researchers sidestep ethical debates over the use of human embryos. Researchers at Advanced Cell Technology (ACT) in Worcester, Massachusetts, report ... that they have isolated the first stem cell lines from primate parthenotes, embryos grown from unfertilized eggs that, in mammals, are not capable of developing into viable fetuses.
To create the parthenotes, the scientists treated 28 macaque ova with chemicals that prevent eggs from ejecting half their chromosomes--as they do when fertilized--and instead spur the eggs to begin dividing. Four of the 28 developed into blastocysts; the team was able to establish a stable stem cell line from the inner cell mass of one of them. From these stem cells, the researchers developed a considerable variety of cells, including dopamine-producing neurons and spontaneously beating cells resembling heart cells...
Wolf says parthenogenesis would actually be simpler than therapeutic cloning for producing genetically compatible material for a patient--at least one with oocytes. 'Of course, with this approach,' he adds, 'you could not produce your own stem cells unless you could also provide your own eggs. Sorry, guys.' "

Xueyan Zhang, Yingxi Zhu, and Steve Granick: Hydrophobicity at a Janus interface. Science 295: 663-666 (2002)
"Water confined between adjoining hydrophobic and hydrophilic surfaces (a Janus interface) is found to form stable films of nanometer thickness whose responses to shear deformations are extraordinarily noisy."

Adrian Cho [ed]: Making a stink. Science 295: 619 (2002)
"President George W. Bush talks of smoking terrorists out of their hiding places, but it may be possible to stink out the bad guys, too. The U.S. military is backing research into substances so foul they could be used in a stink bomb...
Stinky substances, which the military calls malodorants, could be used to disperse crowds without causing the injuries sometimes associated with tear gas and other irritants, says Capt. Joe Kloppel of the Joint Non-Lethal Weapons Directorate at the Pentagon. But Kloppel says the technology isn't yet ripe enough to become a part of the Pentagon's arsenal."

Maureen A, Rouhi: exploring the chemical senses. Chemical & Engineering News 80: 24 - 29 (2002)
"In the aftermath of the Sept. 11 attacks on the World Trade Center, Wall Street Journal reporter Stefan Fatsis wanted to know what was causing the "persistent and weird" odor in New York City. To find out, he turned to the Monell Chemical Senses Center in Philadelphia.
The center is the world's first research institute devoted to the multidisciplinary study of the chemical senses. Work there includes probing human pheromones, inquiring about food cravings, sniffing out body odors, understanding chemically induced sensations beyond taste and smell, and controlling environmental malodors. The center attracts the interest of companies in the food, fragrance, beverage, tobacco, chemical, pharmaceutical, and personal care industries."

Ken Garber: Taking Garbage In, Tossing Cancer Out? Science 295: 612-613 (2002)
"The proteasome [not to be confused with the proteome] is the cell's garbage shredder, a barrel-shaped enzyme that sucks in damaged or short-lived proteins and dismembers them for eventual disposal or recycling. It's absolutely essential for survival. So when ProScript, a tiny, privately held company leasing a basement office in Cambridge, Massachusetts, discovered a drug in 1995 that could treat cancer by blocking the proteasome, the idea met with almost universal skepticism: The treatment seemed likely to kill patients along with their tumors. The company persevered, however, getting encouraging results in animals and eventually persuading the National Cancer Institute (NCI) to fund clinical trials of its drug, PS-341....
Already, it's clear that PS-341 is not the ideal proteasome inhibitor, because the drug indiscriminately raises levels for hundreds of proteins without regard to their anticancer effect. Millennium is now trying to develop inhibitors upstream of the proteasome, by tagging proteins for survival even before they're sent to the proteasome for destruction. If a drug could inhibit specific enzymes that attach ubiquitin to individual proteins (ubiquitin chains mark proteins for destruction in the proteasome), it could, in theory block degradation of only those proteins thought to have a direct anticancer effect--for example, tumor suppressor gene products.
So proteasome inhibition, in all its guises, has arrived as an anticancer strategy, although no one, including Millennium, is quite sure how best to apply it. 'They have a golden nugget, but they're going to have to figure out how to make it into a golden ring,' says Berenson. Only time will tell if PS-341 ultimately proves useful in the clinic, but the drug has already shown that playing with garbage has its rewards."

Lockergnome's Weekly Windows Digest (from Chris Pirillo), January 26, 2002:
"There is no one true definition of a blog - which is short for Web log. To blog is to post your deepest thoughts, experiences, pictures, feelings, and opinions to a Web page using software which will handle everything for you but the actual composition. It's a public diary. You write, it publishes. It? Yes, a blogging tool. The beauty of the blogging community is that they're constantly in touch with one another, linking to each other's most interesting entries. Blogs put people in touch with people who have similar interests. You quickly become an essential part of your online community, exchanging ideas on your respective sites with the click of a button. So, what makes this different from the "old" way of doing things? For one, it's infinitely easier. There's no HTML code to learn. With some tools, there's no installation required. I've mentioned Blogger.com as a starting point many times before. Jump in - the water's fine!"

At Blogger.com we find the following definitions:

What is a weblog/blog?
"A blog is a web page made up of usually short, frequently updated posts that are arranged chronologically -- like a what's new page or a journal. The content and purposes of blogs varies greatly -- from links and commentary about other web sites, to news about a company/person/idea, to diaries, photos, poetry, mini-essays, project updates, even fiction.
blog posts are like instant messages to the web.
Many blogs are personal, "what's on my mind" type musings. Others are collaborative efforts based on a specific topic or area of mutual interest. Some blogs are for play. Some are for work. Some are both."

What is Blogger?
Blogger is a free, web-based tool that helps you publish to the web instantly -- whenever the urge strikes. Blogger is the leading tool in the rapidly growing area of web publishing known as weblogs, or "blogs," as we like to say.

Bert Vogelstein: When a Clone Is Not a Clone HMS Beagle, January 18, 2002
"The clear distinction between therapeutic cloning and human cloning is again becoming lost in reactions to reports that scientists are breaking new ground in the effort to obtain stem cells from cloned human embryos. Without an understanding of the differences between the two, policy makers and the public risk curtailing research that may lead to effective treatments and even cures for debilitating diseases. Therapeutic cloning is an unfortunate term that describes a method for creating stem cells to produce tissues that are less likely to be rejected by the immune system of a transplant recipient. Creating stem cells to treat humans is not the same as creating a human being...
The term therapeutic cloning is a misnomer, and one that scientists don't like to use, because it implies the creation of a human clone. Instead, using a process known as somatic cell nuclear transfer, scientists place the cell nucleus of the potential transplant recipient into an egg that has had its nucleus removed. Then, in a culture dish, they try to coax the remade cell into dividing like a fertilized egg to produce stem cells, which could be harvested and grown into organs or tissues that are almost genetically identical to the transplant recipient. In theory, the body should not reject tissue derived from stem cells that are a genetic match. These techniques are far too risky and rudimentary to use for anything but potential medical therapies."

"A Webinar is a live or replayed interactive multimedia presentation conducted from a Web site. The term combines Web with seminar. A Webinar typically uses some combination of:

• The presenter speaking (usually with streaming audio)
• The presenter also presented visually (streaming video)
• A panel of presenters
• A chat session that shows typed-in questions and answers as a live Webinar progresses or the entire session when it is played from an archive
• A slide presentation that can be viewed simultaneously
• For a small group, a whiteboard that allows the presenter and auditors to draw pictures
• For a small group, PC cameras and microphone that allow some of the auditors to talk to the presenter
• Conference telephone connections to the presenter"

Found at searchWebManagement.com, a TechTarget site for Web Management professionals.

"At Ascent we know that it takes more than clinical research and modern technology to improve children's medicine. it takes the right attitude - pediatude and we know it is this key ingredient that can truly make a difference in children's medicine."

"Anadya Pharmaceuticals Inc. ... employs proprietary technologies in microbial genomics (GATE^TM), affinity-based compound screening against targets of both known and unknown function (ATLAS^TM), world-class high-output medicinal chemistry, and cheminformatics including proprietary software (PROTOS^TM) to develop a portfolio of novel anti-infective products. The company also intends to become a sector leader in the emerging field of Riboproteomics^TM, the study of RNA-protein interactions and the development of novel therapeutic compounds that target these interactions. RNA has been validated as a target for the treatment of infectious diseases with approved drugs such as neomycin and tobramycin."

"Riboproteomics Opportunity
"Riboproteomics^TM is the systematic characterization and annotation of RNA-protein interactions that affect RNA metabolism, including RNA transport, splicing, translation and decay. There is untapped opportunity in Riboproteomics^TM to accelerate the discovery and development of novel drugs because RNA-protein interactions have been largely overlooked as viable drug targets. RNA targets present new opportunities for discovery and development of novel drugs with high selectivity and specificity, and opportunities to address many different diseases. Small molecule modulation of RNA metabolism essentially permits the pharmacological control of expression and function of protein drug targets. Because Riboproteomics^TM addresses disease processes at an earlier step in gene expression, this approach offers new intervention strategies."

Have you noticed a recent remarkable increase in terms ending in "omic"? You are not the only one -- in fact, the Cambridge Healthtech Institute has compiled a long Glossary of -omes & -omics terms.

In the preamble to this glossary the authors also point out that omic studies often are discouraged in favor of single molecule studies as Fishing Expeditions (with reference to a Science article of the same title by John N. Weinstein), whereas in reality both scientific approaches [the hypothesis-driven, focused as well as the road map studies] are valid and needed. I couldn't agree more.

Robert F. Service: Searching for recipes for protein chips. Science 294, 2080-2082 (2001).
"... using a protein, antibody or otherwise, to capture another protein has its drawbacks. This approach makes it tricky to detect where target proteins bind on a chip: Both the capture molecules and the targets are proteins, so a simple protein-staining technique would light up each spot. That forces many companies to use more complex assays, such as creating fluorescent compounds that have to bind to target proteins to light up. SomaLogic's Gold says a better solution is changing the probe molecules laid down on the grid to aptamers, short stretches of nucleotides that can twist, fold, and bind to target molecules much like proteins do. A key advantage, Gold says, is that once an aptamer binds to a protein, researchers can forge a tight covalent bond by hitting it with ultraviolet light, allowing them to wash excess protein off the chip surface and scan for the tight binders that remain."

Guidant Cardiovascular Medical Products:

"There are different technologies, and then there are difference technologies. Technologies that make a difference in how, or if, someone lives."

Isaac Ginsburg: The Disregard Syndrome: A Menace to Honest Science? The Scientist 15[24]:51, Dec. 10, 2001

"It might have been expected that a careful literature search--in Index Medicus, Medline, Biological Abstracts, or in the electronic journals--would guarantee that a lack of regard for already published data would not occur and that authors would also consider with respect all viewpoints expressed. But it transpires that mainly because of the information overload of scientific publications, expert referees nominated by journal editorial boards are unable to cover the vast literature to prevent duplications of already published data. This might well provide a haven for redundant scientific information.
Can we identify the main roots and motivations behind the unethical and self-defeating disregard syndrome, discussed in 1991 by Eugene Garfield, founder of The Scientist?1 [Columbia University sociologist Robert K Merton also called it citation amnesia.] Can we prescribe a prophylactic or an antidote and means for its application? Also, can one guarantee that reliance solely on computer database abstracts, without the reading of the full texts of articles and a thorough scrutiny of the lists of references cited by authors, might not lead to acceptance for publication of previously performed research, not to mention a waste of precious public funding and journal space. There is a growing concern that the disregard syndrome has already contributed to the disappearance of whole lines of research from the awareness of investigators."

Paula Park: Dealing in Relationships. The Scientist 15[24]:43, Dec. 10, 2001

"Joseph Schlessinger would hardly fit most people's definition of the unworldly scientist. Originally a physicist, Schlessinger has conducted groundbreaking work in identifying and characterizing molecules in the signaling pathways of receptor tyrosine kinases. Elected to the National Academy of Sciences in 2000, Schlessinger, William H. Prusoff professor and chairman of pharmacology at Yale University, has achieved the acclaim some scientists yearn for. Yet in 1991, when he set out to build a company based on scientific discoveries made by himself and his associates, the negotiations with financiers left him flummoxed. 'I acted like any other scientist who was naïve on the business side,' he relates."

Webster's: Old Slang; to confuse, perplex.

Beckey Worley: 'Badtrans' Worm Continues Spread - Password-stealing Worm Worse Threat Than Nimda. TechTV, November 30, 2001

"If you've been hit with Badtrans, SARC has removal instructions posted.
Users should protect themselves from Badtrans because it has a pretty nasty payload and could steal sensitive data.
The executable file Badtrans installs consists of a key logger that can record account numbers and passwords. Keystroke loggers record every detail of a computing session -- literally every key that is typed.
For example, a logger could record a user's online banking account number and password. In the case of Badtrans, the program then emails the logged data back to the virus writer or attacker at a myriad of anonymous email accounts."

Hal Cohen: Speeding up the Evolutionary Process - Biotech firm uses patented method to accelerate development. The Scientist 15[23]:12, Nov. 26, 2001

"From TV dinners to computers, improving speed and efficiency are deemed the true hallmarks of progress. The same tenet holds true in science: Why wait thousands of years for nature to do its work when it can be done in a few months? This is the concept behind the new biotech firm Morphotek. Using a patented technology platform called morphogenics, the company has given evolution's normal crawling pace a rocket-powered backpack.
Philadelphia-based Morphotek creates genetically altered host organisms using morphogenics, a technology that alters the genome of a wide range of host cells including microbes, plants, and mammals. The resulting evolution is accelerated and the gene pool is then skimmed for the offspring that exhibit viable traits, say company officials...
When bacterial DNA is damaged from mutagens such as ultraviolet light, the DNA will switch from its normal replication system to the S.O.S. system. Several proteins transiently increase the mutation rate by greatly increasing the number of errors made in copying DNA sequences. 'The S.O.S. system induces many more genetic changes in progeny in the hope that a greater genetic variability will help the organism adapt to its environment,' says Pigliucci...
'We've essentially circumvented the need for the screening of thousands of genomes to understand their function,' says Nicoladies. 'Instead of figuring out what genes are important to the trait desired, we have the phenotype and sort out what the genes are.'

spectroscopyNOW Spectral Lines 7, 2001

"British and Czech scientists have demonstrated that flowing-afterglow mass spectrometry (FA-MS) can be used to check a patient's body water levels.
Water imbalance is not just about being thirsty, for patients with severe dehydration there can be serious problems...
The system is based on dosing patients with non-radioactive heavy water - water in which the hydrogen atoms have been substituted for deuterium - and uses flowing afterglow mass spectrometry (FAMS) to measure respired levels of heavy water. The whole procedure takes less than two hours to give an accurate figure and could be used on a daily basis to monitor a patient."

Varmai Seto et al.: Development of generic liquid chromatography-mass spectrometry methods using experimental design. J. Am. Soc. Mass Spectrometry, November 19, 2001
"Standard approaches to development of liquid chromatography-mass spectrometry (LC-MS) methods, either ion-pairing or reversed-phase liquid chromatography, have been through trial and error or intentional variation of experimental factors. These approaches to method optimization fail to take into account interactions between experimental factors and therefore the results may not be optimal for the combination of experimental factors. Another approach to optimization is through the use of chemometrics. Chemometric approaches can be more efficient than trial and error or intentional variation because chemometrics make use of multivariate designs; experimental factors are varied simultaneously at the various levels. Therefore chemometrics can take into account interactions between factors. The goal of this study was to develop a generic ion-pair LC-MS method for the analysis of acidic compounds using a chemometric approach called design of experiments (DOE)."

The exact definition of Chemometrics has been a matter of debate for some time, however, the chair of the InCINC'94, the first International Chemometrics InterNet Conference, offered the following definition:

Chemometrics is the science of relating measurements made on a chemical system or process to the state of the system via application of mathematical or statistical methods.

Those who want to know more are referred to the Chemometrics Tutorials page.

Steven Brown (Univ. Delaware): Soft Modeling in Latent Variables. Chemometrics Primer, July 12, 2001
"Many of the methods employed in chemometrics are based on the concept of soft modeling, a linear modeling method that originated in the field of multivariate statistical analysis but which has become synonymous with the term chemometrics. The focus of the soft modeling method on the properties of the signal rather than on the noise help to distinguish chemometrics from statistics, where the emphasis is usually on the structure and properties of the error term. Chemists often confuse the two fields, but remembering the difference in focus makes distinguishing them relatively simple."

First the following clarification, which was was found at Chowhound.com:
"Everyone has one in his or her life: the brother-in-law with a collection of 800 takeout menus, the coworker who's always late from lunch because she HAD to trek to one end of town for the best soup and to the other for the best sandwich. Chowhounds know where the good stuff is, and they never settle for less than optimal deliciousness, whether dining in splanky splendor or grabbing a quick slice of pizza. They are the one in ten who live to eat.
We're not talking about foodies. Foodies eat where they're told; they eagerly follow trends and rarely go where Zagat hasn't gone before. Chowhounds, on the other hand, blaze trails, combing gleefully through neighborhoods for hidden culinary treasure. They despise hype, and while they appreciate refined ambiance and service, they can't be fooled by mere flash."

Shawn Hubler and Melinda Fulmer: A Monument to the Good Life in Napa. Los Angeles Times, November 17, 2001
"Copia: The American Center for Food, Wine & the Arts will be the nation's first major museum devoted exclusively to sustenance, in all its variations. What that means isn't exactly clear.
Not everyone here gets it yet, and its backers have been accused of elitism. Scholars, foodies and others are hailing its opening as a benchmark in America's appreciation of the art of living well. 'It's, uh, unique,' Mayor Ed Henderson said with a laugh, fresh from a preview of the corrugated-metal-and-glass center, which looks like a cross between an agricultural lab and a swank warehouse. 'Is it pretty? I don't know. It's different. I sound like a mayor, don't I? Tell you what--come see for yourself' ".

Janis Weeks: Metamorphosis - How steroid hormones transform caterpillar neurons BioMedNet News, November 15, 2001

"According to brand-new work from the lab, the hormone caused the APR neurons to self-destruct by digesting itself from within - a poorly understood mechanism known as autophagy. Unlike the more familiar type of cell suicide, apoptosis, cells undergoing autophagy exhibit a strange clumping of their mitochondria. 'We have no clue what that means,' she said. But studying these neurons as they self-destruct should yield important clues about autophagy in all sorts of cells."

Suppressive Chemistry from the Earth and the Sea. The Alchemist, November 15, 2001

"These compounds, often described as second-generation immunosuppressants (steroidal and DNA synthesis suppressors being the first), work by binding to intracellular proteins known collectively as immunophillins. Cyclosporin A and FK506 bind to different immunophillins but the end result is the same: the resulting complexes bind to and inhibit calcineurin, the enzyme at the start of the chain reaction that leads to the production of T lymphocytes, the front-line immune weapons."

Web site for German wine

"As far as ampelography (the description of vines) is concerned, Traminer and Gewürztraminer are one and the same variety. The distinct differences in maturity and bouquet are obviously based on slight variations whithin one variety."

Nick Atkinson: Out on a Limb, or a New Branch of Signalling Theory? HMS Beagle, November 9, 2001

"Could it be that one of nature's most dazzling displays is just a "keep out" sign to insects? According to Hamilton and Brown's recent analysis [1] of published data, the autumnal change in leaf color of temperate deciduous trees is a handicap signal to their insect pests, revealing the commitment of the trees to defense. This is the first costly handicap signal to be proposed in plants [2]. In animals, handicap signals are often behavioral: stotting in Thompson's gazelles being the most commonly cited example. The scope for handicap signals in plants is perhaps more limited, at least to our current view, but the area of plant-herbivore interactions is one in which they could evolve...
Autumn will never be the same again."

Pamela Weintraub: Autoimmunity in a New Vein? - Pathobiotek. HMS Beagle, November 9, 2001

"Lindner was, to put it mildly, intrigued. 'The general dogma in medicine up until very recently,' he explains, 'is that the bloodstream in normal people is sterile. It was not supposed to have bacteria floating around in it, but there they were...'
One result of culture advancements has been the finding that the organism is present, in low number, in all or nearly all people. 'We can grow them from everyone,' he states. The Lindner team has also learned that the organisms consist of three or four closely related species of Methylobacteria, a class usually found living in the environment. 'So far we haven't found a particular species or strain to correlate with whether or not the patient has symptoms,' Lindner adds, 'though we continue to look. And although we have been looking fairly hard, we have yet to find any mechanism that would explain why certain patients have symptoms while others do not. We are now working on quantitative PCR to see whether we can confirm our original, crude associations in a more precise way...'
The company is also trying to understand the mechanism of the cell-wall pump that can respond to antibiotics by making some patients especially ill. 'We don't know what the pumps are moving in and out of the bacteria,' says Lindner, 'but we've found that some solvents influence their behavior, flipping them back and forth.' What's more, he notes, 'certain patterns of diet may do the same.' The group has learned, for instance, that niacin tends to turn up the pumps, stimulating growth of the bacteria. Other nutrients may do the reverse.
Finally, Pathobiotek is working hard to identify antibiotic sensitivity levels in autoimmune patients, a prerequisite for delivering therapeutic treatment at all. Already, the team has discovered that one antibiotic, clarithromycin, is likely to stimulate bacterial growth in most patients."

Katie Hafner: A Paternity Dispute Divides Net Pioneers. The New York Times, November 8, 2001

"Few inventions are immune from claims and counterclaims of precedence. Thomas Edison was embroiled in a number of patent disputes. It took years for the Wright brothers to secure their rightful claim to aircraft-powered flight.
Now a dispute is churning around credit for a modern scientific breakthrough: packet switching, the technology that breaks all data that travels over the Internet into discrete bundles that are then sent along various paths around the network and reassembled at their destination."

Adam Bostanci: Super Antibodies Arrest Anthrax Toxin Science Now, May 31, 2002
"When diagnosed in time, anthrax can be cured by giving large doses of antibiotics. But when treatment is started too late, patients often die: not from Bacillus anthracis bacteria itself, but from their toxin, which wreaks havoc even after the bugs have been killed. Now, researchers have come up with a second line of defense by creating potent antibodies that stop the toxin in its tracks...
Whereas unprotected rats died 1.5 hours after they had been given 10 times the lethal dose of anthrax toxin, rats injected with the antibody fragments survived for 5 hours--enough time, the researchers say, for the kidneys to filter the antibody-bound toxin out of the bloodstream. Georgiou now plans to engineer the protective antibody fragment into human antibodies. Those could be tested for efficacy in human patients if bioterrorists strike again, he says."

James Glanz: Particles Are Tiny, but Damage Can Be Great. The New York Times, October 30, 2001
"Until anthrax spores started spreading through the mail, few people gave much thought to the minuscule particles that drift almost invisibly in the atmosphere, infiltrate buildings and plunge deep into lungs. Not so for environmental scientists, who have spent decades studying the physics and physiology of particles very much like those in the most dangerous forms of biological weaponry.
From the coal dust that causes black lung disease to the bacteria-laden droplets that spread Legionnaires' disease to second- hand cigarette smoke and plain old air pollution, particles from about 0.05 microns to 10 or 20 microns in size have long been at the focus of those scientists' attention. A micron is a millionth of a meter, or an inch divided into 25,400 parts.
Those tiny particles crop up in environmental science and germ weaponry for virtually identical reasons. Once released, particles of that size can stay aloft almost indefinitely and seep into poorly sealed buildings, greatly increasing the chances of the particles' being inhaled by people.
What is more, the peculiar microscopic physics shared by all those particles makes it certain that some of them, within a highly specific range of sizes, will be able to slip past protective nose hairs, avoid sticky bronchial walls and be deposited in the deepest reaches of the lungs, where great damage can be done.
'A particle is a particle,' said Dr. Joe Mauderly, a toxicologist at the Lovelace Respiratory Research Institute in Albuquerque, where he is director of the National Environmental Respiratory Center...",br> Once the particle does land, its exact composition Ñ whether it is harmless, chemically toxic or biologically infectious Ñ comes very much into play. Of course, much is known about that process too, especially through studies of Legionnaires', tuberculosis and other bacterial diseases that are transmitted through the air on particles that are, not coincidentally, a few microns in size.
The existence of all this knowledge, freely available in unclassified literature, is double-edged, the scientists say. It may sap germ warfare of some of its mysteriousness, but it also shows how widely available much of the information needed to design the weaponry is.


David Wade: CAMELs Against Anthrax. ChemWeb Preprints, November 7, 2001
"CAMELs are a group of novel synthetic antibiotic peptides that may be effective substitutes for ciprofloxacin in the treatment of anthrax infections."


Jeff Carpenter: Rapid Anthrax Test -- It is now possible to identify anthrax in just 30 minutes, scientists announced today. abcNews.com, November 5, 2001
"The test involves a process known as polymerase chain reaction, or PCR, which has the ability to amplify tiny amounts of DNA. In this case, suspicious substances or human samples can be tested for the presence of anthrax DNA.
Other PCR tests require days to determine if the amplified DNA is in fact anthrax. The new test involves an early detection method that identifies anthrax DNA in as little as 30 minutes.
While this particular technology has been around for years, this is the first time PCR is being applied for the rapid identification of infectious diseases, such as anthrax, strep throat and herpes."


Portable Endospore Detection System for Rapid Anthrax Detection
"The EDS2000 tests for the presence of dipicolinic acid (DPA), which is extracted from the endspores when they're added to a reagent in a disposable test vial. DPA is unique to bacterial endospores and makes up as much as 10% of the endospore's dry weight. 'While the EDS2000 test is not specific to anthrax, the test is a very useful screening tool for substances that are suspected to be concentrated forms of the anthrax spore,' said Ocean Optics president Mike Morris. 'When high concentrations of these endospores are detected in a suspicious place, it's a serious indication of foul play...'
Analysis begins by swabbing the potentially infected surface. The swab is swirled in a disposable plastic cuvette containing the special reagents. The cuvette is placed into the system's cuvette holder and exposed to UV light provided by a pulsed xenon lamp. The software compares the fluorescent pattern of a standard with the sample and displays the spectra of the sample and the results -- positive, possible or negative -- within seconds of the analysis."


Eytan Elhanany et al.: Detection of specific Bacillus anthracis spore biomarkers by MALDI-TOFMS. (PDF file) Rapid Communications in Mass Spectrometry 15: 2110-2116 (2001)
"These markers, corresponding to a molecular weight of 2528.3, 2792.4, 3077.4, and 3590.7 Da, have not been observed in extracts of the three closely related Bacillus species - B. cereus, B. thuringiensis, and B. mycoides. These unique B. anthracis biomarkers, which were isotopically resolved and reproducibly detected in the highly accurate MALDI-TOFMS reflectron mode, may be useful as a basis for rapid and specific identification of B. anthracis strains."


Stephan R. Ritter: Ousting anthrax - Combined chemical, irradiation methods likely will be used to decontaminate mail and buildings. Chemical & Engineering News 79 (48), 24 - 26 (November 26, 2001)
"In addition to gases, there are a handful of commercially available inexpensive liquid decontamination products that can neutralize chemical agents and/or kill most microbes within a few minutes of exposure. One of the best known of these is a foam invented at Sandia National Laboratories by chemists Mark D. Tucker and Maher E. Tadros.
The nontoxic, noncorrosive Sandia foam, developed in the late 1990s, is a combination of a surfactant and water-soluble polymers that supports proprietary nucleophilic reagents and mild oxidizing reagents, such as hydrogen peroxide. It already has been proven to be very effective against anthrax spores. The researchers believe the foam's surfactant damages the spores' protective protein membrane, specifically breaking phosphate and sulfide bonds, which allows the oxidizing agent to attack DNA inside the spores."

Stu Borman: Anthrax toxin deciphered -Structure, mechanism of third toxin component determined. Chemical & Engineering News 80 (4), 13 (January 28, 2002)
"Three proteins from the bacterium Bacillus anthracis, known collectively as anthrax toxin, are responsible for the microorganism's toxic and potentially lethal effects. Two--protective antigen and lethal factor--had been structurally analyzed previously. Now, after a three-year effort, scientists have determined the crystal structure and mechanism of action of the catalytic portion of the third component, edema factor."

Below are some references found at Medscape's Anthrax site:

Morton N. Swartz: Recognition and Managment of Anthrax (PDF file). New England Journal of Medicine, November 29, 2001 (electronic version November 6, 2001)

Cutaneous Anthrax Infection (PDF file with image). New England Journal of Medicine, November 29, 2001 (electronic version November 6, 2001)

What Should I do if I Receive an Anthrax Threat by Mail?
Advise from the US Postal Service
Advice from the CDC

Wendy Orent: Today's Germ War, Yesterday's Weapons - Research suggests that smallpox could be easily genetically altered--in which case vaccinations might not protect us. Los Angeles Times, October 28, 2001

"Unlike Soviet bioweaponeers, who were trying to build more lethal agents, the Australian scientists stumbled on their results. Working on a high-tech method of mouse fertility control, they inserted a gene that produced a mammalian hormone, interleukin-4 (IL-4), into mousepox, a disease of mice that's related to smallpox. The engineered mousepox killed most of the mice injected with it, including those mice that, through vaccination or heredity, were supposed to be immune.
'Monster mousepox,' as pox virologist Mark L. Buller of Saint Louis University calls it, kills not by changing the virus itself, but rather by subverting the mouse's immune system. This experiment raises the specter of diabolical new biological weapons. Humanity evolved alongside certain diseases, smallpox among them, in an arms race between germs and our species. Over millennia, human populations developed resistance to particular diseases. But what if those evolved defenses--and vaccine-induced immunity, as well--could be shut down by a gene incorporated into the pathogen itself?"

Barnaby J. Feder and Andrew C. Revkin: Killing Anthrax - Post Offices to Install Devices to Destroy Deadly Organisms. The New York Times, October 25, 2001

"The Postal Service said last night that it would buy devices that would use powerful beams of high-energy electrons to kill anthrax or other deadly organisms in sacks of mail collected and delivered to mail-processing centers.
The technology, often known as ion beam sterilization, is already used in the food and medical-device industries. The machines will initially be installed at a small number of unidentified sites where the Postal Service believes there are clear threats of encountering tainted mail, said Sue Brennan, a spokeswoman...
In addition to ion beams, equipment used to irradiate food, sterilizing gases and X-rays can all do the job, according to product sterilization consultants. In fact, such systems are likely to be effective not just against anthrax but also a wide range of bacteria and viruses that might be used as weapons...
Except for the gas-based units from companies like Andersen Products and Vacudyne, a unit of Altair, most of the competing systems work on similar principles. High-energy gamma rays, electron beams or X- rays penetrate the mail and rapidly strip electrons from molecules inside the bacteria, a process known as ionization. Once DNA and other crucial molecules in the bacteria have been ionized, the organisms cannot survive long enough to cause deadly infections.
The far slower gas-based systems, most of which use ethylene oxide, take a day or more to sanitize mail. The highly reactive gas breaks down the DNA of spores, bacteria and viruses, but it must seep into the mail to reach them. Such technology is the cheapest option and has been widely used for decades -- the Smithsonian Institution uses it to disinfect exhibits -- but the gas is toxic and flammable, according to James Gibson, a consultant in Odessa, Fla."

Barnaby J. Feder: Intel Develops a New Way to Produce Silicon Chips. The New York Times, October 8, 2001

"Today's processors are mounted on packaging that consists of three layers. In a standard silicon processor like Intel's Pentium chip, droplets of solder carry electrical current from the chip to the package. The grid of droplets, called bumps, connects to a network of tiny copper wires in the top layer of the package; the wires are routed to copper links that drop vertically through a plastic middle layer, or core...
The invention Intel is announcing does away with the top layer of the package and the bumps of solder by connecting copper wiring directly from the core of the package to the processor.
The new structure, which Intel calls BBUL, for bumpless buildup layer, is thinner and lighter because the silicon chip is embedded in the packaging where the top connecting layer used to sit. Intel said the new design could operate at higher frequencies, use less power and move signals around the silicon chip more efficiently."

Paul Meller: EU sets rules for online marketing of financial services. InfoWorld.com, September 27, 2001

"Ministers of the 15 EU member states agreed to ban inertia selling, which involves sending unsolicited financial products or services to a consumer and charging them for these before the consumer has agreed to buy them. The ministers also agreed to introduce an opt-in rule that would prohibit companies from using unsolicited e-mail to sell their wares. At present an opt-out rule applies, which allows companies to assume that a consumer wants to receive its direct marketing literature unless they specify otherwise."

Martin Holcik: Deadly Revenge - Uptake of Oncogenes from Apoptotic Bodies.
HMS Beagle, September 14, 2001

"The role of apoptosis in a multicellular organism is to remove unwanted, damaged and potentially harmful cells. So why don't we acquire bad mutations and genes from all those dying cells in our bodies? Fortunately for us, cells have evolved potent safeguard mechanisms, such as the protection of the genome by p53, that prevents normal cells from undergoing unwanted transformation. The acquisition of mutations in genes involved in the control of genome integrity would therefore make cells more vulnerable to the effects of foreign DNA. Compromised genome integrity is frequently associated with cancer cells. Horizontal gene transfer could therefore be one mechanism that contributes significantly to the further accumulation of genes necessary for malignant transformation and tumorigenesis."

Sharon Levy: Elephant Seals.
HMS Beagle, September 14, 2001

"For Castellini, the breathing pattern of elephant seals snoozing ashore is a window into their adaptation as divers. It's difficult to study the physiology of seals diving in the wild. But northern elephant seals come ashore for a few weeks each year, on islands off the coast of California and Mexico, to breed and molt. As they sleep on the beach, they alternate periods when they cease breathing - apnea - with periods when they breathe rapidly to replenish their oxygen supply - eupnea. Their bodies cope during sleep apnea in much the same way they do during long dives."

Webster's: pieces of pork or veal that are skewered and breaded, and cooked by braising or baking.

First seen in the menu of the web site of the Softwarepatent-Arbeitsgruppe (Not really American English, I know, but nevertheless interesting).

"Political Economy of the Patent System: the Mechanisms of Patent Inflation
During the last 200 years, the patent system has continually expanded. This expansion is not so much the result of conscious economic policy but rather to self-propagating mechanisms similar to monetary inflation or to the arms race. This article analyses the mechanisms of patent inflation, traces their evolution and points to possible paths of escape."

Jane Perlez, David E. Sanger and Thom Shanker: From Many Voices, One Battle Strategy. The New York Times, September 23, 2001

"Mr. Cheney, secretary of defense in the first Bush administration, has presented the president with military, diplomatic and political choices, and from the inside he is viewed as the steady hand. Secretary Powell, chairman of the Joint Chiefs of Staff in the gulf war, was a strong cautionary voice then and has been an advocate of prudence again now. Mr. Rumsfeld was arguing even before Sept. 11 that the military needed to be reconfigured for asymmetrical threats Ñ which is exactly what crashed into his building."

Celestine Bohlen: Thinkers Face the Limits of a Just War. The New York Times, September 22, 2001

"Still, each new war brings another moral quandary and another round of debate. This time, as several scholars have noted, the issue lies in the asymmetrical balance of forces. On one side is a modern superpower with a full arsenal of high-tech weapons restrained by popular moral revulsion at the prospect of inflicting unintended damage on innocent bystanders. On the other is a shadowy network of conspirators who may lack modern weapons but have no qualms about killing thousands of victims."

From a briefing by Defense Secretary Donald Rumsfeld at the Pentagon, as recorded by The New York Times: The New York Times, September 20, 2001

"...I've said before and I'll say it again: What we're engaged in is something that is very very different from World War II, Korea, Vietnam, the Gulf War, Kosovo, Bosnia, the kinds of things that people think of when they use the word war or campaign or conflict.
We really almost are going to have to fashion a new vocabulary and different constructs for thinking about what it is we're doing. It is very different than embarking on a campaign against a specific country within a specific time frame for a specific purpose...
I would just add that the problem that we've talked about from the day that I've arrived of asymmetrical threats of terrorism and ballistic missiles, cruise missiles, cyberattacks and weapons of mass destruction are something that are front and center to us because of the problem of proliferation and the problem that with the end of the cold war there was a relaxation of tension and almost anything that people want they can get their hands on if they're determined and if they have the money."

Barnaby J. Feder: Exploring Technology to Protect Passengers With Fingerprint or Retina Scans. The New York Times, September 19, 2001

"Governments and airlines seeking to reduce the threat of airplane hijackings by terrorists have a wide range of security technologies to choose from.
Much of the spotlight will be on biometrics systems, which identify travelers by fingerprints, the patterns in their retinas, their voices or other individual characteristics. Privacy concerns have slowed the development of such technology, but investors apparently expect that to change: the stocks of the few publicly traded biometrics companies soared Monday while most of the stock market declined."

Ephraim Schwartz: Parasitic grid wireless movement may threaten telecom profits. InfoWorld.com, August 24, 2001

"The major goal is to build up the 802.11b infrastructure inside the city. If you have a home that is connected to the Internet, for example, I use your connection and you can use mine,' said Matt Westervelt, one of the originators of what he likes to call a symbiotic grid rather than a parasitic grid.
Westervelt talks about a network of volunteers deploying, at their own expense, a wireless access point on the outside of their home, or at worst at a window, with the access point connected to the volunteer's PC.
The access point, as the name implies, gives users within range of any one of these access points who have a wireless LAN card in their mobile device a connection to any other device or node on the same LAN.
Once a more or less complete grid of access points are put up around a city, grid participants could connect into the LAN to access numerous services, including a free alternative to fee-based cellular networks. Voice services over 802.11b are typically referred to as VoIP (voice over IP).
Other services envisioned include information distribution for city services, free e-mail for all citizens, and, for a budget-strapped city government, inexpensive access to Internet terminals in public places such as libraries.
'Presumably these free metro wireless access could help to erase the digital divide,' said Scott Kennedy, one of nine candidates for mayor for the city of Seattle and owner of the BitStar Cafe in the city."

Jennifer S. Lee: Postdoc Trail - Long and Filled With Pitfalls. The New York Times, August 21, 2001

"...As the annual number of doctorates awarded in science nationwide has greatly outpaced the growth in the number of faculty jobs over the last 20 years, scientists like Dr. Dugan are finding that their postdoctoral years are stretching out for a discouragingly long time.
What used to be two or three years of career development often becomes five or more years in one post after another. Many of the postdocs are almost 40 before they start their first permanent positions and begin saving for retirement...
Postdocs often fall through the institutional cracks at universities, largely because of the debate of who should take responsibility for them -- whether it is the universities, the individual laboratories or the organizations paying for the research, like the National Institutes of Health.
Last November, the National Academy of Sciences, the National Academy of Engineering and the Institute of Medicine issued a report that said it was in the long-term interests of American science for postdocs to get better treatment."

Steve Lohr: I.B.M. Making a Commitment to Next Phase of the Internet. The New York Times, August 2, 2001

"I.B.M. is announcing today a new initiative to support and exploit a technology known as grid computing, which the company and much of the computer research community say is the next evolutionary step in the development of the Internet.
The grid vision is that everyone at a desktop machine or hand-held computer could eventually have the power of a supercomputer at his or her fingertips, by amassing the processing power and information resources attached to networks. Although the idea has been around for some time, the types of computer hardware and software to achieve it are only now coming within reach."

Tom Sullivan: Compaq partners with Platform Computing to back global grids. InfoWorld, November 7, 2001

"Grid computing got a big boost on Wednesday when Platform Computing made the open-source Globus toolkit commercially available and pulled together through partnerships another grid solution that Compaq will sell.
The vision of grid computing is that computer systems the world over, from desktops to the heartiest of supercomputers, will be connected in a manner much like power grids. With that type of structure in place, users and systems then can plug into the grid to access software, services, and unused computing cycles.
Industry experts are coining the phrase Great Global Grid as a future generation of the World Wide Web, only far more powerful. But thus far, grids have largely been relegated to the academic and scientific communities."

Brenda Sandburg: Battling the Patent Trolls. The Recorder @ Law.com, July 31, 2001

"Peter Detkin's spin sounds surprisingly like something out of the Brothers Grimm.
In the sleepy village of Santa Clara, Calif., there lived a very wealthy but very frightened giant named Intel. Intel was plagued by a fearsome band of evil trolls -- patent trolls, to be exact -- who wanted a glittering pot of gold in exchange for doing absolutely nothing. And they were very powerful because they said they owned the patent on some of the magic Intel used to become rich.
The true story behind the fairy tale, at least Detkin's version of it, unfolds like a case study on a patent system run amok. The assistant general counsel at semiconductor titan Intel Corp., Detkin spends much of his time these days fighting off claims of patent infringement by companies that have never made a semiconductor device. In 1999 alone, the claims topped $15 billion, Detkin said, and he hurls the epithet "patent trolls" at the companies that want Intel to pay up. He even keeps a couple of troll dolls on his desk in the gray warren of buildings at Intel's Santa Clara headquarters just as a reminder of his company's legal enemies.
'We were sued for libel for the use of the term patent extortionists so I came up with patent trolls,' Detkin said. 'A patent troll is somebody who tries to make a lot of money off a patent that they are not practicing and have no intention of practicing and in most cases never practiced.'"

The above story was reported by Hartmut Pilch on the Patents mailing list, who had this to say:

"TechSearch, a company that has sued Greg for patent infringement, is now biting Intel using software patents. The Intel patent department is calling them patent trolls. A nice word, which should be reserved for those people at Intel and in other big companies, who have been letting their patent lawyers run loose and lobby for unlimited patentability. Now they are getting the punishment they deserve, from people who are probably not trolls but just clever and unscrupulous businessmen."

Rick Weiss: The Repercussions of Taking Genetic Control. Los Angeles Times, July 30, 2001

"As of now, there are no outside authorities--governmental or otherwise--stepping into decisions on whether, when or how to use PGD (preimplantation genetic diagnosis) technology. Nor are there likely to be any soon.
'Do you really want to start assessing people's motives for having kids?' says Jeff Kahn, an ethicist at the University of Minnesota, summing up the consensus in the field. 'Good luck. We just don't do that, and we shouldn't. Try to tell me if having a kid to do work on a farm is a better reason than having one to save the life of a 6-year-old.'
Kahn's comments reflect an emerging view that there's nothing inherently unethical about human beings taking control of their genome--what matters is how they use that control. And ethicists and scientists have no trouble identifying reasons to be concerned about embryo screening. The most obvious reason is the idea of the designer baby, with its echoes of the eugenics movement of early 20th century America and its later adoption by the Nazis."

Kenneth Chang: Clever Wiring Harnesses Tiny Switches. The New York Times, July 17, 2001

"Two years ago, scientists at Hewlett- Packard and U.C.L.A. announced that they had created a custom-designed, carbon-based molecule called rotaxane that could act as a switch. A ring-shape structure slides up or down along the rest of the molecule, changing its electrical resistance. The switch mechanism consisted of rotaxane molecules between two crossed wires.
The rotaxane switches developed by Hewlett-Packard could not be reset, but the following year, the U.C.L.A. scientists developed a different molecule, with two interlocking rings; groups of those molecules could be switched back and forth between the on and off positions.
Because of the thickness of the wires used in its experiments to date, the switches Hewlett-Packard has used so far actually consist of millions of molecules each. Research published last month by scientists at Rice University and Penn State indicate that the switches can be scaled down to a single molecule."

Steve Bunk: Change of Expression. For proteomics predictions, mRNA transcripts won't do. The Scientist 15[14]:17, Jul. 9, 2001

"...Aebersold and colleagues developed a new technique to identify and quantify proteins in mixtures. It relies on reagents called isotope coded affinity tags (ICAT) that can be synthesized in either isotopically heavy or light forms. Aebersold explains that the 2D gel approach is limited by the total amount of protein that can be loaded onto the gel before its resolution breaks down. This means lower-abundance proteins, such as those involved in various regulatory activities, cannot be analyzed if very complex mixtures are being separated. The ICAT-based process virtually eliminates this problem."

Barnaby J. Feder: Pursuing a New Line in Optical Research. The New York Times, July 7, 2001

"...For all its marvels, the current generation of fiber is expensive to operate because it requires powerful amplifiers and signal repeaters to keep the light moving through its solid core. Hollow fiber, if it can be perfected, could enable light to be pumped virtually unimpeded down tiny corridors of air stretching thousands of miles.
Operators of systems with hollow fibers would not only do away with many of the supporting components of today's networks, they figure that they could cram more lightwaves into the fibers at higher energy levels before dispersion causes the lightwaves to interfere with one another.
That is the theory, anyway...
OmniGuide has a high-powered board of advisers, including John D. Joannopoulos, an M.I.T. physicist who is an expert on photonic crystals, as the materials used in hollow-core fibers are known. Also on board is James A. Harrington, a Rutgers University optics expert whose research programs have groomed many young photonics engineers for Corning and its rivals."

Roc’o Sanchez-Fernandez and Philip A. Rea: Do Plants Have More Genes Than Humans?. HMS Beagle, July 6, 2001

"No one knows why the number of open-reading-frames (ORFs) in the Arabidopsis genome (25,500) [4] is only slightly less than that estimated for the human genome (31,500) [2,3] - specifically, how humans can get by with so few genes - but we can answer Messing's opening question 'Do plants have more genes than humans?' in the affirmative in at least some cases. The ATP-binding cassette (ABC) proteins are a case in point, many of which are modularly constructed membrane proteins containing idiotypic nucleotide-binding folds (NBFs). By compiling the first complete inventory of the ABC protein superfamily from Arabidopsis [5] - the first complete inventory of ABC proteins from any multicellular organism - we have determined that the genome of this plant encodes 129 ABC proteins, which fall into 13 subfamilies (figure 1). This gene count far outstrips those for the human genome and for any other animal genome sequenced to date. The human genome is estimated to encode a mere 51 ABC proteins; those of Caenorhabditis elegans (19,000 ORFs) and Drosophila melanogaster (13,600 ORFs) only 58 and 55, respectively."

Found in Yahoo's Financial Glossary

"A measure of the goodness of fit of the relationship between the dependent and independent variables in a regression analysis; for instance, the percentage of variation in the return of an asset explained by the market portfolio return. Also known as R-square.

R square (R2)
Square of the correlation coefficient. The proportion of the variability in one series that can be explained by the variability of one or more other series a regression model. A measure of the quality of fit. 100% R-square means perfect predictability.

Correlation coefficient
A standardized statistical measure of the dependence of two random variables, defined as the covariance divided by the standard deviations of two variables."

Rick Perera: Hackers delay censorship-busting software. InfoWorld, June 28, 2001

"A groups of hackers has delayed introducing its planned Web software that is meant to allow users to evade government censorship of the Internet. The delayed project, code-named 'Peekabooty,' was originally scheduled for launch next month at the hackers' convention Def Con, the group Cult of the Dead Cow (CDC) said in an e-mail message to journalists...
CDC said it will demonstrate the current version of Peekabooty at Def Con, which takes place on July 13 to 15 in Las Vegas, for 'selected journalists and opinion leaders, mostly to avoid any charges of vaporware.' "

So what is vaporware?

The Jargon Dictionary dryly states:
Products announced far in advance of any release (which may or may not actually take place).
See also brochureware:
Planned but non-existent product like vaporware, but with the added implication that marketing is actively selling and promoting it (they've printed brochures). Brochureware is often deployed as a strategic weapon; the idea is to con customers into not committing to an existing product of the competition's. It is a safe bet that when a brochureware product finally becomes real, it will be more expensive than and inferior to the alternatives that had been available for years.

And here a real-life example:

Scott Rosenberg: Microsoft's .Net: Visionary or vaporware? Salon.com, June 30, 2000

"Microsoft's leaders themselves had trouble defining the '.Net vision' at the rollout event last week. There was a lot of talk about 'the cloud' -- a network engineer's term meaning 'the whole mess of stuff that's out there somewhere on the Net' -- and the cloudiness seemed to seep into the language every time someone tried to explain .Net to the crowd. Here, for instance, is Microsoft CEO Steve Ballmer attempting to clarify:

Joris Evers: Windows XP to get fewer Microsoft Smart Tags outside United States. InfoWorld, June 21, 2001

"The Smart Tags feature in Office XP, launched in late May, is designed to scan users' documents and add -- among other things -- links to relevant information on the Web. Windows XP and the upcoming version of Web browser Internet Explorer (IE) also will support the feature, which in the case of IE will result in Smart Tags appearing on Web pages.
The feature is controversial; critics have said Microsoft could bundle a bunch of Smart Tags with its software to promote its online properties. Local Microsoft subsidiaries, however, are responsible for Smart Tags in their own areas, and many U.S.-specific tags were removed from Office XP."

Rick Perera: Microsoft caves to criticism, drops Smart Tags. InfoWorld, June 28, 2001

"Microsoft has decided to drop the controversial Smart Tags feature from its forthcoming Windows XP release. The feature will not appear in the final version of the operating system, scheduled for release Oct. 25, or in the new Web browser Internet Explorer 6.0, the company said Thursday...
Smart Tags already operate in Office XP, launched in late May, providing, for example, links from company stock symbols to relevant information on Microsoft's MSN MoneyCentral site.
'We still very much believe in the possibilities and the techniques that Smart Tags will bring to users of Office and Windows at a later stage,' Schaap said. 'Having said that, we feel that looking at the user experience, there needs to be a balance in what the user actually uses and experiences to the needs and the demands by the content providers ... and we feel that we did not adequately get that balance between those two groups.' "

Webster: ontology: the branch of metaphysics dealing with the nature of being, reality, or ultimate substance.

Michael A. Hiltzik: Birth of a Thinking Machine. Los Angeles Times, June 21, 2001

"Most of Lenat's programmers are trained not in computer engineering but in fields related to logic and human thought: The staff includes about 20 philosophers and smaller teams of experts in subjects ranging from theology to physics.
Among them is Charles Klein, 33, a University of Virginia-trained metaphysician who joined Cycorp in 1999 after finding its want-ad for ontological engineers in a meager professional quarterly called Jobs for Philosophers.
In a room he shares with a large monitor displaying Cyc's characteristic rows of logical queries and responses, Klein spends hours inculcating the system with such abstract concepts as "belief"--a difficult notion for a computer program to grasp, possibly because it has more to do with point of view than with anything true or false about the real world.
'People who do this enjoy the process of decoding thought,' he says of his daily routine of typing assertions into Cyc's database and replying to the computer's minute requests for clarifications. It is the kind of work that only a specialist could love. 'Take the phrase: I like to go shopping,' Klein says. 'Connecting each word to a concept is fascinating to any philosopher who's interested in the structure of thought and inference.' "

Marla Dickerson: A Nutty but Natural Power Source. Los Angeles Times, June 16, 2001

"The concept of using plant oils for a fuel source might seem a little nutty. But when Rudolph Diesel unveiled his now-famous engine at the 1900 World Exhibition in Paris, he ran the contraption on peanut oil.
Then, as now, the world was powered by oil and gas. Thus, Diesel watched the technology that bore his name become synonymous with dirty fossil fuel. But he never gave up the dream that plants, not petroleum, would someday gain widespread acceptance with the motoring public. 'The use of vegetable oils for engine fuels may seem insignificant today,' Diesel said in a 1912 speech. 'But such oils may become in the course of time as important as petroleum and the coal tar.'
Nearly nine decades later, Shaq Diesel is better known than biodiesel in the United States, where petroleum-based products maintain a huge cost advantage. The average price for a gallon of diesel fuel in Southern California is about $1.63, while a gallon of biodiesel can cost upward of $3 a gallon.
High taxes on petroleum products have narrowed the gap substantially in Europe, where automotive biodiesel technology is flourishing. But interest began growing in the U.S. in the early 1990s, when Congress passed the Energy Policy Act of 1992."

AP Science Writer: Lab Study Finds Vitamin C Dangers. Los Angeles Times, June 15, 2001

"In the study, Blair and his colleagues analyzed the effects of vitamin C on lipid hydroperoxide, a compound produced in the body from fat in the diet. Lipid hydroperoxide can be converted in the cell into agents, called genotoxins, that can damage DNA. Blair said his group found that vitamin C was highly efficient in converting lipid hydroperoxide into the gene-damaging toxins."

You can read more about this in Science 292, 2083-2086 (2001)

Ricki Lewis and Barry A. Palevitz: Genome Economy. The Scientist 15[12]:21, Jun. 11, 2001

"The Human Genome Project's discovery that the human body runs on an instruction manual of a mere 35,000 or so genes--compared to the worm's 19,000, the fruit fly's 13,000, and the tiny mustard relative Arabidopsis thaliana's 25,000--placed humanity on an even playing field with these other, supposedly simpler, organisms. It was a humbling experience, but humility quickly gave way to awe with the realization that the human genome might encode 100,000 to 200,000 proteins. Scientists base this number on the analysis of DNA sequences--called expressed sequence tags, or ESTs--that are reverse-transcribed from mRNAs. The question is, where is the information for all those extra proteins?"

Karen Young Kreeger: Scientific, Ethical Questions Temper Pharmacogenetics. The Scientist 15[12]:32, Jun. 11, 2001

"The field of pharmacogenetics, the study of inherited differences that influence a person's response to drugs, rivals bioinformatics in claims about how it will revolutionize pharmaceutical research. To be sure, pharmacogenetics and its allied discipline, pharmacogenomics (the use of tools such as microarrays and proteomics to study drug response) has opened a wealth of research questions and job opportunities. But scientists are still working to untangle the ethical and research complications that delay the development of new medications....
Nevertheless, the complexity of drug development relates to the difficult study of responses to treatment, which involves differences in effectiveness, resistance, side effects, and drug metabolism. Single genes do not determine most of the effects of medications and not all responses have inherited roots. What's more, amassing databases of human genetic profiles creates enormous ethical and privacy problems. The genetic revolution in pharmaceuticals may be on the horizon, but science remains in the murky predawn. 'It has a lot of potential, but so did nuclear energy,' says Mellors. 'It's a great area, but to think we'll be able to tell a person's individual response to an aspirin tablet or a new drug in the next few years, forget it. [The advances] will be incremental.' "

The Pharmacogenetics Research Network defines pharmacogenetics as follows:
"Pharmacogenetics is the study of how genes affect the way people respond to medicines, including antidepressants, chemotherapy treatments, asthma drugs, and many others. The ultimate goal of pharmacogenetics research is to help doctors tailor doses of medicines to a person's unique genetic make-up. This will make medicines safer and more effective for everyone." Or in short: "One Size Doesn't Fit All."

Carbon Sinks' Usefulness Limited, Scientists Say. UN Wire, May 24, 2001

"The potential use of forests as carbon "sinks" to offset carbon dioxide emissions is seriously limited, according to two US studies published today in Nature. International climate talks in November in The Hague broke down in part because of a disagreement between advocates of carbon sinks -- including the United States, the world's leading carbon dioxide emitter -- and sink opponents (Alex Kirby, BBC Online, 23 May)."

Anne Eisenberg: What's Next: Batteries Push Paper Into Electronics Age. The New York Times, May 24, 2001

" 'This is a conventional zinc-manganese dioxide battery, with the usual anode and cathode,' said Baruch Levanon, chief executive of Power Paper, the private company that developed the battery. 'The difference is in the formula for the electrolytes,' Mr. Levanon said. 'We call it our Coca-Cola formula because the chemistry of the ink we used to print the electrolytes is a secret.'
Usually the moist paste of electrolytes must be encased in metal. Here, though, the electrolytes, like the anode, cathode and conductors, are printed in layers directly on the paper or plastic surface. The cell, which is about as thick as the paper in a milk carton, produces 1.5 volts and has a shelf life of two and a half years, Mr. Levanon said. It is not rechargeable and is designed to be used with disposable products with modest current requirements for powering things like an L.C.D. or a small microprocessor. Because the battery is so flat, its capacity is proportional not to its volume, as would be the case, for instance, in D-size batteries, but to its area. To produce as much energy as an AA alkaline battery, for instance, the paper battery would need to cover about a square foot...
The paper battery, or ones similar to it, may one day be used in the nascent field sometimes called paper electronics, helping to produce electronic books or newspapers on thin, flexible pages that can be thumbed through nearly as easily as printed pages."

Chris Gaither: Intel Hones Larger Wafer for a Cheaper Chip. The New York Times, May 14, 2001

"In a few weeks, a 26,000-pound machine will begin shooting ions into silicon wafers like lightning bolts, one process in hundreds that silicon must undergo during its transformation into a computer chip.
The immense machine, called an implanter, will be a small piece of the Intel Corporation's newest semiconductor factory here, scheduled to begin mass production early next year."

Richard A. Bond: Is Paradoxical Pharmacology a Strategy Worth Pursuing? BioMedNet, May 14, 2001

"Although -adrenoceptors are desensitized in patients with CHF, these receptors still respond to agonist infusions with an increase in contractility. Therefore, the paradox remains as to why impeding a contractile system results in an increase in contractility. Although various theories exist on why -blockers are useful in CHF, on the surface these effects appear to be paradoxical.
Other isolated instances exist where paradoxical pharmacology has become accepted. For example, stimulants such as methylphenidate and amphetamines are used to treat hyperactivity in children, and skin irritants such as retinoic acid and benzoyl peroxide are used to treat acne, which is an inflammatory skin condition."

Dave Wilson: Free Stuff on Web Gives Way to Profit Motive. Los Angeles Times, May 13, 2001

"When Web browsing software such as Mosaic opened the Internet to the masses, the rush was on. Investment money inundated Web site operators who could provide numbers -- any numbers -- suggesting that consumers were aware of the site.
The idea was that, in the future, when everybody was on the Internet, such mind share would pay off handsomely and anyone who tried to set up a competing Web site later in the same product category would be doomed to failure.
Jack Marshall, a co-founder of Photoloft.com, one of the first sites allowing users to share their snapshots on the Web, said the obsession with being first to market and building mind share reached such absurd proportions that many companies paid for the privilege of providing products or services."

Paul Krugman: Unrefined truth about gasoline. Inland Valley Daily Bulletin/The New York Times, May 11 & 9, 2001

"In the wake of the energy crisis in the 1970's, ordinary people in the United States began conserving energy Ñ not as a "sign of personal virtue," as Mr. Cheney sneeringly puts it, but because they wanted to save money. Cars, in particular, became much more fuel-efficient. Meanwhile the oil industry was subject to refinery creep, the tendency of refining capacity to grow through incremental improvements even when no new refineries are built. The result was excess capacity and squeezed margins, right up to the late 1990's.
What finally brought us up against capacity constraints was a surge in demand that was partly due to the economic boom of the later Clinton years, but mainly due to the renewed enthusiasm of Americans for huge, gas-guzzling vehicles Ñ an enthusiasm, er, fueled by cheap gas."

Aaron Zitner: Sniffing at Empty Nose Idea. Los Angeles Times, May 10, 2001 "...At professional conferences, one group of physicians has been trying to build a case that removal of too much turbinate tissue can cause an illness the doctors call empty nose syndrome, which they say has appeared only in recent years. Other specialists doubt that the syndrome exists. They say that turbinates have been removed for 100 years with few problems and that the pain patients report must come from some other cause."

Click to see full graphic.

"One day in the summer of 1994, Kern was showing X-rays of these patients to a visiting Swedish surgeon, Monica Stenquist. "I put up the X-rays, and they show there's nothing in the nose," Kern recalled.
"And Monica said, 'Oh, that looks like an empty nose.' "
Empty nose syndrome had been given its name.
Eventually, Kern--with Dr. Eric J. Moore and other colleagues--conducted a look-back study of all 242 patients they had seen from 1982 to 1999 with a diagnosis of atrophic rhinitis. The study found that in 85 of the patients, the deterioration of nose function had been caused by normal aging, inflammatory disease or by infection. For the other 157 patients, however, the cause was not any of those things. Every one of the 157 patients had undergone surgery in which turbinates were pared back or removed.
Kern reasoned that the surgery had caused a new and discrete ailment: empty nose syndrome."

Jeff Madrick: Economic Scene: Each Generation Has Its Own New Economy. The New York Times, May 10, 2001

"What was the genesis of the idea? Research I recently completed at the Joan Shorenstein Center on the Press, Politics and Public Policy at Harvard shows that the press, business economists and economics authors have been using the term new economy since the 1970's to describe many different and often unrelated things. Sometimes it was about computer technology. But it has also been used to describe a service economy, globalization, the two-worker family, stagnating wages, the rise of small companies, deindustrialization and corporate restructuring...
It was the rising stock market, not economic analysis, that pressed the new economy indelibly into the nation's consciousness. High-tech stocks soared in 1999, and references to the new economy in the business press tripled, to more than 3,000...
Now, the economy is slowing, dot-coms are failing, venture capital has dried up, fortunes are lost, as is a goodly portion of retirement savings, and doubters are rising from the woodwork. Is a more clear-headed age upon us?
It is not likely. We economics writers cannot seem to get out of the way. The Wall Street Journal recently wondered, for example, whether there would be a "New Economy growth recession."

Bill Gates seems to think differently:

Bob Trott: Gates touts 'information economy' over New Economy. InfoWorld.com, May 23, 2001

"Chairman Bill Gates on Wednesday gave a roomful of fellow business leaders a short economics lesson at Microsoft's CEO Summit, saying intellectual property -- an issue close to Microsoft's heart -- is the linchpin of the information economy.'
Gates told the 160 CEOs, including eBay's Meg Whitman, Compaq's Michael Cappellas, and Disney's Michael Eisner, at the two-day conference that the recent economic downturn had separated the wheat -- the information economy - from the chaff -- the New Economy."

See also: Susan Stellin: New Economy: Privacy Concerns for Google Archive.

Elizabeth Shogren: 'Clean' Electricity: Coal Emerging From Black Cloud. Los Angeles Times, May 9, 2001

"Experts say the nation's generating capacity needs to grow 45% by 2020. Coal-fired plants already pro