Saturday, February 23, 2008

Whither the revered scientist?

Of greater interest now that
Nature magazine has sounded off
on Canada's science agenda in
the federal Conservative government.

No one reads science daily do they?
Nor visits Cisti once a week down
Montreal Road for a quick read and
some chatter with the free services?

Sad, really.

[ And I wonder how Calami could stand
sitting so long on a panel with those
new hips. ]

X-URL: http://www.thestar.com/News/article/273340

Sunday, November 04, 2007 | Toronto Star
SOCIETY
TheStar.com | News | Whither the revered scientist?

Down the tubes, the public seems to think, in the face of market
pressures, bungled crises, ethical lapses

Nov 04, 2007 04:30 AM Peter Calamai Science Writer

After two days of provocative ideas and spirited exchanges at an
international gathering recently in Toronto, British museum curator
Robert Bud neatly summed up the collective wisdom.

"The scientists are terrified."

This widespread angst among scientists has been sparked by evidence
that the traditional social compact between science and the public has
been irrevocably sundered. Put bluntly, much of the public no longer
implicitly trusts either scientists or their pronouncements about
everything from climate change to the safety of children's vaccines.

<span class="fullpost">
And that matters, not just because of the call on taxpayers to fund
increasingly costly research, but also because the impact of science
and technology on our lives seems to mount by the minute.

"It is difficult to think of anything we do in public life that
doesn't pass through the window of science and technology," observed
Sheila Jasanoff, a professor at Harvard's John F. Kennedy School of
Government who delivered one of two evening public lectures at the
CBC's Glenn Gould Studio.

Yet judging from the tenor of the meeting, restoring some measure of
the lost trust will require scientists to rethink the basic tenets of
their calling and to fundamentally renegotiate their relationships
with the public.

The public, too, will need to accept a more active role, examining
critically issues such as who benefits from advances in science and
technology, who owns the intellectual property, and how it will be
applied.

"Being better informed is not enough, the public must also be
empowered," said Peter Broks, author of Understanding Popular Science.

Public unease and outright mistrust concerning science has repeatedly
cropped up in opinion polling in recent years::

Almost one in four of 1,000 adults surveyed for the British Royal
Society in 2002 didn't trust scientists in general to tell the truth.

A 2004 survey of 2,000 adult Canadians for federal science departments
found almost 30 per cent expressing concern that science is "going too
far and is hurting society rather than helping it."

The largest ever survey of public values and attitudes toward science
and technology involved face-to-face interviews in 2005 with almost
33,000 adults in 32 European countries. Four in five said that the
authorities should formally oblige scientists to respect ethical
standards, a result widely interpreted as indicating a lack of trust
in scientists to police themselves.

Reasons put forward for this unease are many and varied, including the
blurring of the lines between science, business and government, the
increasing complexity of questions that science is called upon to
answer and a general societal mistrust of institutions.

As further evidence of how seriously this angst is being taken, the
Toronto meeting came on the heels of publication of a seven-point
ethics code for research scientists portrayed as the counterpart of
the Hippocratic Oath for physicians.

This new code already binds all government scientists in Britain,
where it was developed, and is being promoted worldwide by Sir David
King, the U.K. government chief scientific advisor.

"We want to get the idea across to the public that scientists can be
trusted," King told an interviewer, "if they live by the code."

It's unlikely to be that simple, judging by the September "Trust in
Science" workshop here, which drew more than 60 participants from
Canada, the U.S. and the U.K. The driving force behind it was
something called the Cluster for the Humanistic and Social Studies of
Science, just launched with $2 million in federal funding.

The participants were overwhelmingly academics from the humanities and
social sciences who examine the history, philosophy and impact of
technology, as opposed to researchers from the natural sciences,
medicine and life sciences. Indeed, knowledge among the participants
about those other sciences was highly variable.

In their own fields, however, the participants have carried out
pioneering work into public trust in science, with case studies
covering such widely varied topics as Toronto's SARS outbreak and the
deadly levee breach in New Orleans.

A repeated theme among workshop participants was that many scientists
still act as if they possess the "facts," while the public merely has
"opinions."

In reality, however, scientists are increasingly expressing opinions,
and laypersons sometimes possess greater expertise than the
scientists, especially in the case of rare medical afflictions.

Philip Mirowski of the University of Notre Dame laid a large part of
the blame for a loss of public trust in science on three factors.
First, the withdrawal of governments from even attempting to manage
science, thus ceding priorities to the whims of the marketplace;
second, outsourcing of research and development by corporations,
meaning the demise of anything that could be called national science
strengths; and third, the transformation of scientific research into a
"fungible" commodity, so it is essentially interchangeable.

"If you buy your science and I buy my science, then how can it act as
an arbiter of anything?" Mirowski asked.

Trust in science also suffers when scientists can't come up with
definitive answers quickly enough to respond to public concerns, as
illustrated by analysis of the 2003 SARS outbreak in Toronto and the
continuing controversy over vaccination and autism in children.

Alan Richardson, a philosophy professor at the University of British
Columbia, reached his conclusions after studying reports from the two
major SARS inquiries. He noted unfounded advice from experts for the
public to stay away from Chinatown.

"All decisions were decisions under ignorance, because there was no
reliable data during the outbreak," he said. "It didn't exist."

But the greatest damage may have been inflicted by the observation in
the reports from both Dr. Andrew Naylor and Ontario Justice Archie
Campbell: that the public health system failed in the SARS outbreak

"The public health system can only work in a structure of public
trust," Richardson said. "Saying it failed probably means that public
compliance will be harder to achieve in any future outbreak."

Jennifer Keelan, a University of Toronto professor of public health
sciences, has been studying the clash between scientists and activists
who blame their children's autism on low levels of mercury
preservative used to avoid contamination in multi-dose vaccines.

"Mistrust is an understatement to describe the level of vitriol in the
debate," she said.

In effect, a scientific stalemate exists. Some research is said to
show an "association" between the mercury preservative and autism in
lab animals. Yet epidemiologists don't have large enough population
surveys to rule out such long-shot adverse reactions.

Keelan said the activists aren't anti-science, like many
anti-vaccination groups. Nor do they promote "junk" science. They
simply want the scientists to investigate different avenues.

"Will the outputs of science be markedly different if the opportunity
exists for citizens to pose questions?" asked Keelan.

Scientists might ask themselves about the erosion of the traditional
trust relationships among researchers, who once readily exchanged
things like specialized strains of mice or reagents, custom chemicals
used in experiments.

Increasingly such exchanges are now circumscribed by material transfer
agreements, complex legal documents that spell out details like
liability and indemnification, due diligence and standards for care.
Some even feature "reach-through" clauses, guaranteeing the supplier
of the materials a share in any subsequent commercialization because
of subsequent research done elsewhere.

Use of these agreements is exploding. In 1998, the University of
Toronto handled about 30. This year, +*officials have reviewed 170.

Similar growth at U.S. universities prompted this wry workshop comment
from Notre Dame's Mirowski:

"Why should the public trust science when it is becoming apparent that
scientists less and less trust each other?"
_______________________________________________________________

Star science writer Peter Calamai, based in Ottawa, was a panellist at
the Trust in Science workshop, which paid his travel expenses to
attend.
</span>

Sunday, November 4, 2007

New science formula STIX Fonts Project Completes Design Phase

So it's a contribution, but yet they don't
have a TeX version. Sounds like a too-late,
too-little project to me.

It would be more useful if their implementation
allowed interactive changes in computation by
the readers.

X-URL: http://www.elsevier.com/wps/find/authored_newsitem.cws_home/companynews05_00769


STIX Fonts Project Completes Design Phase

Melville, NY, October 31, 2007 - A group of scientific publishers
today announced the release of the full complement of the Scientific
and Technical Information Exchange (STIX) Fonts in a beta test
version. This free, comprehensive set of special characters - mainly
mathematical or scientific - represents a significant breakthrough in
scientific, technical, and medical publishing. Following a short beta
test period, the final production release of the STIX Fonts should
occur before the end of 2007.

The successful completion of the STIX Fonts project will alleviate the
need for publishers to assemble symbols from a variety of fonts. When
posted to a Web site, documents using the STIX Fonts will be properly
rendered, regardless of the fonts installed on a particular computer,
saving editors' valuable time.

The six publishers that collaborated to design, fund and manage the
STIX project include the American Chemical Society (ACS), the American
Institute of Physics (AIP), the American Mathematical Society (AMS),
the American Physical Society (APS), Elsevier, and the Institute of
Electrical and Electronics Engineers (IEEE). The beta version can be
downloaded from the STIX Fonts web site at
[24]http://www.stixfonts.org.

The technical development of the STIX Fonts Project was handled by
MicroPress, Inc., a respected font designer, which has created and
delivered nearly 8,000 characters/glyphs required for these
comprehensive fonts. Glyphs designed by Elsevier for an earlier
project push the final glyph total to 8,047.

"Given the scope of this ambitious undertaking, it's not surprising
that completion of the STIX Fonts project took more than 10 years,
more than one million dollars in donated staff time, and the combined
efforts of a half dozen well-respected scholarly publishers," said
Fran Zappulla, Staff Director, IEEE Publishing Operations. "The end
result is a font set that is the most comprehensive of its kind,
encompassing so many sub-ranges of the Unicode(TM) standard and
enabling data to be transferred securely through many different
systems without corruption."

.....By making the fonts freely available, the STIX project hopes to
encourage the development of widespread applications that make use of
these fonts. In particular the STIX project will create a TEX
implementation that TEX users can install and configure with minimal
effort. TEX is a computer language designed for typesetting, with
particular application to mathematics and other technical material.
The TEX version of the fonts is being developed by a sub-contractor,
and should be available soon after the production version is released.

For more information visit the STIX Fonts web site at
[25]http://www.stixfonts.org

Sunday, October 28, 2007

NASW or BASW?

Just got back from the annual (U.S.) National Association of Science Writers, or from the looks of the audience, the Barely Adequate Science Writers.
Far too many attendees were the PR flacks from U.S. Uni or company Pravda offices.
While the (U.S.) NASW has 3000 members, only 300 people attended this meeting of workshops.
I was surprised by the number of nutters with causes in attendance.
I was not surprised by vast math ignorance, or no idea of scale.

Friday, December 15, 2006

Rationalizing Pi

Found an old Hemmi Mannheim type slide rule in the lab the
http://www.sphere.bc.ca/test/build.html [ slide rules ]
other day.

On the back was a series of settings to approximate the ratios
better than the eye and setting C1 or D1 to a number.

Linkname: pi is irrational
URL: http://www.lrz-muenchen.de/~hr/numb/pi-irr.html

Linkname: Math Forum - Ask Dr. Math
URL: http://mathforum.org/library/drmath/view/58725.html

Linkname: Pi -- from Wolfram MathWorld
URL: http://mathworld.wolfram.com/Pi.html

Linkname: Pi - Wikipedia, the free encyclopedia
URL: http://en.wikipedia.org/wiki/Pi

Interesting, for 3 figures, but for 2, mental is as good
and more interesting to the idea of Fermi question resolves.
Linkname: Fermi questions
URL: http://mathforum.org/workshops/sum96/interdisc/sheila1.html

Linkname: Fermi Questions / Fermi Problems
URL: http://www.vendian.org/envelope/dir0/fermi_questions.html

Some of the Hemmi slide rule conversion factors

Dia circle Circum
226 710
710 / 226
:= 3.14159292035398230088
vs. 3.141592653589793238462643383279502884 ...

from : http://www.geocities.com/SiliconValley/Pines/5945/facts.html

The fraction (22 / 7) is a well used number for Pi. It is accurate
to 0.04025%.
Another fraction used as an approximation to Pi is (355 / 113)
which is accurate to 0.00000849% [ same as the above 710/226 ]
A more accurate fraction of Pi is(104348 / 33215). This is accurate
to 0.00000001056%.

Other conversions were:
Side of sq diag of square
70 99

inches mm
5 127

feet metres
292 89

yards metres
35 32

miles km
87 140

...
cu ft imp gal
17 106

cu ft us gal
234 1750

cu ft litres
3 85
etc. etc.

Friday, December 1, 2006

Further to "Science in Germany"

Having the ESA might be an 'encourager'
for space science. Or they might be
doing more aurora work.

I can see Physics because of Desy, CERN.
And the farming lobby has Plant and Animal
research (Compare the neighbouring Swiss).

The 'negatives' in this listing would be
papers that are predominately in German
for this English-dominated index from
Thomson/ISI.

Subject: SCI-BYTES: Science in Germany, 2001-05
X-URL: http://www.in-cites.com/research/2006/may_15_2006-2.html

47]in-cites - an editorial component of Essential Science Indicators
Citing URL: http://www.in-cites.com/research/2006/may_15_2006-2.html

[49]SCI-BYTES What's New in Research: May 15, 2006

Science in Germany, 2001-05

Germany's world share of science and social-science papers over the
last five years, expressed as a percentage of papers in each of 21
fields in the Thomson Scientific database. Also, Germany's relative
citation impact compared to the world average in each field, in
percentage terms.
Field

Percentage of papers from Germany
Relative impact
compared to world
% Impact(%)
Space Science 14.95 +27
Physics 11.26 +36
Molecular Biology 10.09 +14
Neurosciences & Behavior 9.76 +3
Geosciences 9.73 +34
Microbiology 9.22 +18
Chemistry 8.99 +19
Clinical Medicine 8.93 +5
Mathematics 8.90 +17
Materials Sciences 8.56 +17

Germany's overall
percent share, all fields: 8.55

Immunology 8.24 +11
Biology & Biochemistry 7.75 +17
Psychology/Psychiatry 7.17 -7
Plant & Animal Science 7.15 +31
Pharmacology 7.11 +11
Computer Science 6.67 +5
Engineering 6.25 +26
Agricultural Sciences 6.24 +9
Ecology/Environmental 6.09 +19
Economics & Business 4.42 -23
Social Sciences 3.20 -21

Between 2001 and 2005, Thomson Scientific indexed 334,831 papers that
listed at least one author address in Germany. Of those papers, the
highest percentage appeared in journals classified under the heading
of space science, followed by physics and molecular biology. In all
three of those fields, and in all but a handful of the rest, the
citations-per-paper average for papers from Germany exceeded the world
average, as the right-hand column shows. (In space science, for
example, Germany's impact average of 9.51 cites per paper surpassed
the world mark of 7.50 by 27%.) Germany's performance was even
stronger in physics (36% above the world mark), geosciences (34%
above), and plant & animal science (+31%), while also being notable in
engineering (+26%), chemistry (+19%), and ecology/environmental
sciences (+19%).

SOURCE: [53]National Science Indicators, 1981-2005 (containing
listings of output and citation statistics for more than 170
countries; available in standard and deluxe versions from the
[54]Research Services Group.

[related-information.gif]
* [quickscience-icon.gif] View the 10-year country rankings for
[55]Germany, 1996-February 28, 2006.

* View the 10-year country profile for [56]Germany, January
1993-April 30, 2003..

References
55. javascript:popUp5ColRank('may_15_2006-4.html')
56. http://www.in-cites.com/countries/germany.html

Thursday, November 30, 2006

View of modern research in Germany

The usual complaints about the Anglo-American
axis of research, but acknowledgement of the
lack of places, because of inflexibility, in
Germany.
Still there is a lack of real research money too.

Subject: Goethe-Institut - Research and Technology - Topics
X-URL: http://www.goethe.de/wis/fut/thm/en1841852.htm


The Helmholtz Association: Research Writ Large
Prof. J?rgen Mlynek
"Our mission is to help solve pressing social, scientific and economic
problems." In September 2005 J?rgen Mlynek took the helm of the
Helmholtz-Gemeinschaft, Germany's biggest scientific organization. In
this interview he advocates greater flexibility in German research and
explains what's special about the Helmholtz Centres.

F: Professor Mlynek, in your capacity as president of the Helmholtz
Association you received the Schr?dinger Award for Interdisciplinary
Research a few days ago. To put it a bit polemically: is there really
any prize-worthy research still going on in Germany today?

A: Germany is still one of the leading nations in science and technology.
Excellent research is going on here, we place well in international
rankings. The situation is better than the prevailing mood would
suggest. Our young researchers are much in demand and we've still got
an edge in many areas of science and technology, as is reflected in
the economy.

F: When you look at the German research scene, in your opinion what are
the most formidable challenges to significantly boosting research in
Germany? Are they of a structural or financial nature?

A: There are essentially two big barriers to overcome. The first is a
matter of mentality: Are we not as good as we think we are? Or do we
not believe we're as good as we actually are? It is, in short, a
matter of self-assurance. The other barrier is that the basic
conditions for research and development need to be changed. There are
too many rules we have to abide by. We've got to loosen up these
rules, cut the red tape. We need more flexibility - when it comes to
remuneration, for example. We need to be able to break away from the
public service union agreement and pay salaries based on individual
results.

F: How important is funding for the next generation of researchers?

A: There are some 80,000 doctoral candidates in Germany. These young
academics are internationally sought-after. We have to make sure they
stay here and don't emigrate to Anglo-American countries. We have to
hold out bright prospects to our researchers, especially those between
the ages of 30 and 35. In the scientific domain, for example, that
means more independence, more autonomy in directing research groups.
That's why I feel junior professorships are a step in the right
direction. The goal should be to establish something akin to the
tenure track system in Anglo-American countries. We've already
introduced something of the sort in our Helmholtz University Young
Investigators Groups. Furthermore, the Habilitation [qualification to
teach at university--TRANSLATOR'S NOTE] ought to be abolished. It's
outmoded. And the process takes longer than initially intended.

F: Five years ago, the Helmholtz Association laid down its main fields of
endeavour for research and funding purposes. They include Energy, the
Earth and Environment, Health, Key Technologies, the Structure of
Matter, and Transport and Space. What are these fields of endeavour
about?

The Helmholtz Association has a mission. We engage in top-level
research to solve major and pressing social, scientific and economic
problems. The fields you mentioned are among the most formidable
challenges facing our society. The 15 Helmholtz Centres address issues
in those fields, often pooling their efforts to that end. They work on
.... [ 66 more lines ]
Translation: Eric Rosencrantz
November 2006
Related links
[44]Helmholtz Association deutsch english russkij
[65]50 Deutsche Stars
Innovations made in Germany. German inventions continue to change the
world today, just as they have been doing for the past 500 years.
Learn more about it.
References

Visible links
44. http://www.helmholtz.de/

65. http://www.goethe.de/wis/fut/prj/dst/enindex.htm

Tuesday, November 21, 2006

Western Blot? Wot that?

A western blot (a.k.a immunoblot) is a method in molecular biology/biochemistry/immunogenetics to detect protein in a given sample of tissue homogenate or extract. It uses gel electrophoresis to separate denatured proteins by mass. The proteins are then transferred out of the gel and onto a membrane (typically nitrocellulose), where they are "probed" using antibodies specific to the protein. As a result, researchers can examine the amount of protein in a given sample and compare levels between several groups. Other techniques also using antibodies allow detection of proteins in tissues (immunohistochemistry) and cells (immunocytochemistry).

The method originated from the laboratory of George Stark at Stanford. The name western blot was given to the technique by W. Neal Burnette (Analytical Biochemistry, 112:195-203, 1981) and is a play on the name Southern blot, a technique for DNA detection developed earlier by Edwin Southern (Journal of Molecular Biology 98 (3): 503-&1975 ) [ See http://garfield.library.upenn.edu/histcomp/southern-em_auth/ for History of Citation ]. Detection of RNA is termed northern blotting.

Western blots allow investigators to determine the molecular weight of a protein and to measure relative amounts of the protein present in different samples.

1) Proteins are separated by gel electrophoresis, usually SDS-PAGE.

2) The proteins are transfered to a sheet of special blotting paper called nitrocellulose, though other types of paper, or membranes, can be used. The proteins retain the same pattern of separation they had on the gel.

3) The blot is incubated with a generic protein (such as milk proteins) to bind to any remaining sticky places on the nitrocellulose. An antibody is then added to the solution which is able to bind to its specific protein. The antibody has an enzyme (e.g. alkaline phosphatase or horseradish peroxidase) or dye attached to it which cannot be seen at this time.

4) The location of the antibody is revealed by incubating it with a colorless substrate that the attached enzyme converts to a colored product that can be seen and photographed.