Monthly Archives: September 2014

LET’S JOIN IN CELEBRATING THE INTERNATIONAL YEAR OF CRYSTALLOGRAPHY!!

 

Schematic of ordering in 1, 2, and 3 dimensions.  Top view looks downward onto the flat object; side view is at 90 degrees and looks onto the edge.  1-D ordering is a row of 5 associated subunits.  2-D ordering has 4 associated rows of 5 subunits. 3-D ordering has a layer of 12 subunits on top of the 20 subunits in the 2-D array.   (http:dr-monsrs.net)
Schematic of ordering in 1, 2, and 3 dimensions. Top view looks downward onto the flat object; side view is at 90 degrees and looks onto the edge. 1-D ordering is a row of 5 associated subunits. 2-D ordering has 4 associated rows of 5 subunits. 3-D ordering has a layer of 12 subunits above the 20 subunits in 2-D array.  (http://dr-monsrs.net)

2014 is the 100th year since the discovery that a beam of x-rays directed onto a single crystal comes out as multiple beams forming discrete spots.  That monumental finding has been called one the most important scientific research discoveries of all time.  Everyone in the entire public now is invited to celebrate this special 2014, designated by the United Nations as the International Year of Crystallography (IYCr2014)!  Below, I give the briefest possible non-mathematical introduction to the basic essentials of crystals and crystallography, along with some recommended internet websites where much further information is available.

What are crystals? 

We all encounter crystals every day, but most know little about them.  Crystals consist of matter whose smallest subunits (i.e., molecules or macromolecules) are very highly ordered in all 3 dimensions (3-D), as depicted in the opening figure above.  Some typical examples of the numerous crystals we commonly see are table salt (sodium chloride), diamonds in rings and jewelry (carbon), ice (water), and small granules of sugar (glucose).  If you have a magnifier, take a look now at what is in your salt shaker and you will observe many tiny crystals!

The 3-D ordering of the components making up crystals is so perfect that each and every subunit has exactly the same orientation and positioning as do all its neighbors.  This means that the atoms making up each subunit also have identical positioning to those in other subunits.  When a beam of x-rays is directed onto a single crystal in a suitable manner, each atom in the highly ordered complex scatters the incoming radiation identically into discrete spots.  The array of different spots produced from one crystal is the sum of the rays scattered by all its component atoms; because the innumerable atoms are so highly ordered, the many scattered rays join to form discrete spots.

What is diffraction? 

Diffraction is a fundamental property of atoms whereby incoming x-rays, electrons, or neutrons are scattered at characteristic angles and intensities.  The numerous scattered rays form an ordered array of diffraction spots and rings known as a diffraction pattern.  A single crystal produces one set of periodic diffraction spots, 2 crystals produce 2 sets of spots (at different rotations), and multiple crystals in polycrystalline materials will produce diffraction rings (i.e., many sets of the same spots at numerous different rotations).  The periodic order in diffraction patterns directly corresponds to the ordered position of the different atoms inside crystals; this means that diffraction patterns show atomic structure of the material making up each crystal.  The diffraction pattern is totally distinctive for each crystalline material, since the locations (atomic spacings) and brightness (kinds and numbers of atoms) of spots or rings are unique for each kind of crystalline matter.

What is crystallography? 

Crystallography is a research methodology for studying crystals.  Diffraction patterns are used in crystallography to tell us about the arrangement of the component atoms inside many different materials.  Since the beginning of x-ray crystallography one century ago, many thousands of materials have been crystallized and examined by crystallography; these include catalysts, enzymes, metals, minerals and biominerals, newly synthesized chemical compounds, proteins, salts, viruses, etc.   Because the atoms inside crystals are so highly ordered in an identical manner, diffraction patterns can be recorded, measured, and then processed by computation to determine structure down to the level of individual atoms.  This atomic structure determination of crystalline matter is the magic of crystallography!

Crystallography is a global activity for both science and industry, and almost all countries have scientists working as crystallographers.  X-ray diffraction is the most frequently used approach for crystallography, and now is quite automated through the use of computers to carry out the extensive numerical calculations needed to define an unknown structure to a high level of resolution.  Crystallography can be performed with laboratory x-ray sources or with very powerful and very fast x-rays produced by synchrotrons.   The hugely expensive synchrotron facilities are rather few in number, but have well-organized programs permitting their use by many visiting scientists.  Diffraction of electrons or neutrons also provides valuable special knowledge about structure at the atomic level.  When all is said and done, crystallography simply is a special way of looking at structure.

Not all materials are crystalline

Not all substances are naturally crystalline or can be induced to form crystals.  If the atoms in some substance are not ordered at all (i.e., they are randomly distributed), then this material is said to be in the amorphous state.  Examples of amorphous materials we see frequently include liquid water, many plastics, and air.  Inducing the formation of very highly ordered crystals is an essential requirement for structure determination by x-ray crystallography, since amorphous materials do not produce any diffraction spots or rings.

How does crystallography matter to you and me? 

Why do research scientists spend so much time and effort to use the magic of crystallography for determining the atomic structure of many kinds of physical, chemical, and biological materials?  The answer is that this knowledge about structure always provides information about functional capabilities and mechanisms for activities.  As one example, consider what can be derived from new knowledge about the high resolution structure of a virus; this will often increase  understanding about its biogenesis, mechanism for infecting host cells, immunoreactivity, and differences from other viruses.  Knowledge about functional capabilities  always is immensely valuable for both science and industry; for example: functioning of some inorganic catalyst or enzyme (e.g., mechanisms for activity and activation), interactions with other ions and molecules (e.g., changed functioning upon binding), formation of functional complexes (e.g., complex multi-protein assemblies), arrangement to form some more complex object (e.g., associations of 2-D polymers), changes producing specific toxic effects, prerequisites for binding to various ligands. sequential steps in genesis, characteristics of new materials (e.g., nano-materials made in university or industrial labs), etc.

Where can more information be found about crystals, crystallography, and IYCr2014? 

In the year-long world-wide celebration of crystallography and crystallographers during IYCr2014, many very fascinating programs for non-scientists now are being featured on the internet.  A large directory of instructive videos about crystals and crystallography for IYCr2014 is available at:  http://iycr2014.org/learn/watch .  Dr.M gives a rating of ‘outstanding’ to “Diving into the Heart of the Molecules of Life”, which shows how modern protein crystallography is done (http://www.youtube.com/watch?v=GfOyZch6llo ); regardless of which branch of science you prefer, Dr.M encourages everyone to see this video.

The International Union of Crystallography, which coordinates the international congresses on crystallography, has a special area on its website explaining the current celebration of IYCr2014 (see  http://www.iycr2014.org/about/video , and,  http://www.iycr2014.org/about  ).  Other large areas provide a listing of many internet resources and web tutorials dealing with crystals and crystallography; these include educational materials for students and teachers, and, recipes and instructions for growing your own crystals ( http://www.iycr2014.org/learn/educational-materials ).  The American Crystallographic Association has annual meetings that always include a special presentation aimed to instruct ordinary people about crystals and crystallography ( http://www.amercrystalassn.org/ ); this and many other national or regional crystallography societies also feature special IYCr2014 programs on their websites.

Visitors to Dr.M’s website are urged to take a look at any of these internet resources.  You don’t have to be a scientist to love crystals!  The IYCr2014 is for everyone, and that includes you!

 

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SCIENTISTS TELL US ABOUT THEIR LIFE AND WORK, PART 6

 

 Cover of 1992 book by Thomas E. Starzl.  Published by the University of Pittsburgh Press, and available from many bookstores and internet booksellers.     (http://dr-monsrs.net)

Cover of 1992 book by Thomas E. Starzl. Published by the University of Pittsburgh Press, and available from many bookstores and internet booksellers. (http://dr-monsrs.net)

 

In this series, I am recommending to you a few life stories about real scientists.  I prefer to let these scientists tell their own stories where possible.  Autobiographical accounts are interesting and entertaining for both non-scientists and other scientists.  My selections here mostly involve scientists I either know personally or at least know about.  If further materials like this are needed, they can be obtained readily on the internet or with input from librarians at public or university libraries, science teachers, and other scientists.  In the preceding segment of this series, the story of a very creative and individualistic research scientist working in Chemistry & Biochemistry was recommended (see “Scientists Tell Us About Their Life and Work, Part 5”).  Part 6 presents the dramatic story of a dynamic clinical researcher in surgical science, who pioneered in human organ transplantation and who now works on basic research studies of immunology.

Part 6 Recommendations:  TRANSPLANT SURGERY & IMMUNOLOGY

Prof. Thomas E. Starzl (1926 – present) developed the complex experimental procedures for human liver transplantation into a practical clinical treatment for human patients with liver failure.  His vigorous research efforts for transplantation of livers involved clinical practice with very endangered infant and adult patients, development of new technical procedures and surgical protocols, innovations of adjunctive manipulations in clinical immunology (i.e., therapeutic immuno-suppression), and logistical coordination of the several different clinical teams involved with each transplant surgery.  This long clinical development followed his preceding surgical career involving the transplantation of several other human organs.  Following his retirement from clinical surgery in 1991, Prof. Starzl turned his research attention to basic laboratory experiments on the immune system; this switch reflects his strong belief in bidirectional interchanges between the clinical hospital and research laboratories.  It is nothing less than astounding that he has authored several thousands of research publications during his long academic career and continues this blistering pace today.  The University of Pittsburgh has named a research building on their clinical campus as the Thomas E. Starzl Transplantation Institute.  Dr. Starzl has received many awards and prestigious honors, including the Medawar Prize (1992), the USA National Medal of Science (2004), and the Lasker-DeBakey Clinical Medical Research Award  (2012).

Much information about this giant in surgical science can be found at The Official Thomas E. Starzl Website      ( http://www.starzl.pitt.edu/ ).  My first recommendation is an illustrated story about his personal life and professional activities.  The second gives a clear exposition about what happens when an entire human organ is transplanted.  My third recommendation presents his account about the development of liver transplantation into a successful surgical treatment for end-stage liver disease, and is well-suited for general adult readers.  The  fourth recommendation is a truly wonderful video showing the very long research process needed to develop modern liver transplantation, and demonstrating how this surgical advance now greatly benefits clinical patients.

(1) The Official Thomas E. Starzl Website, 2014.  About Thomas E Starzl, M. D., Ph. D.  Available on the internet at:  http://www.starzl.pitt.edu/about/starzl.html .

(2) The Official Thomas E. Starzl Website, 2014.  Statement of impact.  Available on the internet at:  http://www.starzl.pitt.edu/impact/impact.html .

(3) Strauss, E., 2012.  Award description for the Lasker-DeBakey Clinical Medical Research Award.  Available on the internet at:  http://www.laskerfoundation.org/awards/2012_c_description.htm .

(4) Lasker Foundation, 2012.  An interview with Thomas E. Starzl.  Available on the internet at:  http://www.laskerfoundation.org/awards/2012_c_interview_starzl.htm


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SCIENTISTS TELL US ABOUT THEIR LIFE AND WORK, PART 5

 

Quote from the 1993 Nobel Prize Lecture in Chemistry by Kary Banks Mullis

Quote from the 1993 Nobel Prize Lecture in Chemistry by Kary Banks Mullis

 

In this series, I am recommending to you a few life stories about real scientists.  I prefer to let these scientists tell their own stories where possible.  Autobiographical accounts are interesting and entertaining for both non-scientists and other scientists.  My selections here mostly involve scientists I either know personally or at least know about.  If further materials like this are needed, they can be obtained readily on the internet or with input from librarians at public or university libraries, science teachers, and other scientists.  In the preceding segment of this series, the life story of a world-renowned research scientist working in Experimental Pathology & Cell Biology was recommended (see “Scientists Tell Us About Their Life and Work, Part 4”).  Part 5 presents the adventures of an energetic individualist whose creative scientific research enabled the molecular genetics revolution to take place in biology and medicine.

Part 5 Recommendations:  CHEMISTRY & BIOCHEMISTRY

Kary Banks Mullis (1944 – present) is an extremely creative free-thinker who invented the polymerase chain reaction (PCR) during his chemical research studies at an industrial research center.  This technological breakthrough enables DNA amplification (i.e., creation of myriad exact copies of some length of DNA), and now has been expanded into many new protocols and new instrumentation for molecular genetics, paternity testing, genomics, and personalized medicine.  The 1993 Nobel Prize in Chemistry was awarded to him for this very influential research discovery.  Dr. Mullis recognized that his Nobel Prize provided the opportunity to be able to freely announce his reasoned viewpoints about controversial topics in science and in ordinary life; he always is a very outspoken scientist and a vibrant individual.  He has preferred to conduct research within industrial laboratories, and currently works as a Distinguished Researcher at the Children’s Hospital and Research Institute in Oakland, California.

A considerable number of very fascinating stories and personal information, as well as a very clear explanation of how the PCR operates, is available on the website of Dr. Mullis (http://www.karymullis.com ).  His childhood interest in chemistry and research is recorded as a most amusing video presentation (see “Sons of Sputnik: Kary Mullis at TEDxOrangeCoast”, available on the internet at:  https://www.youtube.com/watch?v=iSVy1b-RyVM ).  The life story of Dr. Mullis epitomizes that many great researchers excel in personal determination, asking provocative questions, and thinking new thoughts (see my earlier article in the Scientists category on “Curiosity, Creativity, Inventiveness, and Individualism in Science”).

My first recommendation is his brief illustrated autobiography.  The second is a very personal account of how the notable discovery of PCR was made, and includes stories about his life as a student and a scientist.   The third is a video interview in 2005, 12 years after he became a Nobel Laureate; this includes some advice for young science students.  My fourth recommendation is his formal Nobel Prize lecture, presenting personal stories about his being a scientist, and including a vivid description of his “eureka moment” when he realized the significance of his amazing new research finding.

(1) Mullis, K.B., 2014.  Biography, and making rockets.  Available on the internet at:
http://www.karymullis.com/biography.shtml ).

(2) Mullis, K.B., 1993.  Autobiography, and addenda.  Available on the internet at:
http://www.nobelprize.org/nobel_prizes/chemistry/laureates/1993/mullis-autobio.html.

(3) The Nobel Prize in Chemistry (1993), 2005.  Interview with Kary B. Mullis – Media Player at Nobelprize.com.  Available on the internet at:  http://www.nobelprize.org/mediaplayer/index.php?id=428 .

(4) Nobel Prize Lecture by K.B. Mullis, 1993.  Nobel Lecture: The polymerase chain reaction.  Available on the internet at:  http://www.nobelprize.org/nobel_prizes/chemistry/laureates/1993/mullis-lecture.html .

 

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WHY ARE UNIVERSITY SCIENTISTS INCREASINGLY UPSET WITH THEIR JOB? PART II.

 

Why is quality researching and teaching now so problematic for university scientists?    (http://dr-monsrs.net)
Why is quality researching and teaching now so problematic for university scientists? (http://dr-monsrs.net)

 

Part I of this essay identifies the chief causes and consequences for the increasing dismay and dissatisfaction of scientists working in universities for researching and/or teaching (see “Why are University Scientists Increasingly Upset with their Job?  Part I”).  Part II now discusses the effects of this condition upon the conduct of experimental research and science education in universities; further, I explain what can be done to deal with this current issue.

What do the changes in Part I mean for scientific research and science teaching in universities? 

The whole nature of science and research at universities recently has changed.  The altered and decreased standards for quality performance in research and teaching means that a decline is inevitable in both activities.  Rather than being a university scientist, members of the science faculty now are forced to become businessmen and businesswomen.  Instead of working at the laboratory bench, far too many successful university scientists become managers doing paperwork while sitting at a desk in an office, but never entering their laboratory.  Acquisition of more and more research grant dollars now is their chief goal, instead of trying to discover more new truths and create valid new concepts through research experiments.

When doctoral research scientists become transformed into business managers, they are then expected to perform activities that all their many years of advanced education and training have not prepared them for (e.g., acquiring money, adjusting experimental data to fit what is wanted, bargaining, composing research grant proposals based only on what is most likely to be funded, handling investments and charting profit margins, interacting with other scientists only as either competitors or collaborators, etc.).  I know of no evidence that being good or clever at making money in business is more than very loosely related to being good or clever at doing research experiments; these two sets of skills and capabilities seem to me to be separate and unrelated.

Science and scientists at universities have been modified to such an extent that activities, performance, and advancement now are being evaluated with very different criteria than were used only a few decades ago.   Even science education is negatively affected, because quality standards for teaching are lowered, students are not taught to think independently and to ask meaningful questions, the development of understanding by students is not fostered, etc.; often, all of these are decreased or even negated.  University scientists concentrating on teaching activities now are evaluated mainly on the basis of their popularity with students, instead of being evaluated for educational quality.  I will never forget the time I was very shocked when a senior faculty teacher once confided to me that he believed his own required first-year medical school course had degenerated into something suitable for high school students.

The overall effect of the enlarging dissatisfaction by science faculty is a progressive decrease in the quality of both researching and teaching.  The activities of professional scientists at universities now are degraded due to the changes and consequences enumerated in Part I (see “Why are University Scientists Increasingly Upset with their Job?  Part I”).

Can university research and science teaching be rescued? 

What should be done to resolve the current predicament of university scientists?  Finding effective solutions for these vexing academic problems certainly is not easy, particularly because academia historically always has been very slow to change anything even when it is totally obvious that changes are badly needed.  Possible solutions could be sought either by (1) rectifying the general policies and practices at modern universities, or by (2) improving the individual situation for each  disgruntled and demoralized scientist.  Since I regretfully do not see how the first possibility can be accomplished at the present time, I will consider here only the second possibility.

Why do I feel that university policies and practices cannot be reformed now?  Universities generally are very happy with exactly the same changes that upset their science faculty, since those maneuvers have significantly elevated the financial position of these institutions (see “Three Money Cycles Support Scientific Research”).  Any large and comprehensive solution for the problems in academia probably must await strong reform measures that can replace the ongoing commercialization of doing research in universities with some modern version of its traditional aims of finding new truth, creating valid new concepts, and, developing new ideas and new technology.  Similarly, in all levels of teaching science in universities, changes that can improve the present decayed educational system seem unlikely until there will be removal of such unrealistic philosophies as “truth is relative”, “all children are equal”, “education should be made easier, so students can learn quicker”, and, “that’s good enough”.  In my view, all such anti-education liberal proclamations really are only excuses for failure to do effective teaching.

What can actually be done to improve job satisfaction for individual faculty scientists? 

My suggestions here are directed towards practical considerations.  Because I believe that the policies for scientific research in universities are very unlikely to be changed or improved for a long time, I suggest that the best approach for individuals is to move out of the way of whatever causes their dissatisfaction.  This entails evaluating the nature of their problematic situation and the amount of change they believe is needed.  Many will find that this ultimately boils down to asking oneself whether it is time to find a better place to work.  I do indeed know personally that this is never an easy question, and that moving usually is very disruptive for the career of any academic scientist.  However, it should be recognized by all the upset university scientists that there now are an increasing number of good employment opportunities for scientists that are quite different from working in traditional roles at universities.  One now can conduct research experiments at the laboratory bench outside universities, or can perform science-related work completely outside research laboratories.  I already have discussed a number of these non-traditional opportunities in recent articles primarily aimed to inform graduate students and Postdocs (see “Other Jobs for Scientists, Parts I, II, and III”).

Dissatisfied university scientists who remain very enthusiastic about continuing to do lab research should seriously look at what is available in industrial research and development centers, and in government laboratories.  Much valuable information about these possibilities can be obtained by directly talking to doctoral scientists now working in these other environments, and personally asking them what they see as being serious local job problems.

Dissatisfied science faculty who still are very committed and enthusiastic about continuing to teach science should try to find a new employer, either at other universities or at non-university sites, where their viewpoints about what constitutes excellent education are shared with the other teachers and are actually put into practice (i.e., lip-service is not enough!).  With the recent development of digital education outlets, educational video programs, non-university course offerings, personal education coaches, private educational organizations, etc., there now are an increasing variety and number of employment opportunities for good science teachers to do new things.

Concluding Remarks for Part II

The increasing levels of job dissatisfaction amongst university faculty researchers and science teachers stem from the recent large shifts in (1) professional identity, (2) job aims and duties, (3) standards for job performance evaluations, (4) career expectations, and, (5) commercialization of academic research and teaching.  These modern changes largely run against what most practicing academic scientists were taught in graduate school, and directly give rise to increasing levels of job frustration and dismay.  The main message here is that these changes also act to decrease the quality of both scientific research and science teaching.  It is nationally important that good solutions to this quagmire must be developed.  It is up to each individual scientist to find a good environment for doing quality research and quality teaching.  The increased variety of job opportunities now available for scientists make non-traditional solutions to this important problem a realistic possibility.

Conclusions for Both Parts I and II

University scientists are increasingly upset with their job due to wholesale changes in many different aspects of researching and teaching.  Science at universities now is being degraded, and the professional roles of faculty scientists increasingly are distorted.  This problem is not some isolated small esoteric issue, but rather involves the purpose of science and research, and, the objective of becoming a doctoral scientist.  These very destructive changes in universities constitute a large portion of the reasons why I have come to believe that science itself now is dying (see my recent article in the Big Problems category on “Could Science and Research now be Dying?”).

 

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