Monthly Archives: September 2015



Both methods and research instrumentation are important for science! (
Both methods and instrumentation are very important for scientific research! (

Detailed methods for conducting research experiments play a very fundamental role for all scientists.  The term, methodology, includes all the numerous different procedures, protocols, and techniques for acquiring and analyzing research data.  This introductory presentation  is for general readers!  It describes how research methods originate, develop, and mature, explains how methodology differs from instrumentation, and, points out the reasons why methodology has so much importance for modern science.

Basics about methodology for scientific research. 

Methods aim to produce research results that are accurate, repeatable, and valid.  Detailed protocols are the heart of methodology; these provide step-by-step instructions for how to collect good data (e.g., measure conversion of A into B, record amount of carbon dioxide as a function of ambient temperature, count the number of non-carbon atoms on graphene sheets, etc.).  To ensure reproducibility of experiments,  methods must be explicitly detailed, utilize a sequential progression of operations, and provide for completion of the data collection; once results start being generated, the scientist or technician then must always follow the protocol exactly, or else unrecognized variables can distort the data.  Analysis of research results constitutes a distinct aspect of any methodology, and often is focused on different statistical parameters.

Some scientists have been honored by Nobel Prizes for inventing very significant new research methods (see: ).  Why are methods important for science?  Methodology is vital because it: (1) permits experiments and data collection to be repeated, (2) details the conditions used to produce results, and (3) explains the reasoning for certain operational choices made for a given experiment or measurement.  Without adequate methodology, research results become disorganized, irreproducible, and unreliable.

How does methodology differ from instrumentation? 

Methodology and instrumentation (see: “Introduction to instrumentation for scientific research” ) are interrelated, but also differ.  Methods tell exactly how to conduct a measurement or record experimental data, while instruments are designed to permit research operations to be carried out.  Accordingly, methods always emphasize “how to do it“, and instruments furnish the “tools to get it done“.  By analogy, methodology is a road map telling the driver how to travel to a certain destination, but instrumentation is the automobile for doing that travel.  Thus, having the latest instrumentation alone is not enough; one also needs good methods to successfully produce valid research results.  Most research instruments come with a detailed users manual, but methodology goes beyond that by specifying the exact conditions for usage of the instrument during specific experiments.  Modern instrumentation often features highly automatic operations such that everything is done without much intervention by the operator; this uses a standardized methodology that is literally built into the instrument.

Where is methodology found? 

Methodology is found all over scientific research!  Most research operations have preferred protocols that give good results.  These protocols are derived from previous usage by numerous scientists, postdocs, graduate students, and technicians.  Some books give a detailed critical examination of research methods (e.g., the long series of volumes, “Methods in Enzymology“).  Certain modern professional journals feature only new methods and protocols for some area of experimental science; other more typical journals usually include a few articles about new methods.  Almost all research reports published in science journals include a section giving a detailed description of the “Materials and Methods” utilized for producing the experimental findings; this section necessarily is very important since experiments need to give the same results when conducted by other scientists in some other lab or country.  Even theoretical research studies need to have some description of the methods utilized.

How do preferred methods develop? 

New research instruments often cause new research methods to develop, and those lead to a burst of new results.  With enough time and sufficient users, certain methods become established as being accurate, efficient, reliable, and not overly expensive.  These are termed standard or preferred methods.  For new research projects, the experiments usually start with an established standard protocol, but then some small changes are tried; this process of ongoing development of methodology is practical science, because sometimes the changes give better results, and at other times they do not work.  Revised methods arise from established protocols whenever many scientists are using some variant condition that gives better results for their investigations; this revision of methodology goes on during actual research studies.

Concluding remarks. 

Detailed methods for conducting research and collecting experimental data are standard components of modern science, and are always undergoing further development.  Methods permit experimental measurements to be made in a reproducible manner that gives useful and reliable results.  Although often hidden from view, good methodology is necessary for research progress to be made in science.



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Wow! Research instrumentation is really fun!! (
Wow!  Research instrumentation is really fun!!   (

Research instruments play a big role in enabling the progress of science.  The term, instrumentation, includes all the different instruments from the many parts of science.  This introductory presentation is for general readers!  It describes how research equipment originates and develops, and, points out why science instruments almost always are an expensive budgetary component of modern research projects in science.

Basics about instrumentation for scientific research. 

Research instruments are tools used to acquire data (i.e., research results) during experimental investigations.  They are fundamental in all branches of science (e.g., cell counters and sorters, microscopes, PCR  machines (polymerase chain reaction), sonogram recorders, etc., in biomedical science; chromatographs, spectroscopes, ultrarapid recorders, x-ray diffractometers, etc., in chemistry; and, atomic force microscopes, electron diffractometers, magnetometers, terrestrial and space telescopes, etc., in physics).  Some research instruments are huge, but are used to examine very small specimens such as atoms and molecules, while other instruments are small, but are used to examine gigantic specimens such as volcanoes and oceans.  Thermometers are simple instruments that continue to be widely used by both scientists and ordinary people.

Science seeks answers to research questions (see: “Fundamentals for beginners: What is science?  What is research?  What are scientists?” ).  Obtaining these answers often uses measurements, images, sonograms, spectra, etc., made by research instruments.  Most such output is quantitative, and high precision always is sought.  Research instruments directly produce and record data, while accessories and related equipment expand the range of applications and enable processing of the raw results with statistics and analysis; nowadays, most science instruments are used with personal computers for control and operation, storage of output, and, analysis of the research data.

Some science instruments have extremely general usage (e.g., balances, light microscopes, mass analyzers, , pH meters, small ovens and freezers, vacuum chambers, etc.).  Other research instruments have only a very specific usage (e.g., cosmic ray detectors, Raman microscopes, space probes, ultra-rapid spectroscopes, etc.); usually these special instruments are much more complex and costly than are general instruments.  The cost to purchase a manufactured research instrument generally is high; this is due largely to their complexity, and to the limited number of potential buyers (e.g., some few hundreds).  High purchase prices of instrumentation are accepted due to the value of the research results produced (see: “Why is science so very expensive?  Why  do research experiments cost so much?” ).

Big science commonly uses unique, special, and very expensive research instruments that serve as a research facility for many scientists (e.g., 3-G synchrotrons; free-electron lasers; neutron diffractometers).  Two of the 3 new giant terrestrial telescopes now are being constructed in the mountains of northern Chile.  Each of the 3 has a total cost of over one billion dollars, and will take 8-10 years to finish their very complex  construction (see excellent article: “Behemoth telescopes build towards first light” by Toni Feder in 2015 Physics Today 68:24-27)).  Because of their fundamental importance for science, these very special research facilities each must be funded by multiple nations and organizations.

General stages in the history of any research instrument. 

The total development of research instruments generally passes through a common sequence of stages: (1) invention and first construction, (2) initial usage by the originator and other scientists, (3) commercial development by engineers, industrial scientists, and manufacturers, and, (4) ongoing development of advanced manufactured versions with additional or better capabilities.

Most research instruments available for purchase today originated with the work of one creative individual, known subsequently as the inventor or originator (i.e., often this person is both a scientist and an inventor).  The origination of science instruments typically results from a wish to acquire data that is not currently available.   The number of research scientists involved in stage 2 is largely determined by current interest in some field and by current attention to the research question(s) involved.  The total time needed for stage 3 is quite variable, and can be months to years.  Stage 4 features modifications and improvements in the commercialized instrument; it can involve establishment of competing manufacturers, each of which claims that their version produces data faster, more accurately, more efficiently, with finer detail, and/or with lower cost, than do the products of other vendors.  Scientist-users often help the manufacturers make significant improvements in instrument capabilities, functioning, and applications.

The fun of using research instruments. 

Using modern research instrumentation to produce good data is not always easy.  Acquiring the ability to become a skilled user of science equipment usually comes from personal hands-on experience and many failed trials.  Once operation of a research instrument is mastered by a scientist or technician, this not only results in production of good data, but also creates personal pride.  However, scientists who are very skillful and experienced experts often are surprised to find they only have an incomplete knowledge about the instrument when they first try to teach a new user how to operate it.  For some researchers, the trials and tribulations of using complex instruments becomes nothing less than fun!  Large, complex, and costly science instruments even can be considered to be wonderful toys by those lucky enough to use them!

Concluding remarks. 

Any research instrument, whether used by only a few or by very many scientists, has a history involving the work of engineers, scientist-users, workers at manufacturing companies, and various others, all of whom add to the accomplishment of the initial inventor(s) who built the first one.  Although there now is a general tendency to make commercial versions of research equipment more automatic and easier to use, that does not deny the scientist-user’s benefit of working to become very skillful in operating a research instrument.



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Asking questions, answering questions, and questioning answers are vital for education! (

Asking questions, answering questions, and questioning answers are vital for science education!   (


Following my recent posts with Q&A for assistant professors in science” , I now present some interesting  questions and answers between you and me!

Dr.M, please tell me why should I care anything about science and research?  It just doesn’t matter to me! 

Dr.M:  It will matter a whole bunch when you run into health problems, when new wars break out using weather as a destructive weapon, when TVs listen to your every spoken word at home, and, when it finally is admitted that you really are poisoning yourself and your children by what you eat and drink!  Due to the very deficient public education about science, you and most other adults have no idea what scientists do or how many of your everyday activities involve the products of science and engineering.  It will be fun for you to explore science; for starters, look on the internet for “NASA pictures from outer space” and, “3-D printing”!

Dr.M. asks you:  What is the thrill of research discovery for a scientist? 

Typical soccer mom:  It is just the same as finding a $50 bill when you are walking from your car into a supermarket!  I guess that research is fun and discovery is pure luck; it looks just like the lottery to me!  Discovery by scientists means they then are famous, can write a textbook, and get rich!

I love to watch science on TV for many hours almost every day because it all is so amusing!  Dr.M, can you please recommend which are the best science shows? 

Dr.M:  Most adults see science and research only as being some fantastic amusement.  Unfortunately, none of these science-as-entertainment shows deal with real scientists or real research. They are only for mindless amusement, and have much too much emphasis on who is the star researcher of the day, what horrible disease might be cured, and how science could solve some new global calamity.  Since I see all of this idiotic garbage as being a total waste of time, I will not recommend any to you!

Dr.M asks an Assistant Professor:  If your university employer turns down your application for tenure, what are you going to do? 

Assistant Professor:  Nobody taught me anything about how to get tenure in grad school.  I thought it was almost automatic so long as you were funded by research grants.  I know I will never win a Nobel Prize, but I still believe I am a successful research scientist!  If I didn’t enjoy lab research so much I would simply quit this nonsense and find a new job in the stock market or selling computers!

My husband and I want our young children to learn about science.  What is the best way to help them do that?  Do you think we should buy them a chemistry set, Dr.M? 

Dr.M: All young children have a strong curiosity, and they often focus that on what they see, hear, smell, taste, and touch.  For these youngsters, encourage them to explore and examine nature, and to learn about the world in your backyard or town (e.g., insects, birds, flowers, seeds, leaves, ponds and rivers, stars, beaches and soil, pollution, lightening, snow, garbage dumps, our moon, stars, etc., etc.).  Much can be done with little expense!  As they grow up they can use a magnifying glass, camera, and personal computer, all of which involve science and engineering.   A chemistry set is good for somewhat older children who show a special interest and liking for chemistry; however, for young kids having no affinity for chemistry it will probably only be a potentially dangerous toy (e.g., What does that taste like?).  Let your kids decide for themselves what they are interested in!

I looked on the internet for info about nanomaterials after reading one of your posts, Dr.M, but I just do not understand most of what I read.  What should I do?

Dr.M:  This situation is due to unfortunate general deficiencies in  science education.  Recognize that you have selected a large topic!  I suggest that you will find it easier if you study only a single more specific subject within the world of nanomaterials (e.g., carbon nanotubes, buckyballs, nanomedicine drug carriers, nanomachines, etc.).  Even without much background, you should be able to understand some descriptive articles about that subject in any Wikisite on the internet; be sure to also take a look at internet diagrams and videos for whatever subject you choose.

Dr.M. asks you:  Do you believe scientists should receive a much smaller paycheck than do star baseball players? 

Teenager:  What are the salary numbers?  Don’t star scientists get several million each year?  Postdocs must be equivalent to minor league players in baseball; what do they get?  Baseball players deserve millions because they bring in many more millions for their team owner.  Good research scientists should be paid at least as much as are professional baseball players!

I haven’t looked at any science since I was in high school.  Now I just retired.  Tell me, Dr.M, why should I spend any time with science now? 

Dr.M:  Science is not something you have to do, but it sure makes life more interesting!  Have you ever heard of 3-D printers?  Do you realize what they can create?  Don’t you wonder how they work?  Aren’t you curious about why your knees now are causing you pain, or why some new medicine might magically be able to give you full mobility again?  Do you realize that your children might not retire until age 80, and could live to be over 100 years old?  All of that is science in action!  Pick any topic that has some personal interest for you, and see what videos are available about that subject on the internet; I can almost guarantee that you will find something fascinating!

Dr.M. asks you:  Do you admire any scientist? 

College undergrad:  No, because I don’t know any scientists, and have no idea what they have done with their research.  I don’t know any Nobel Prizers or local scientists.  They all mean nothing to me!

I tried to read about research on new batteries, but I just cannot understand all the special terms and concepts.  Are there any translations available just for ordinary folks, Dr.M? 

Dr.M:  You are totally correct that all the special terminology creates a barrier preventing many people from reading about science.  The closest to actual translations are simplified articles found in some science magazines and news websites.  Take a look at such internet sites as: “ScienceNews for Students” ( ), and “Popular Science Magazine” ( ).   Good luck!

Dr.M. asks you:  What is the purpose of scientific research? 

Hollywood celeb:  I really have absolutely no idea, but I do love to watch science on TV!  It’s just so funny!  Research scientists must be mad!  I always laugh my head off and cannot believe these guys and gals are for real!

I appreciate science and would like to help scientific research, but I am not wealthy.  Tell me, Dr.M, how can I help out? 

Dr.M:  Even small financial contributions to promote scientific research always are welcome at science research organizations, universities, high schools, science societies, research workshops, museums, and other special science organizations.  Some people like to donate via contributions to crowd-funding organizations (i.e., search with any internet browser for “crowdfunding for science”).  Money-free ways to support science and research are to attend public presentations and discussions by professional scientists, or, sign up for a free subscription to specialized science journals, magazines, and websites (e.g., Microscopy Today ( ), “Microscopedia” ( ), SciTechDaily ( ), and, “Chemical and Engineering News” ( ).  You also can volunteer to personally participate in research projects at a nearby field site or laboratory.  Last, but definitely not least, encourage your own children and young relatives to  have some interest in science!

Dr.M. asks you:  Why can’t scientists agree about whether global warming is real? 

Aunt Maggie:  I guess they just love to argue!  Why don’t they do more research and less yapping?  Last winter was really cold, so I don’t believe whatever they say!  Maybe they are arguing about nothing?  It doesn’t matter much to me, anyhow!

Dr.M. asks you:  Why do some scientists cheat? 

Uncle Joe:  Probably they are after more money!  There are only small penalties if they do get caught, so why shouldn’t they take a chance on getting rich faster?  Everybody else today cheats at their work,  so why shouldn’t scientists?

Dr.M, Why won’t you allow any comments and e-mails on your website?

Dr.M:  I refuse to waste my valuable time dealing with lonely souls, morons having an empty life, or hungry entrepreneurs, as announced on November 14, 2014 (see: “Special Notice to All from Dr.M!” ).  Although It was necessary to do that, if 99.9% of 100,000 comments to you were ads for other websites or duplicate messages disguised as comments, then I believe you also would ban them.  It still amazes me that on any one day I used to receive multiple word-for-word identical messages from several different continents!  The blogosphere certainly is polluted by spamming on botnets!



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