TEACHING STUDENTS BASIC LAB SKILLS FOR A REGULATED ENVIRONMENTBIOMAN 2007Lisa SeidmanMadison Area Technical CollegeMadison, WI
WHY THE BASICS?Needs of studentsNeeds of employers
MYTH 1Basics means simple, easy, obviousIf this were true, far fewer problems in companies and in research labs
MYTH 2Most of this does not apply in research labs
MYTH 3We all learn the basics in high school, or someone elses class, or by osmosis
MYTH 4Basics are boring
BASICSWhat are basics?Different answers, but some common themes
HOW TO TEACH BASICS?ConsciouslySystematically model 1: way teach children musicmodel 2: way grad students are taughtUnderlying principles
THIS WORKSHOPTeaching basics consciouslySystematicallyUnderlying principles
TOPICS FOR THIS WORKSHOPQuality Basic lab task making a solutionMetrology (unifying principles)
STORY OF FRANCES KELSEYCase study
Purpose:introduce GMPintroduce process of developing drugmost important: idea of qualityBureaucrat who understood quality
QUALITY: THE BIG (BUT BRIEF) PICTURE
WHAT IS BIOTECHNOLOGY?The biotechnology industry transforms scientific knowledge into useful products
OVERVIEW Talk about product quality systemsIn broad wayApply ideas to the various work places we talked about
Broad systems of regulations, standards, or policies that ensure the quality of the final productGMP/GLP/GCP are examples of quality systems
WHAT IS PRODUCT QUALITY? What is a good product in biotechnology?That dependsConsider biotech:Research labsTesting labs Production facilities
QUALITY PRODUCT: RESEARCH LABResearch lab, knowledge is product:Knowledge of nature (basic research)Understanding of technology (applied research, R&D)
QUALITY SYSTEMS IN RESEARCH LABSQuality system in researchEnsure meaningful datahas been around a long timeIt is called:
DOING GOOD SCIENCE
Less formalized than other quality systemsNo one book spells it outNo laws to obeyBut it exists
INFORMAL SYSTEMConsequences of poor quality product not life-threatening soGovernment seldom involved in monitoring research qualityOversight not generally by outside inspectors or auditors
BUT THERE IS OVERSIGHTOversight is by peersGrant reviewPublicationsReputation
Compare and contrast situation in research labs and other work places
PRODUCT QUALITY: TESTING LABTesting lab:Information about samples Good product = result that can be relied on when making decisions
CONSEQUENCESA poor quality product can be life-threatening or have serious effects
QUALITY SYSTEMS IN TESTING LABSInclude most of what we call doing good science plusSpecific formal requirementsPersonnelEquipment TrainingFacilitiesDocumentation
You can find a book that spells it out for:Clinical labsForensic labsEnvironmental labs
ENFORCEMENT: TESTING LABSSince consequences of poor product can be life-threateningIs outside oversightFBIEPAEtc.
PRODUCT QUALITY: PRODUCTION FACILITYMake tangible itemsQuality product fulfills intended purpose Ex.: reagent grade salt vs road salt vs table salt
QUALITY SYSTEMS IN PRODUCTION FACILITIESDepends on nature of productPoor product may or may not have life-threatening consequences
SO, FOR EXAMPLEProducts for research use, not generally regulatedAgricultural products are regulated in one wayPharmaceutical products are regulated in another
VOLUNTARY STANDARDSCompanies that are not regulated may choose to comply with a product quality system for business reasons
ISO 9000ISO 9000Formal product quality systemExtensiveExists in a series of booksCompanies comply voluntarily to improve the quality of productsand to make more money
OVERSIGHT: ISO 9000Oversight by outside auditors, paid by company
BIOTECH AND MEDICAL PRODUCTSMany biotech companies that make money make medical/pharmaceutical productsConsequences of poor product can be life-threatening
SOThese products are highly regulated by the governmentBut, it wasnt always this way
HOW IS QUALITY BUILT INTO A PRODUCT?No single answerRequires:Skilled personnelWell-designed and maintained facilityWell-constructed processesProper raw materialsDocumentationChange controlValidation
ENFORCEMENTCompliance is enforced by governmentFDA
QUALITY IS BASICDetails may not be essential right nowIdea of quality is essential
LETS GO TO THE LABVERY BASIC LAB TASKS1. Write procedure to make 100 mL of a buffer solution that is:100 mM Tris, pH 7.5 2% NaCl10 g/mL of proteinase KQC your solution by checking its conductivityCheck the pH of a Tris buffer solution
PROCEDUREFor 100 mL of 100 mM Tris solution (FW 121.1) weigh out 1.211 g of Tris base. Dissolve in about 60 mL of water and adjust pH to 7.5.Add 2g of NaCl 10 g/mL of proteinase K X 100 mL = 1000 g = 1 mg. Weigh and add to Tris. Dissolve, BTV, check pH
VARIABILITY IN APPROACHES?Value of SOPs in ensuring consistencyValue of communicating among various lab workersDocumentation
WHAT DO STUDENTS NEED TO KNOW?ConceptualWhy they are making solution, contextHow to interpret recipeBasic calculationsInstrumentationHow to maintain, use, calibrate balanceHow to maintain, use, calibrate pH meterHow to measure volumeHow to maintain, use, calibrate conductivity meterQuality controlHow to ensure that solution is what it should beHow to document work
TEACHINGConcrete skillscalculationsusing equipmentetc.These are activities in the lab manual to systematically build these skills
UNDERLYING PRINCIPLES Quality ideas (e.g. reducing variability and documentation, following directionsSOPs)Math calculations/ideas that repeat over and over againSafety practicesMetrology principles
INTRODUCTION TO METROLOGYLisa SeidmanBioman 2007
DEFINITIONSMetrology is the study of measurements
Measurements are quantitative observations; numerical descriptions
OVERVIEWBegin with general principles
Next: weight, volume, pH, light transmittance (spectrophotometry)
WE WANT TO MAKE GOOD MEASUREMENTSMaking measurements is woven throughout daily life in a lab.
Often take measurements for granted, but measurements must be good.
What is a good measurement?
EXAMPLEA man weighs himself in the morning on his bathroom scale, 172 pounds. Later, he weighs himself at the gym,173 pounds.
QUESTIONSHow much does he really weigh?Do you trust one or other scale? Which one? Could both be wrong? Do you think he actually gained a pound?
Are these good measurements?
NOT SUREWe are not exactly certain of the mans true weight because:Maybe his weight really did change always sample issuesMaybe one or both scales are wrong always instrument issues
DO WE REALLY CARE?Do you care if he really gained a pound?
How many think give or take a pound is OK?
ANOTHER EXAMPLESuppose a premature baby is weighed. The weight is recorded as 5 pounds 3 ounces and the baby is sent home.
Do we care if the scale is off by a pound?
GOOD MEASUREMENTSA good measurement is one that can be trusted when making decisions.
We just made judgments about scales.
We make this type of judgment routinely.
IN THE LABAnyone who works in a lab makes judgments about whether measurements are good enough but often the judgments are made subconsciously differently by different peopleWant to make decisionsConsciousConsistent
QUALITY SYSTEMSAll laboratory quality systems are concerned with measurements
All want good measurements
NEEDAwareness of issues so can make good measurements.
Language to discuss measurements.
Tools to evaluate measurements.
METROLOGY VOCABULARYVery precise science with imprecise vocabulary(word precise has several precise meanings that are, without uncertainty, different)
Words have multiple meanings, but specific meanings
VOCABULARYUnits of measurement
Accuracy Precision Errors Uncertainty
UNITS OF MEASUREMENTUnits define measurementsExample, gram is the unit for massWhat is the mass of a gram? How do we know?
DEFINITIONS MADE BY AGREEMENTDefinitions of units are made by international agreements, SI systemExample, kilogram prototype in FranceK10 and K20 at NIST
EXTERNAL AUTHORITYMeasurements are always made in accordance with external authorityEarly authority was Pharaohs arm length
A standard is an external authorityAlso, standard is a physical embodiment of a unit
STANDARDS ARE:Physical objects, the properties of which are known with sufficient accuracy to be used to evaluate other items.
STANDARDS ARE AFFECTED BY THE ENVIRONMENTUnits are unaffected by the environment, but standards areExample, Pharaohs arm length might changeExample, a ruler is a physical embodiment of centimeters Can change with temperature But cm doesnt change
STANDARDS ALSO ARE:In chemical and biological assays, substances or solutions used to establish the response of an instrument or assay method to an analyte
See these in spectrophotometry labs
STANDARDS ALSO ARE:Documents established by consensus and approved by a recognized body that establish rules to make a process consistentExample ISO 9000ASTM standard method calibrating micropipettor
CALIBRATION IS:Bringing a measuring system into accordance with external authority, using standardsFor example, calibrating a balanceUse standards that have known massesRelate response of balance to units of kgDo this in lab
PERFORMANCE VERIFICATION IS:Check of the performance of an instrument or method without adjusting it.Do this in lab.
TOLERANCE IS:Amount of error that is allowed in the calibration of a particular item. National and international standards specify tolerances.
EXAMPLEStandards for balance calibration can have slight variation from true valueHighest quality 100 g standards have a tolerance of + 2.5 mg99.99975-100.00025 gLeads to uncertainty in all weight measurements
TRACEABILITY IS:The chain of calibrations, genealogy, that establishes the value of a standard or measurement
In the U.S. traceability for most physical and some chemical standards goes back to NIST
TRACEABILITYNote in this catalog example, traceable to NIST
VOCABULARYStandardsCalibrationTraceabilityTolerancePlay with these ideas in labs
MEASUREMENTWhat are the characteristics of good measurement?AccuracyPrecision
ACCURACY AND PRECISION ARE: Accuracy is how close an individual value is to the true or accepted valuePrecision is the consistency of a series of measurements
% error = True value measured value X 100% True value
Will calculate this in volume lab
EXPRESS PRECISIONStandard deviation (p. 187-190)Expression of variabilityTake the mean (average)Calculate how much each measurement deviates from meanTake an average of the deviation, so it is the average deviation from the meanTry this in the volume lab
ERROR IS:Error is responsible for the difference between a measured value and the true value
CATEGORIES OF ERRORSThree types of error:GrossRandomSystematic
RANDOM ERRORIn U.S., weigh particular 10 g standard every day. They see:9.999590 g, 9.999601 g, 9.999592 g .
What do you think about this?
RANDOM ERRORVariability No one knows why They correct for humidity, barometric pressure, temperatureError that cannot be eliminated. Called random error
RANDOM ERRORDo you think that repeating the measurement over and over would allow us to be more certain of the true weight of this standard?
RANDOM ERRORYes, because in the presence of only random error, the mean is more likely to be correct if repeat the measurement many times
Standard is probably really a bit light
Average of all the values is a good estimate of its true weight
RANDOM ERROR AND ACCURACYIn presence of only random error, average value will tend to be correct
With only one or a few measurements, may or may not be accurate
THERE IS ALWAYS RANDOM ERRORIf cant see it, system isnt sensitive enough
Less sensitive balance:10.00 g, 10.00 g, 10.00 gVersus 9.999600 g
SOCan we ever be positive of true weight of that standard?NoThere is uncertainty in every weight measurement
RELATIONSHIP RANDOM ERROR AND PRECISIONRandom error Leads to a loss of precision
SYSTEMATIC ERRORDefined as measurements that are consistently too high or too low, bias
Many causes, contaminated solutions, malfunctioning instruments, temperature fluctuations, etc., etc.
SYSTEMATIC ERRORTechnician controls sources of systematic error and should try to eliminate them, if possibleTemperature effectsHumidity effects Calibration of instrumentsEtc.
In the presence of systematic error, does it help to repeat measurements?
SYSTEMATIC ERRORSystematic error Does impact accuracy
Repeating measurements with systematic error does not improve the accuracy of the measurements
Match these descriptions with the 4 distributions in the figure: Good precision, poor accuracyGood accuracy, poor precisionGood accuracy, good precisionPoor accuracy, poor precision
ANOTHER DEFINTION OF ERROR IS:Error = is the difference between the measured value and the true value due to any cause
Absolute error = True value - measured value
Percent error is:True value - measured value (100 %)True value
ERRORS AND UNCERTAINTYErrors lead to uncertainty in measurementsCan never know the exact, true value for any measurement.Idea of a true value is abstract never knowable.In practice, get close enough
UNCERTAINTY IS:Estimate of the inaccuracy of a measurement that includes both the random and systematic components.
UNCERTAINTY ALSO IS:An estimate of the range within which the true value for a measurement lies, with a given probability level.
UNCERTAINTYNot surprisingly, it is difficult to state, with certainty, how much uncertainty there is in a measurement value.
But that doesnt keep metrologists from trying
METROLOGISTSMetrologists try to figure out all the possible sources of uncertainty and estimate their magnitude One or another factor may be more significant. For example, when measuring very short lengths with micrometers, care a lot about repeatability. But, with measurements of longer lengths, temperature effects are far more important
REPORT VALUESMetrologists come up with a value for uncertaintyYou may see this in catalogues or specificationsExample: measured value + an estimate of uncertainty
UNCERTAINTY ESTIMATESDetails are not important to us now
But principle is: any measurement, need to know where the important sources of error might be
SIGNIFICANT FIGURESOne cause of uncertainty in all measurements is that the value for the measurement can only read to a certain number of places
This type of uncertainty. It is called resolution error. (It is often evaluated using Type B methods.)
SIIGNIFICANT FIGURE CONVENTIONSSignificant figure conventions are used to record the values from measurementsExpression of uncertaintyAlso apply to very large counted valuesDo not apply to exact valuesCounts where are certain of valueConversion factors
ROUNDING CONVENTIONSCombine numbers in calculationsConfusingLook up rules when they need them
RECORDING MEASURED VALUESRecord measured values (or large counts) with correct number of significant figuresDont add extra zeros; dont drop ones that are significantWith digital reading, record exactly what it says; assume the last value is estimatedWith analog values, record all measured values plus one that is estimatedDiscussed in Laboratory Exercise 1
ROUNDINGA Biotechnology company specifies that the level of RNA impurities in a certain product must be less than or equal to 0.02%. If the level of RNA in a particular lot is 0.024%, does that lot meet the specifications?
The specification is set at the hundredth decimal place. Therefore, the result is rounded to that place when it is reported. The result rounded is therefore 0.02%, and it meets the specification.
GOOD WEB SITE FOR SIGNIFICANT FIGURES http://antoine.frostburg.edu/cgi-bin/senese/tutorials/sigfig/index.cgi
THERMOMETERSLook at the values for the thermometers on the board.Significant figure conventions can guide us in how to record the value that we read off any measuring instrument.With these thermometers, correct number of sig figs is _______.
Were they accurate? How could we figure out the true value for the temperature?
REPEATING MEASUREMENTSWould repeating measurements with these thermometers, assuming we did not calibrate them, improve our ability to trust them?Is their error an example of random or systematic error?
CALIBRATIONCalibration of the thermometers could lead to increased accuracyThis is a type of systematic errorIn the presence of systematic error, repeating the measurement will not improve its accuracy
TOLERANCEHere is a catalog description of mercury thermometers.Are these thermometers out of the range for which their tolerance is specified?
Were they precise? How could precision be measured?Would calibration help to make them more precise?
CALIBRATION Calibration would probably not improve their precision
RETURN TO OUR ORIGINAL TYPE OF QUESTIONAre our temperature measurements good measurements?How do you make that judgment?Can we trust them?
THERMOMETERS GOOD ENOUGH?Are times that we need to be very close in temperature measurements. For example PCR is fairly picky.Other times we can be pretty far off and process will still work.
EXPLORE SOME OF THESE IDEASIn lab:Calibrate instrumentsUse standardsCheck performance of pipettorsRecord measurement valuesCalculate per cent errorsCalculate repeatability
SAME IDEAS APPLYA good assay is one can trust when making a decisionAccuracy and precisionLinearityLimits
Teaching Basic Lab Skills ~ Lisa SeidmanBIOMAN 2007 ~ NHCTC Porstmouth NH