Protocol (natural sciences) - AbsoluteAstronomy.com

In the natural sciences a protocol is a predefined written procedural method in the design and implementation of experiments. Protocols are written whenever it is desirable to standardize a laboratory method to ensure successful replication

Reproducibility

Reproducibility is the ability of an experiment or study to be accurately reproduced, or replicated, by someone else working independently...

of results by others in the same laboratory or by other laboratories. Detailed protocols also facilitate the assessment of results through peer review

Peer review

Peer review is a process of self-regulation by a profession or a process of evaluation involving qualified individuals within the relevant field. Peer review methods are employed to maintain standards, improve performance and provide credibility...

. In addition to detailed procedures and lists of required equipment and instruments, protocols often include information on safety precautions, the calculation of results and reporting standards, including statistical analysis and rules for predefining and documenting excluded data to avoid bias. Protocols are employed in a wide range of experimental fields, from social science to quantum mechanics

Quantum mechanics

Quantum mechanics, also known as quantum physics or quantum theory, is a branch of physics providing a mathematical description of much of the dual particle-like and wave-like behavior and interactions of energy and matter. It departs from classical mechanics primarily at the atomic and subatomic...

. Written protocols are also employed in manufacturing to ensure consistent quality.

Overview

Formal protocols are the general rule in fields of applied science, such as environmental and medical studies that require the coordinated, standardized work of many participants. Such predefined protocols are an essential component of Good Laboratory Practice

Good Laboratory Practice

In the experimental research arena, the phrase good laboratory practice or GLP specifically refers to a quality system of management controls for research laboratories and organizations to try to ensure the uniformity, consistency, reliability, reproducibility, quality, and integrity of chemical ...

(GLP) and Good Clinical Practice

Good clinical practice

Good Clinical Practice is an international quality standard that is provided by International Conference on Harmonisation , an international body that defines standards, which governments can transpose into regulations for clinical trials involving human subjects.Good Clinical Practice guidelines...

(GCP) regulations. Protocols written for use by a specific laboratory may incorporate or reference standard operating procedures (SOP) governing general practices required by the laboratory. A protocol may also reference applicable laws and regulations that are applicable to the procedures described. Formal protocols typically require approval by a laboratory official before they are implemented for general use.

Manufacturing protocols are required by current good manufacturing practice

Good Manufacturing Practice

"Good manufacturing practice" or "GMP" are practices and the systems required to be adapted in pharmaceutical manufacturing, quality control, quality system covering the manufacture and testing of pharmaceuticals or drugs including active pharmaceutical ingredients, diagnostics, foods,...

(cGMP) for manufacture of food

Food

Food is any substance consumed to provide nutritional support for the body. It is usually of plant or animal origin, and contains essential nutrients, such as carbohydrates, fats, proteins, vitamins, or minerals...

s, pharmaceuticals, and medical device

Medical device

A medical device is a product which is used for medical purposes in patients, in diagnosis, therapy or surgery . Whereas medicinal products achieve their principal action by pharmacological, metabolic or immunological means. Medical devices act by other means like physical, mechanical, thermal,...

Safety

Safety precautions are a valuable addition to a protocol, and can range from requiring goggles to provisions for containment of microbes, environmental hazards, toxic substances, and volatile solvents. Procedural contingencies in the event of an accident may be included in a protocol or in a referenced SOP.

Procedures

Procedural information may include not only safety procedures but also procedures for avoiding contamination, calibration of equipment, equipment testing, documentation, and all other relevant issues. These procedural protocols can be used by skeptics to invalidate any claimed results if flaws are found.

Equipment

Equipment testing and documentation includes all necessary specifications, calibrations, operating ranges, etc. Environmental factors such as temperature, humidity, barometric pressure, and other factors can often have effects on results. Documenting these factors should be a part of any good procedure.

Calculations, Statistics and Bias

Protocols for methods that produce numerical results generally include detailed formulae for calculation of results. Formula may also be included for preparation of reagents and other solutions required for the work. Methods of statistical analysis

Statistics

Statistics is the study of the collection, organization, analysis, and interpretation of data. It deals with all aspects of this, including the planning of data collection in terms of the design of surveys and experiments....

may be included to guide interpretation of the data.

Many protocols include provisions for avoiding bias in the interpretation of results. Approximation error

Approximation error

The approximation error in some data is the discrepancy between an exact value and some approximation to it. An approximation error can occur because#the measurement of the data is not precise due to the instruments...

is common to all measurements. These errors can be absolute errors from limitations of the equipment or propagation errors from approximate numbers used in calculations. Sample bias is the most common and sometimes the hardest bias to quantify. Statisticians often go to great lengths to ensure that the sample

Sample (statistics)

In statistics, a sample is a subset of a population. Typically, the population is very large, making a census or a complete enumeration of all the values in the population impractical or impossible. The sample represents a subset of manageable size...

used is representative. For instance political polls are best when restricted to likely voters and this is one of the reasons why web polls cannot be considered scientific. The sample size

Sample size

Sample size determination is the act of choosing the number of observations to include in a statistical sample. The sample size is an important feature of any empirical study in which the goal is to make inferences about a population from a sample...

is another important concept and can lead to biased data simply due to an unlikely event. A sample size of 10, i.e. polling 10 people, will seldom give valid polling results. Standard deviation

Standard deviation

Standard deviation is a widely used measure of variability or diversity used in statistics and probability theory. It shows how much variation or "dispersion" there is from the average...

and variance

Variance

In probability theory and statistics, the variance is a measure of how far a set of numbers is spread out. It is one of several descriptors of a probability distribution, describing how far the numbers lie from the mean . In particular, the variance is one of the moments of a distribution...

are concepts used to quantify the likely relevance of a given sample size

Sample size

. The mass media

Mass media

Mass media refers collectively to all media technologies which are intended to reach a large audience via mass communication. Broadcast media transmit their information electronically and comprise of television, film and radio, movies, CDs, DVDs and some other gadgets like cameras or video consoles...

and the public often use average
Average
In mathematics, an average, or central tendency of a data set is a measure of the "middle" value of the data set. Average is one form of central tendency. Not all central tendencies should be considered definitions of average....

and mean
Arithmetic mean
In mathematics and statistics, the arithmetic mean, often referred to as simply the mean or average when the context is clear, is a method to derive the central tendency of a sample space...

values interchangeably, which can lead to dubious and even misleading arguments. The placebo effect

Placebo effect

Placebo effect may refer to:* Placebo effect, the tendency of any medication or treatment, even an inert or ineffective one, to exhibit results simply because the recipient believes that it will work...

and observer bias often require an experiment to use a double blind protocol and a control group.

Blinded protocols

A protocol may require blinding to avoid bias.

A single blind protocol requires that the experimenter does not know the identity of samples or animals during the testing and calculations. It is appropriate when no human subjects are involved.

A double blind protocol comes into play when human subjects are tested and requires insuring neither the experimenter nor experimental subjects have knowledge of the identity of the treatments or the results until after the experiment is complete.

An experimenter may have latitude defining procedures for blinding and controls but may be required to justify those choices if the results are published or submitted to a regulatory agency. When it is known during the experiment which data was negative there are often reasons to rationalize why that data shouldn't be included. Positive data are rarely rationalized the same way.

Reporting

A protocol may specify reporting requirements. Reporting requirements would include all elements of the experiments design and protocols and any environmental factors or mechanical limitations that might effect the validity of the results.