Protocol (natural sciences)

In the natural sciences a protocol is a predefined written procedural method in the design and implementation of experiments. This should establish standards that can be adequately assessed by peer review and provide for successful replication of results by others in the field. It should include safety, procedural, equipment, and reporting standards. A major part of this protocol is predefining and documenting excluded data to avoid bias. This protocol is not the same but motivated by the Scientific method to the degree possible.

Overview
Many fields such as medical research has a standard operating procedure (SOP). These should be incorporated into the protocol and may in some cases be subject to laws and regulations, such as stem cell research. Statistics plays an almost universal role in all natural sciences from the efficacy of drugs to the accuracy of a given measurement. Their role cannot be underestimated from social science to Quantum Mechanics. Statistics can be a major source of bias even when the researcher is not trying to deceive and is often abused in mass media to make nonexistent or dubious claims.

Safety
Safety issues can range from simple goggles to huge investments in containment for bacterial, environmental, and volatile materials. For instance a simple torsion bar experiment would require little safety measures while biological hazards like the Hanta virus would require Hazmat suits, oxygen tanks, airlocks, showers, ultraviolet sterilizers, to just name a few. A medical kit should always be available in any circumstance. Procedural contingencies in the event of an accident are just as important.

Bias
Outside of safety the protocol is primarily concerned with avoiding bias. These issues will be scrutinized carefully by skeptics for errors and unknowns of all kinds. All the following issues will deal with this in some form. Although fraud is very rare careers have been lost or greatly harmed from reporting unreproducible results. This is most often a failure to adhere to good protocol practice. Researchers will often spend months or even years insuring their results are reproducible. Making sure the claims are not overinflated and the limitations of the equipment and data are properly reported can also save careers.

Procedural
Procedural issues 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 specs, calibrations, operating ranges, etc. Environmental factors such as temperature, humidity, barometric pressure, and other factors can often have effects on the results. Documenting these factors should be a part of any good procedure.

Using Statistics
The use and understanding of statistics is the backbone of most experimental science. The application is so general that statisticians represent a field of science in itself. The approximation error 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 insure that the sample used is representative. For instance political polls are best when restricted to likely voters. This is why web polls cannot be considered scientific. The sample size is another important concept and can lead to biased data simply due to an unlikely event. You are not likely to get a good poll with a sample size of 10, i.e. polling 10 people. The standard deviation and variance are concepts used to quantify the likely relevance of a given sample size. In the mass media and public the average and mean values are often used interchangeably often leading to dubious and even misleading arguments. The placebo effect and observer bias often require the experiment to use a double blind protocol and a control group.

Double Blind
The double blind protocol requires insuring not neither the experimenters or any subjects involved knows the outcome until after the experiment is complete. It also includes a control group in where it is not known by anyone involved which is the real experiment and which is the control experiment. An experimentalist has some latitude in how to define blinding and controls but may be requires to justify those choices if the results are published. 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 is rarely rationalized the same way. The actions of an experimentalist that know what is happening can also give any subjects clues about how to respond consciously or unconsciously. Although these effects are best know in the medical, social, and parapsychology fields they are just as important in the physical sciences. If you have a new gravimeter and run control readings every morning and experimental readings every evening can you be sure temperature and humidity changes are not responsible for any anomalous effects?

Reporting
Reporting should include all elements of the experiments design and protocols and any environmental factors or mechanical limitations that might effect the validity of the results. If the results are found to be in error due to factors that were properly reported and discussed it should have no negative impact on the scientist. If the errors are found contrary to the claims of the scientist it may have a large negative impact on that scientist career. In general report everything and honestly discuss any factors that might impact the results.

Ethics
Ethical issues include but are not limited to scientific misconduct. They can also include human and Animal experimentation. Many of these ethical issues are a matter of law and researchers are responsible for understanding these laws as it applies to them. Failure to properly apply scientific methods and procedures can also imply ethical misconduct.

Sites and Journals
There are many scientific journals that publish methods and protocols. There are also open-access sites where researchers can download their protocols and many research groups publish their protocols on their websites. Examples of these are listed below:

Open-access sites

 * SyntheticPages
 * TAIR Protocol Search (is part of the The Arabidopsis Information Resource site)
 * Nature Protocols also has section called Protocols Network where researchers are invited to upload their protocols. These protocols are freely available..

Scientific Journals

 * CSH Protocols
 * Nature Protocols
 * Nature Methods
 * Current Protocols
 * Methods
 * Analytical Chemistry
 * Analytical biochemistry
 * Organic synthesis
 * BioMed Protocols