Thinking Scientifically

—Reliable ways of knowing

Introduction


Certain approaches to examining reality are reliable ways of learning about the universe we live in. Although these approaches are described here as “Thinking Scientifically” they are useful for reliably determining factual information in a variety of areas including the sciences, historical research, journalism, forensic investigations, legal proceedings, economics, policy development, making personal or business decisions, solving problems, choosing beliefs, and evaluating moral alternatives.

Objectives
lbeaumont The objectives of this course are to:
 * Encourage you to wonder about how our world works;
 * Improve your understanding of reality;
 * Help you
 * evaluate ways of knowing;
 * develop and adopt reliable ways of knowing;
 * recognize assumptions, bias, illusion, and fantasy;
 * learn about the universe we live in;
 * think more clearly;
 * understand what is;
 * Encourage you to adopt reliable ways of knowing and abandon unreliable ways of knowing.

All students are welcome and there are no prerequisites to this course. If you are having difficulty with any of the material, it may be beneficial to begin your studies at the beginning of the Clear Thinking curriculum.

The course contains many hyperlinks to further information. Use your judgment and these link following guidelines to decide when to follow a link, and when to skip over it.

This course is part of the Applied Wisdom curriculum and of the Clear Thinking curriculum.

If you wish to contact the instructor, please click here to send me an email or leave a comment or question on the discussion page.

OK, let’s begin thinking scientifically!

Guiding Principles
People have been exploring ways of knowing for millennia and have evaluated various methods by assessing how well results correspond with reality. From this extensive experience, clear thinkers have come to value:

Wonder, curiosity, exploration, and discovery over disinterest, apathy, and complacency;

Empirical evidence over preserving ideologies;

Embracing facts over denying inconvenient truths;

Investigation and experimentation over assumption, excuse, and storytelling;

Learning from mistakes over never making mistakes.

Representative evidence over anecdotes, narratives, and cherrypicked examples;

Doubt and a skeptical stance over certainty or gullibility;

Verification and falsification over assumption, gullibility, indifference, and apathy;

Seeking falsification over seeking confirmation;

Describing uncertainty over claiming certainty;

Replication and transparency over isolated reports and anecdotal reports;

Collaboration and interactions over isolation;

Humility over vanity and arrogance;

Expertise over authority;

Forming, testing, and rejecting hypothesis over salvaging failed hypotheses;

Continuous learning over preserving entrenched dogma;

Superseding falsified concepts over defending false beliefs;

General explanatory power over situational explanations;

Predictive power over post hoc rationalizations;

Explanation based on causal mechanisms over magical causes;

Natural mechanisms over supernatural mechanisms;

Consistency, convergence, and the unity of knowledge over inconsistencies, contradictions, and fragmented beliefs;

Coherence over incoherence;

Fewer assumptions over ad-hoc explanations;

Universal principles over situational rules;

Firm beliefs based on representative evidence over rigid beliefs based on entrenched dogma;

Objectivity over bias.

That is, while the items on the right may have some role, clear thinkers value the items on the left more.

To proceed, we must make some sort of assumption, implicitly or explicitly, about the sort of world we are in. Thinking scientifically is based on assumptions about the nature of the world that best accords with, and supports, empirically successful theories.

People who are thinking scientifically follow these principles:

Reality exists.
 * We live in the real world.
 * We can explore, investigate, examine, observe, measure, and probe that real world.
 * Reality is coherent, the most certain of all basic principles is that contradictory propositions are not true simultaneously.
 * Our highest epistemic priority is to explore reality and produce true descriptions of things in the world.
 * Correspondence with reality is the objective arbiter of disputes, truth, and knowledge.

The next sections expand on these guiding principles.

Wonder
French philosopher René Descartes offered that “Wonder is the first of all the passions.”

When we allow wonder to guide us our curiosity springs to life, we ask questions, we explore our surroundings, and we discover new ways to think about our world. This contrasts with indifference, disinterest, complacency, magical thinking, and certainty which favor stasis and even entrenchment of ideas and understanding.

When we are open to experience we are original, likely to come up with new ideas, curious about many different things, have an active imagination, and are inventive, reflective, and enjoy playing with ideas.

“The scientist is humble in the face of nature, not beholden to dogma, obeys only his eyes, and follows the truth wherever it leads.”

Young Isaac Newton wondered why apples fall down rather than up or sideways and continued to wonder if the same force that causes apples to fall toward the center of the earth could also keep the moon and planets in orbit. Albert Einstein wondered how the world would look to someone chasing after a beam of light and later developed his special theory of relativity.

Steven Gimble notes “Discovery commences with the awareness of anomaly, i.e. with the recognition that nature has somehow violated the paradigm-induced expectations that govern normal science.”

The remark “The most exciting phrase in science Is not ‘Eureka!’ but ‘That’s funny …’” highlights the importance of investigating anomalies and is attributed to several sources, including Isaac Asimov.

It is also helpful for journalists to wonder, explore, and notice anomaly.

On June 17, 1972, Watergate Complex security guard Frank Wills noticed tape covering the latches on some of the complex's doors, removed it, and discovered an hour later that someone had re-taped the locks. Wondering what was going on, he called police. This led to the arrest of five men. Washington Post reporters Bob Woodward and Carl Bernstein also wondered what was going on and their curiosity and explorations discovered information suggesting that knowledge of the break-in, and attempts to cover it up, led deeply into the upper reaches of the Justice Department, FBI, CIA, and the White House. The Watergate scandal unfolded and resulted in the resignation of president Richard Nixon.

When we wonder we are demonstrating our love of knowledge, exercising our curiosity, and keeping an open mind. Scientific thinking values wonder, curiosity, exploration, and discovery over disinterest, apathy, and complacency.

Assignment

 * 1) Recall an occasion when wonder, curiosity, exploration, and discovery resulted in you learning something new.
 * 2) Recall an occasion when disinterest or complacency resulted in you overlooking some important information or insights.

Embracing Reality
Scientific thinking embraces reality as the objective arbiter of disputes, speculation, and conjecture. Representative and reliable empirical evidence supersedes speculation. In his book What is This Thing Called Science, Alan Chalmers states “I believe that once we have the appropriate notions of confirmation and empirical evidence, the distinguishing feature of science lies precisely in the sense in which it is empirically supported.”

Investigation is the systematic exploration of reality.

Reality exists. Reality reminds us of its existence every time we bump into it by stubbing our toe, falling down the stairs, getting stuck in traffic, enjoying the cool breeze of a summer day, talking on the phone, reading under an electric light, comparing actual results to planned results, seeing our favorite sports teams win or lose, and by accepting all that we cannot change despite our wishful thinking.

Our perceptions are personal, and a reality exists independent of anything anyone happens to say or think about the matter. Daniel Patrick Moynihan reminds us that “Everyone is entitled to his own opinion, but not his own facts.” John Adams noted that “Facts are stubborn things; and whatever may be our wishes, our inclinations, or the dictates of our passions, they cannot alter the state of facts and evidence.”

Because science aims to produce true descriptions of things in the world correspondence with reality is the final arbiter of disputes. For example, Sam says the Eiffel tower is 250 meters tall, Joe says it is 350 meters tall, and Sue say it is 300 meters tall. Appealing to reality by accurately measuring the height of the Eiffel tower can settle this dispute. Reality is the objective and unbiased reference.

Truth is correspondence with reality. Facts are accurate statements about reality. Denial and delusion describe an insistence that something is not true despite overwhelming evidence. Embrace reality. Learn from reality. Yield to reality.

Products that are designed and tested in real-world conditions work well. Electric lights help us see at night, refrigerators keep food cold, bridges allow us to safely travel across rivers, airplanes transport us safely, smart phones connect us, global positioning systems are reliable navigational aids, the New Horizons mission photographed Pluto, and other engineering achievements are successful because they are built based on how the world really is. Designers learn each time new products encounter harsh realities, uncover design weaknesses, and improve product designs.

The germ theory of disease, the naturally occurring process of biological evolution, plate tectonics, the heliocentric structure of our solar system, the unfolding of the universe, and the standard model of particle physics were all discovered by carefully examining what is real, despite compelling contradictory ideas held by powerful people attached to alternative explanations and mechanisms. Unfounded assumptions were falsified as more accurate descriptions of reality emerged. Facts are stubborn because reality exists.

The reality of DNA evidence led to the freeing of more than 350 wrongfully convicted people through the work of the innocence project. The reality and extent of child sex abuse in the Catholic archdiocese of Boston was exposed by the investigations of the Boston Globes “spotlight” team. Inconvenient truths became accepted, and the sometimes-difficult work of embracing reality could proceed.

Scientific evidence informs the policy recommendations made by the Abdul Latif Jameel Poverty Action Lab. The research center draws on results from randomized impact evaluations to answer critical questions of how best to reduce poverty, and builds relationships with governments, Non-governmental organizations, and donors to share this knowledge and scale up effective programs.

To better understand reality, scientific thinking values:
 * Empirical evidence over preserving ideologies
 * Embracing facts over denying inconvenient truths
 * Investigation and experimentation over assumption, excuse, and storytelling
 * Representative evidence over anecdotes, narratives, and cherrypicked examples

Assignment

 * 1) Recall a time when an encounter with reality falsified your firmly held conviction. How did reality intrude on your fantasies, hopes, dreams, best laid plans, speculations, misconceptions, and greatest fears? What changed your mind? How long did this take? Describe how you overcame denial. What did you learn? How did you learn?
 * 2) Read the essay Height of the Eiffel Tower.
 * 3) Read the essay Perceptions are Personal.
 * 4) Complete the Wikiversity course Facing Facts.
 * 5) Complete the Wikiversity course Evaluating Evidence.
 * 6) Complete the module on Examining Ideologies.
 * 7) Independently verify information you receive through friendly persuasion.
 * 8) Ensure reality supersedes conjecture.
 * 9) Ensure ideologies yield to representative empirical evidence.
 * 10) Rely on careful evaluation of representative evidence to decide matters of fact.

Understanding Evolves
Scientific thinking is based on a provisional understanding that is supported by corroborating evidence and may be discarded and transformed through falsification. Consider what it would take to prove any theory of gravity. You can drop any number of things, lift weights, fall from a chair, watch apples drop from trees, and use a theory of gravity to precisely describe, explain, and predict the motion of planets throughout the solar system. Newton’s law of universal gravitation was very powerful and useful. When that was shown to be inadequate it was refined and superseded by Einstein’s general theory of relativity. These laws of gravity have been examined and found to be correct not only on earth, but in travel to the moon, many successful missions to Mars, and navigating the New Horizons mission to fly by Pluto. Yet the theory of gravity is still unproven because it is possible that some future falsification of the theory by reliable empirical evidence would need it to be refined and superseded. Despite the success of our theories of gravity the current theories are known to be incorrect or incomplete, based on several observed anomalies and discrepancies.

Scientific thinking begins with a deep-seated doubt that is carefully eroded over time by corroborating evidence and failed attempts at falsification. The result is a justified confidence in those theories that have withstood the rigors of intensive scrutiny fueled by doubt. Indeed, the scientific method boils down to making earnest efforts to prove existing models false.

A key characteristic that differentiates scientific methods from other forms of investigation is the "skeptical stance"—the viewpoint that the purpose of observation and experiment is to disprove a hypothesis, not to confirm it. This is the essential characteristic that distinguishes valid scientific investigations from demonstrations intended to confirm or defend pseudoscience claims, conspiracy theories, or religious dogma. “If claims are to be borne out by evidence then they must be genuinely tested against rather than accommodated to that evidence.”

More accurately scientific thinking is an on-going process of updating Bayesian probabilities. At any point in time people who are thinking scientifically adopt the theory that is best supported by all the available evidence. The dominant paradigm is eventually superseded when the evidence for some new paradigm overtakes the consensus. Sean Carroll reminds us that “all evidence matters” and a theory that must exclude certain evidence to avoid falsification is not likely to be correct.

As a school student you probably learned that Christopher Columbus discovered America. That was your provisional understanding. As you investigated history more closely, you might have wondered how the Native Americans were able to greet Columbus if indeed he had discovered America. Also, you may have learned that Leif Erikson traveled to North America and colonized Vinland, in present-day Newfoundland, several centuries before Columbus visited America. Your understanding becomes more complete, correct, and refined as you begin to understand the complexity of real events.

News commentator Walter Cronkite was often cited as “the most trusted man in America”. He conscientiously reported news on the course of the Vietnam war based largely on reports government officials provided him. He began to doubt his sources and traveled to Vietnam in February 1968 to see for himself what was happening. During that visit, General Creighton Abrams, then commander of all forces in Vietnam, told Cronkite, "we cannot win this Goddamned war, and we ought to find a dignified way out." Cronkite revised his thinking and upon his return reported to the American people “We have been too often disappointed by the optimism of the American leaders, both in Vietnam and Washington, to have faith any longer in the silver linings they find in the darkest clouds. … it seems now more certain than ever that the bloody experience of Vietnam is to end in a stalemate.”

Several weeks later, President Johnson, who sought to preserve his legacy and was now convinced his declining health could not withstand growing public criticism, announced he would not seek reelection.

For many years it was widely believed that peptic ulcer disease was caused by excess acid in the stomach. During that time acid control was the primary treatment for peptic ulcer disease, to only partial success. After many years of research, in 2005 Barry Marshall and Robin Warren were awarded the Nobel Prize in Physiology or Medicine for their discovery that peptic ulcer disease was primarily caused by the bacteria Helicobacter pylori. This new understanding transformed peptic ulcer disease treatment protocols. Our understanding evolves through creative destruction.

The skeptical movement seeks to evolve our understanding toward true beliefs by thinking scientifically and challenging popular but untrue beliefs.

So that our understanding continues to evolve, scientific thinking values:
 * Doubt and a skeptical stance over certainty or gullibility
 * Verification and falsification over assumption, gullibility, indifference, and apathy
 * Seeking falsification over seeking confirmation

Assignment

 * 1) What new evidence would be sufficient to prove the theory of gravity?
 * 2) What new evidence would be sufficient to disprove the theory of gravity?
 * 3) Reflect to recall examples where your understanding of some topic was refined or transformed by further investigation.

Openness
Thinking scientifically values openness—welcoming the assistance, guidance, insights, expansions, confirmation, criticism, cautions, and critical thinking of others.

“Science is a systematic search for knowledge whose validity does not depend on the particular individual but is open for anyone to check or rediscover.”

Each of the following sections focuses on an aspect of openness. Many examples of projects that illustrate the benefits of an open approach to research are described.

Collaboration
Collaboration is the process of two or more people or organizations working together to complete a task or achieve a goal. Teams that work collaboratively often access greater resources, recognition and rewards when facing competition for finite resources.

Many projects that have achieved excellent outcomes from collaborative efforts are briefly described here.

The Human Genome Project was an international scientific research project with the goal of determining the sequence of nucleotide base pairs that make up human DNA, and of identifying and mapping all the genes of the human genome from both a physical and a functional standpoint. It remains the world's largest collaborative biological project.

The associated Bermuda Principles set out rules for the rapid and public release of DNA sequence data.

The sequencing of the human genome holds benefits for many fields, from molecular medicine to human evolution. The Human Genome Project, through its sequencing of the DNA, can help us understand diseases including: genotyping of specific viruses to direct appropriate treatment; identification of mutations linked to different forms of cancer; the design of medication and more accurate prediction of their effects; advancement in forensic applied sciences; biofuels and other energy applications; agriculture, animal husbandry, bioprocessing; risk assessment; bioarcheology, anthropology and evolution along with the commercial development of genomics research related to DNA based products, a multibillion-dollar industry.

The Hubble Space Telescope was launched into low Earth orbit in 1990 and remains in operation. Hubble is one of the largest and most versatile and is well known as both a vital research tool and a public relations boon for astronomy. All Hubble data is made publicly available after the six-month-long exclusive access period of the principle investigator expires. Over 15,000 papers based on Hubble data have been published in peer-reviewed journals, and countless more have appeared in conference proceedings.

The Encyclopedia of Life (EOL) is a free, online collaborative encyclopedia intended to document all the 1.9 million living species known to science. It is compiled from existing databases and from contributions by experts and non-experts throughout the world. EOL's goal is to serve as a resource for the general public, enthusiastic amateurs, educators, students and professional scientists from around the world.

Citizen science is scientific research conducted, in whole or in part, by amateur (or nonprofessional) scientists. Citizen science is sometimes described as "public participation in scientific research," participatory monitoring, and participatory action research. It takes collaboration to its logical limits.

The Wikimedia Foundation has the stated goal of developing and maintaining open content, wiki-based projects and providing the full contents of those projects to the public free of charge. Hundreds of thousands of volunteers from around the world collaborate to create and continuously improve the content and make it freely available to anyone with an internet connection.

Various crowdsourcing projects encourage volunteers to collaborate in creating some cumulative result. Examples include creative works, software development, problem solving, and project funding.

Collaborations among many contributors conducting open research and working within open source models result in the development and sharing software and other creative developments, such as the Public Library of Science.

Investigators often collaborate to solve crimes. Law enforcement agencies cooperate at the local, regional, national, and international levels to gather evidence and share information. Citizens are sometimes recruited to help in searching large outdoor crime scene areas. Information is solicited from the public using publicity systems such as the list of FBI Ten Most Wanted Fugitives, TV Shows such as American’s most wanted, and publicizing missing children on milk cartons.

Assignment

 * 1) In what ways do you collaborate to solve problems?
 * 2) Which, if any, results from collaborative projects do you make use of and benefit from?

Peer review
Peer review is the evaluation of work by people of similar competence to the producers of the work—the author’s peers. It is a form of self-regulation by qualified members of a profession within the relevant field. Peer review methods are employed to maintain standards of quality, improve performance, and provide credibility.

Robust peer review is an important process for ensuring quality in published reports. They improve the accuracy, clarity, and reliability of published reports. They promote expert application of scientific thinking by assessing how well the methods used and the evidence gathered support the claims made. Peers that represent a variety of viewpoints can help to clarify the novelty, scope, and applicably of the work and identify weak arguments or other areas where the work can be improved. Peers that are expert in the field can assess the methods used, the sources cited, the relationship to other work in the field, and the novelty and importance of this work. Peer reviewers are encouraged to look at the robustness of the study and the results, including whether the methodology and analysis were appropriate and whether the results support the conclusions. Peer review helps to filter out incomplete or poorly done work and identify the best work. As a result, “peer review thus supports the system that routes the better papers to the better journals and this allows academics to focus their reading on a manageable number of core journals in their field.”

Robust peer review requires reviewers who:
 * seek true beliefs and base their decisions on careful evaluation of evidence,
 * are expert in the field of research pertaining to this work,
 * are independent of the work being reviewed, and
 * can dedicate the time and attention required to thoroughly assess the work.

Robust peer review is often, but not always effective in separating science from pseudo-science. Unfortunately, the peer review process can be manipulated, and failures occur. Poor work, and even hoaxes sometimes slip through and are published. When seeking true beliefs, references that have been improved by a robust peer review process are almost always more reliable than other sources.

Assignment
When choosing reliable references to support some belief, examine the peer review process each reference has undergone.

Publication
Publishing results makes newly acquired knowledge available to other researchers. This is helpful when the published results accurately report on reality. It is not helpful when the published results are unreliable.

Unfortunately, the most readily available publications are often the least reliable. Therefore the reader bears the burden of evaluating the reliability of each publication. To seek true beliefs, it is important to assess the reliably of the publications being referenced. The Wikipedia policy on identifying reliable sources provides useful guidance in assessing source reliability.

Open access publishing seeks to make reliable publications widely available and affordable.

Assignment
Assess the reliability of references you use to learn from, attain your beliefs, or to inform important decision-making.

Transparency
Transparency, as used in science, engineering, business, the humanities and in other social contexts, is operating in such a way that it is easy for others to see what actions are performed. It has been defined simply as "the perceived quality of intentionally shared information from a sender". Transparency implies openness, communication, and accountability.

The goals of transparency include sharing information, promoting collaboration, accelerating learning, inviting examination and scrutiny of methods, encouraging replication of results, and advancing research. Transparency exposes errors and discourages fraud.

Full transparency, as described in an open science taxonomy, requires open access, open data, open and reproducible research, open science evaluation, open science polices, and open science tools.

Assignment
Because transparency increases accountability, be cautious of projects that lack transparency.

Describing Uncertainty
Various levels of uncertainty are inherent in every observation and measurement. If a friend asks you “how cold is it outside” you can step outside and estimate the temperature, you can look at one or more outdoor thermometers, you can check the weather forecast, or perhaps you can make use of some precision temperature measuring equipment. Because these readings are likely to differ, you will need some reliable basis for interpreting the range of results. The accuracy of the result will depend on the method used. People who think scientifically consider the accuracy of the instruments used and are careful to report measurement uncertainty as they report each measurement.

People who are thinking scientifically pay attention to the significant figures used when reporting results. The distinction among, “It feels cool”, “Its in the 40’s”, "its about 44 degrees”, “its 44.2 degrees Fahrenheit” and “our best measurement is 44.22345 degrees Fahrenheit” is meaningful and is carefully reported, understood, and interpreted.

Error bars are graphical representations of the variability of data and are used on graphs to indicate the error or uncertainty in a reported measurement.

When conclusions are drawn from statistical samples, such as survey results, or clinical trials, it is important to report on the statistical significance of the results.

It is careless and misleading to report more accuracy than was observed, or to ignore the reported range of uncertainty when interpreting results. It is important to describe uncertainty and not to claim a level of precision that has not been achieved.

Reproducibility
The remarkable facts that objects fall to the earth, magnets attract, and the sun rises above the horizon each morning are uncontroversial because these observations are readily reproduced. Reproducibility of results is so important that the philosopher of science Karl Popper noted briefly in his book The Logic of Scientific Discovery that “non-reproducible single occurrences are of no significance to science.” Beginning with the work of Robert Boyle in the 17th century, it has become standard practice for scientific papers to include a Methods section sufficiently detailed that other researchers can repeat the experiment and replicate the result.

Galileo’s observations of the moons of Jupiter were controversial largely because they corroborated the Heliocentric plan of the solar system. Fortunately, these observations could be replicated by any careful observer with access to a sufficient telescope and have become universally accepted.

While reproducing results has bolstered most scientific claims, several promising claims have been discredited because the results could not be reproduced.

In March 1989, University of Utah chemists Stanley Pons and Martin Fleischmann reported the production of excess heat that could only be explained by a nuclear process that became known as "cold fusion". The report was astounding given the simplicity of the equipment. The news media reported on the experiments widely, and it was a front-page item on many newspapers around the world. Over the next several months others tried to replicate the experiment but were unsuccessful.

Here are several other examples where the inability to reproduce the results has disproved the original claim:
 * Stimulus-triggered acquisition of pluripotency, which was revealed to be the result of fraud
 * GFAJ-1, a bacterium that could purportedly incorporate arsenic into its DNA in place of phosphorus
 * MMR vaccine controversy – a study in The Lancet claiming the MMR vaccine caused autism was revealed to be fraudulent
 * Schön scandal – semiconductor "breakthroughs" revealed to be fraudulent
 * Power posing – a social psychology phenomenon that went viral after being the subject of a very popular TED talk but was unable to be replicated in dozens of studies.

Lack of reproducibly is an important indicator of pseudoscience. Science craves reproducibility, pseudoscience shuns it.

Because openness shines a light on discoveries, scientific thinking values:
 * Replication and transparency over isolated reports and anecdotal reports.
 * Collaboration and interactions over isolation

Assignment
Remain skeptical of results that are not replicated.

Humility
Humility is a willingness to admit your limitations. Humility is the realization that although we are each very special, we are nobody special. At its core, humility is openness to learning based on knowledge of your own ignorance. Intellectual humility is deciding that facts are more real and more important than ego. It is the opposite of ego involvement. Because arrogance sustains ignorance, humility is a prerequisite to learning. Humility allows facts to become more important than hopes, fears, preconceptions, ideologies, loyalty, habit, and ego. Humility allows expertise to challenge authority. A lack of humility allowed authority to suppress expertise when the space shuttle Challenger was launched on January 28, 1986 and broke apart 73 seconds into its flight, killing all seven crew members. Try to model after Richard Feynman and not the idiotic pompous military men who carelessly did not take the science seriously. The authority was so simple-minded that Feynman would go into their office and crack the safe with top secret military information because their password was almost visible in plain sight. Scientists should rule the world, and not the one percent rich or useless pollutant causing military.

Intellectual humility requires motivations toward true belief which exceed any motivations toward social status. Humility contrasts with vanity and arrogance.

Pope Paul V lacked humility when the Roman Inquisition tried Galileo in 1633 and found him "vehemently suspect of heresy", sentencing him to indefinite imprisonment. A lack of humility was evident when on February 24, 1616 the theologins who were asked to examine Galileo’s work delivered their unanimous report: the proposition that the Sun is stationary at the center of the universe is "foolish and absurd in philosophy, and formally heretical since it explicitly contradicts in many places the sense of Holy Scripture".

A humbler Pope would have worked to replicate Galileo’s observations supporting heliocentrism, learned from facts, and would not have obstructed learning. Scientific thinking values humility over arrogance and expertise over authority.

Assignment

 * 1) Recall an occasion when your vanity or arrogance prevented you from seeking true beliefs.
 * 2) What caused your motivations toward ego preservation to exceed your motivations toward true belief in that occasion?

Universality
Theories with greater explanatory power are preferred over a collection of ad-hoc explanations tailored to each situation that emerges. Newton’s law of universal gravitation provides a simple formula that describes many observations ranging from falling apples to the motions of the planets. Minor discrepancies between Newton’s theory and careful observations have been resolved by Einstein’s more general theory of general relativity. These theories have been tested at the farthest extent of our solar system by the New Horizons interplanetary space probe flyby of Pluto.

Similarly Maxwell's equations are a set of four equations that, together with the Lorentz force law, provide a mathematical model for electric, optical and radio technologies, such as power generation, electric motors, wireless communication, lenses, radar etc. Maxwell's equations describe how electric and magnetic fields are generated by charges, currents, and changes of the fields.

Contrast the universality of the gravitation laws and Maxwell’s equations with the complexity, specificity, and limited scope of rules for English-language spelling. For example the complex rule: i before e, Except after c, Or when sounded as "a," As in neighbour and weigh. has a narrow scope and many exceptions.

Other theories with great explanatory power and broad applicability include:
 * Cell theory is the historic scientific theory, now universally accepted, that living organisms are made up of cells.
 * Evolution is change in the heritable characteristics of biological populations over successive generations.
 * The germ theory of disease is the currently accepted scientific theory of disease. It states that many diseases are caused by microorganisms.
 * Genetics describes genes, genetic variation, and heredity in living organisms.
 * In chemistry and physics, atomic theory states that matter is composed of discrete units called atoms. The periodic table of the elements describes the chemical elements that constitute all of the ordinary matter of the universe.
 * The Big Bang theory is the prevailing cosmological model for the observable universe from the earliest known periods through its subsequent large-scale evolution. The model describes how the universe expanded from a very high-density and high-temperature state and offers a comprehensive explanation for a broad range of phenomena, including the abundance of light elements, the cosmic microwave background, large scale structure and Hubble's law.
 * The theory of relativity usually encompasses two interrelated theories by Albert Einstein: special relativity and general relativity. Special relativity applies to elementary particles and their interactions, describing all their physical phenomena except gravity. General relativity explains the law of gravitation and its relation to other forces of nature. It applies to the cosmological and astrophysical realm, including astronomy.
 * In theoretical physics, quantum field theory is a theoretical framework that combines classical field theory, special relativity, and quantum mechanics and is used to construct physical models of subatomic particles (in particle physics) and quasiparticles (in condensed matter physics).
 * Plate tectonics is a scientific theory describing the large-scale motion of seven large plates and the movements of a larger number of smaller plates of the Earth's lithosphere, since tectonic processes began on Earth between 3 and 3.5 billion years ago

Scientific thinking values general explanatory power over situational explanations and predictive power over post hoc rationalizations.

Coherence
Coherence is the quality of being logical, consistent, and forming a unified whole. One of the aims of science is to find models that will account for as many observations as possible within a coherent framework.

Aristotle’s law of noncontradiction and the principle of consilience are statements of coherence that are firmly at the foundation of scientific thinking. The law of noncontradiction is simply stated as: "The most certain of all basic principles is that contradictory propositions are not true simultaneously." Whenever a contradiction is uncovered, scientists jump into the gap and investigate thoroughly until the contradiction can be understood and resolved. Examining inconsistency can bring us to the threshold of insight and new understanding.

The perihelion precession of the planet mercury is a good example of carefully examining an inconsistency. An analysis of mercury’s orbit reported in 1859 showed a shift in the point of closest approach to the sun—known as the perihelion—differed from what was predicted by Newtonian physics. Several ad hoc and ultimately unsuccessful solutions were proposed, but they tended to introduce more problems. Eventually Albert Einstein showed that general relativity agrees closely with the observed amount of perihelion shift. This is an example where examining inconsistency brought us to the threshold of insight and new understanding.

Another manifestation of coherence is the role played by the principle of consilience—the unity of knowledge. There is an expectation that accurate investigations will result in broadly compatible results. Theories are typically overdetermined by a variety of evidence before they are widely accepted. An example of this is the response to the faster-than-light neutrino anomaly. Scientists worked diligently to resolve the contractions between the experimental results and the prevailing theories.

Because of consilience, the strength of evidence for any particular conclusion is related to how many independent methods are supporting the conclusion, as well as how different these methods are. Those techniques with the fewest (or no) shared characteristics provide the strongest consilience and result in the strongest conclusions. This also means that confidence is usually strongest when considering evidence from different fields, because the techniques are usually very different.

For example, the theory of evolution is supported by a convergence of evidence from genetics, molecular biology, paleontology, geology, biogeography, comparative anatomy, comparative physiology, and many other fields. In fact, the evidence within each of these fields is itself a convergence providing evidence for the theory. (As a result, to falsify evolution, most or all these independent lines of evidence would have to be found to be in error.) The strength of the evidence considered together as a whole, results in the strong scientific consensus that the theory is correct. In a similar way, evidence about the history of the universe is drawn from astronomy, astrophysics, planetary geology, and physics.

Finding similar conclusions from multiple independent methods is also evidence for the reliability of the methods themselves, because consilience eliminates the possibility of all potential errors that do not affect all the methods equally. This is also used for the validation of new techniques through comparison with the consilient ones. If only partial consilience is observed, this allows for the detection of errors in methodology; any weaknesses in one technique can be compensated for by the strengths of the others. Alternatively, if using more than one or two techniques for every experiment is infeasible, some of the benefits of consilience may still be obtained if it is well-established that these techniques usually give the same result.

A currently unsolved problem in physics is the search for a coherent theory of quantum gravity. Physicists are confident in the basic principles of quantum physics, and the current understanding gravity is based on Albert Einstein’s general theory of relativity. However, these two theories are not consistent, and no current theory reconciles relevant experimental observations. Confidence in the coherence of the universe propels the search for consistent theory.

Because scientific thinking values coherence over incoherence, scientific thinking values consistency, convergence, and the unity of knowledge over inconsistencies, contradictions, and fragmented beliefs. Inconsistencies are vigorously investigated, not dismissed as intractable mysteries.

Parsimony
Explanations that require the fewest new assumptions are parsimonious. Occam's razor is the problem-solving principle that the simplest solution tends to be the correct one. When presented with competing hypotheses to solve a problem, one should select the solution with the fewest assumptions.

A paraphrasing of this principle, often attributed to Albert Einstein, is "Everything should be kept as simple as possible, but not simpler."

A parsimonious theory that is correct can explain a wide range of observations without having to be fixed up by adding ad hoc hypothesis to accommodate each new observation. For example, a parsimonious theory of leprechauns is that “leprechauns do not exist.” This is simple and seems to be correct. An alternative theory that “leprechauns do exist” requires augmentation with several ad hoc assumptions including: 1) they are invisible, 2) they are silent, 3) they eat very little, 4) they work only in secret, 5) they communicate in magical ways, 6) their motives are complex, etc. From ancient times until the 17th century a geocentric model placed earth at the center of the universe. This seemed simple, obvious, correct, and complete. Eventually, however, careful astronomical observations by Galileo, Tycho Brahe and others were difficult to explain with a geocentric model. The complex epicycles in Ptolemy’s geocentric model were insufficient to accommodate these emerging observations. Eventually work by by Copernicus, Kepler, and Newton lead to acceptance of a parsimonious heliocentric model with planets travelling around the sun in elliptical orbits.

Favoring fewer assumptions over ad-hoc explanations often, but not always, leads to better scientific thinking.

Assignment
What, if any, ad-hoc hypotheses do you rely on to sustain your beliefs? Is there some more parsimonious explanation you can explore that corresponds more closely to reality?

Objectivity
Because science is an attempt to uncover truths about the natural world by eliminating personal biases, attachments, and false beliefs, objectivity is essential to scientific thinking. To be considered objective, the results of measurement must be communicated from person to person, and then demonstrated for third parties, as an advance in a collective understanding of the world.

Because work is done by researchers who are human, elements of human nature such as confirmation bias, subjectivity, loyalty, motivated reasoning, assumptions from existing world views, attachments, selective attention, and fatigue make it difficult to attain objectivity.

Scientific thinking employs many countermeasures to overcome human biases and improve objectivity. These methods include embracing reality as the primary objective reference, openness in the form of peer review, publication, transparency, and reproducibility. Research techniques such as random sampling, double-blind trials, and randomized controlled trials increase objectivity.

Robert Trivers notes that “The success of science appears in great part to be due to a series of built-in devices that guard against deceit and self-deception at every turn.” None-the-less, Max Planck quipped that “science advances one funeral at a time” after he was frustrated to observe “a new scientific truth does not triumph by convincing its opponents and making them see the light, but rather because its opponents eventually die, and a new generation grows up that is familiar with it.”

Objectivity is especially important to a fair criminal justice system. In 1990 five juvenile males—four African American and one Hispanic—were convicted of raping a jogger in Central Park by juries in two separate trials. Subsequently, known as the Central Park Five, they received sentences ranging from 5 to 15 years. In 2002, Matias Reyes, a convicted murderer and serial rapist in prison, confessed to raping the jogger, and DNA evidence confirmed his guilt. Convictions of the Central Park Five were vacated in 2002 based on this new, objective evidence.

Because scientific thinking values firm beliefs based on representative evidence over rigid beliefs based on entrenched dogma, objectivity is valued over bias.

Intellectual Honesty
Thinking scientifically requires intellectual honesty—a deep commitment to seek real good. Intellectual honesty requires a primary motivation to seek true beliefs. Our duty toward intellectual honesty is especially important when we share ideas that can inform or persuade others.

Assignment
Part 1:
 * 1) Complete the Wikiversity course on Intellectual Honesty.
 * 2) Be intellectually honest.
 * 3) Expect others to be intellectually honest. Help others become intellectually honest. Hold people who are deliberately dishonest accountable for their dishonesty.

Part 2:
 * 1) Scan this list of scientific misconduct incidents. Choose one incident to study for this assignment.
 * 2) Identify instances of intellectual dishonesty in the incident you chose to study.
 * 3) How could the negative effects of this incident have been prevented?

Continuous Improvement
Scientific methods are continuously improved.

Improvements in methods, tools, techniques, skills, equipment, insights, and all aspects of thinking scientifically are continuously sought out, shared, explored, and evaluated. These advancements are adopted whenever there is an opportunity to improve our ability to learn about the universe we live in.

Thinking scientifically requires wondering, exploring, and discovering how we can improve our abilities to think scientifically.

Limitations
Although thinking scientifically remains the most reliable way of knowing, it is difficult to apply in several important domains.
 * 1) Read the essay /The role and limitations of scientific reduction/.
 * 2) Remain aware of the domains of inquiry where thinking scientifically is most useful and less useful.

A Useful Metaphor

 * 1) Read the essay Science is like a living tree.
 * 2) What role do the various guiding principles play in the metaphor?

Summary
Practice thinking scientifically…
 * Enjoy wondering how the universe works.
 * Embrace reality. Face facts. Use realty as the objective arbiter of disputes.
 * Allow your understanding to evolve as you learn more about reality.
 * Learn from other scientific thinkers and share what you know.
 * Remain humble so you are ready to learn what is.
 * Understand the scope and limits of each rule you follow and each belief you hold. Avoid overgeneralizing.
 * Know that reality is coherent. Examine and resolve inconsistencies. Integrate your knowledge into a single integrated model of the universe.
 * Be suspicious of ad-hoc assumptions.
 * Accept that you and every human is inherently biased. Work to increase objectivity and seek to compensate for your inherent biases.
 * Choose reliable ways of knowing.
 * Be intellectually honest.
 * Improve your skills at thinking scientifically.