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Page Introduction to Biochemistry Subtopics • Science, Scientific Method • What Is Mathematics? Introduction to biochemistry Subtopics Science, scientific method What is mathematics? Demarcation problem Classification of Science Definition and scope of biochemistry Historical perspective Applications and careers in biochemistry What is life? Chemical Vs. biochemical reactions Hierarchical organization Science and Scientific method What is Science? Science is an intellectual and practical activity encompassing the systematic study of the structure and behavior of the physical and the natural world through observation and experiment. Science is the pursuit and application of knowledge and understanding of the natural and social world following a systematic methodology based on evidence. Science is a body of knowledge attained through the scientific method. The scientific method The scientific method is a set of principles and procedures for the systematic pursuit of knowledge involving the recognition and formulation of a problem, the collection of data through observation and experiment, and the formulation and testing of hypotheses. Scientific method is an empirical and systematic method of acquiring knowledge based on evidence. The scientific method is a continuous process that has five basic elements. These elements can be illustrated by the discovery of the structure of DNA. These are 1. Problem identification: 1 | P a g e The scientific method begins with defining a question or a particular problem. Examples: Why is the sky blue? How can we design a drug to cure Corona Virus? How can we stop expansion of the Desert Locust? Previous investigation of DNA had determined its chemical composition (the four nucleotides), the structure of each individual nucleotide, and other properties. In 1950 Gregor Mendel showed that genetic inheritance had a mathematical description. DNA had been identified as the carrier of genetic information by the Avery–MacLeod–McCarty experiment in 1944 (Oswald Avery's transforming principle) but the mechanism of how genetic information was stored in DNA was unclear. 2. Formulating a hypothesis A hypothesis is a proposed explanation suggesting a possible correlation between or among a set of phenomena made on the basis of limited evidence as a starting point for further investigation. A hypothesis is a suggested explanation of a phenomenon, or alternately a reasoned proposal. Formulating a hypothesis involves induction based on previous observations. The hypothesis to be tested is called statistical or alternative hypothesis. The null hypothesis states the alternative hypothesis is false. Scientists want to show that the null hypothesis is false. A scientific hypothesis must be falsifiable, implying that it is possible to identify a possible outcome of an experiment or observation that conflicts with predictions deduced from the hypothesis. Examples: The scattering of blue light by air molecules make the sky blue. Poultry drugs can be modified for human use to fight corona virus. Toxic plants can be used to poison the Desert Locust. Equivalence principle formulated by Albert Einstein Linus Pauling proposed that DNA might be a triple helix. This hypothesis was also considered by Francis Crick and James D. Watson but discarded. Crick and Watson hypothesized that DNA had a double helical structure. DNA makes RNA makes protein formulated by Francis Crick 2 | P a g e 3. Derive predictions Predictions are specific but logical consequences of the formulated hypothesis. Predictions are deductions drawn from the hypotheses. Predictions must be able to distinguish the hypothesis from other likely hypotheses. Prediction: If DNA had a helical structure, its X-ray diffraction pattern would be X-shaped. This prediction was determined using the mathematics of the helix transform, which had been derived by Cochran, Crick and Vand (and independently by Stokes). This prediction was a mathematical construct, completely independent from the biological problem at hand. 4. Test predictions: Hypothesis testing involves conducting experimental and measurement-based testing to check the validity of the predictions. Evidences are generated by empirical experiments. The purpose of an experiment is to determine whether observations agree with or conflict with the predictions derived from a hypothesis. Experiments should be designed to minimize possible errors, especially through the use of appropriate scientific controls. For example, tests of medical treatments are commonly run as double-blind tests. Personnel are unaware of the recipients of the desired test drugs and placebos. Hypothesis testing involves careful observation, applying rigorous skepticism about what is observed, given that cognitive assumptions can distort how one interprets the observation. Experiment: Rosalind Franklin crystallized pure DNA and performed X-ray diffraction to produce photo. The results showed an X-shape. Watson and Crick showed an initial (and incorrect) proposal for the structure of DNA to a team from Kings College – Rosalind Franklin, Maurice Wilkins, and Raymond Gosling. Franklin immediately spotted the flaws which concerned the water content. Later Watson saw Franklin's detailed X-ray diffraction images which showed an X-shape and was able to confirm the structure was helical. This rekindled Watson and Crick's model building and led to the correct structure. 5. Analyze the findings to draw conclusions Analysis is done to compare the predictions of the alternative hypothesis to those of the null hypotheses. Various statistical tests are employed to draw conclusions leading to refinement (or elimination) of the hypotheses based on the experimental findings. Analysis: When Watson saw the detailed diffraction pattern, he immediately recognized it as a helix. He and Crick then produced their model, using this information along with the previously 3 | P a g e known information about DNA's composition and about molecular interactions such as hydrogen bonds. Watson and Crick were able to infer the essential structure of DNA by concrete modeling of the physical shapes of the nucleotides which comprise it. They were guided by the bond lengths which had been deduced by Linus Pauling and by Rosalind Franklin's X-ray diffraction images. 6. Report the results The findings are published and communicated to other scientists through a process of peer review for cross-checking and reproducibility. The paper describing the structure of DNA was published in 1953. The discovery became the starting point for many further studies involving the genetic material, such as the field of molecular genetics, and it was awarded the Nobel Prize in 1962. Properties of scientific method Objective observation: Measurement and data (possibly although not necessarily using mathematics as a tool) Reproducible evidences: repetition of experiment and/or observation as benchmarks for testing hypotheses Induction: reasoning to establish general rules or conclusions drawn from facts or examples Verification and testing: critical analysis, critical exposure to scrutiny, peer review and assessment Mathematics According to Galileo Galilei, the father of modern science, the laws of nature are written in the language of mathematics… measure what is measurable and make measurable what is not so. Mathematics is a language of nature and a language of science but it is not science. Mathematics is a conceptual framework for logical comprehension of the natural world Mathematics use patterns to formulate other patterns through its own proof. The demarcation problem Demarcation problem refers to properties to distinguish scientific beliefs from non-scientific beliefs (religious beliefs, wishful-thinking and artistic imagination). There three basic properties to distinguish scientific knowledge from non-scientific beliefs. 4 | P a g e 1. Logical positivism: scientific beliefs are based on empirically verifiable statements. 2. Falsification: scientific beliefs are base on statements that can be proved false and refuted by invalidating observations or arguments. Science is open to falsification. 3. Uncertainty: scientific measurements are usually accompanied by estimates of their uncertainty. The scientific method is iterative. At any stage it is possible to refine its accuracy and precision. Classification of science Scientific fields are broadly divided into natural sciences (the study of natural phenomena) and social sciences (the study of human behavior and society). Natural sciences are further divided into biology, chemistry, physics and earth sciences. Biochemistry As the name indicates, biochemistry is an interdisciplinary science. Biology is the science of living organisms and it so far has no first principle. The unifying principle in biology is the theory evolution by natural selection. Chemistry is the science of atoms and molecules and the first principle in chemistry is the quantum theory of matter. Biochemistry is the science of the atoms and molecules as governed by the laws of quantum chemistry in living organisms which are unified by the theory of evolution. Biochemistry is the chemistry of life processes; it deals with chemical processes within and related to living organisms. It studies the structure, composition, and chemical reactions of substances in living systems. Scope of biochemistry Historically, classical biochemists were a succession of hunters; microbiologists were microbe hunters, where as biochemists were vitamin hunters followed by enzyme hunters and gene and crystal hunters. Contemporary biochemistry has four main
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