Misplaced Pages

#438561

139-450: Biostatistical modeling forms an important part of numerous modern biological theories. Genetics studies, since its beginning, used statistical concepts to understand observed experimental results. Some genetics scientists even contributed with statistical advances with the development of methods and tools. Gregor Mendel started the genetics studies investigating genetics segregation patterns in families of peas and used statistics to explain

278-443: A consequent . P is the assumption in a (possibly counterfactual ) What If question. The adjective hypothetical , meaning "having the nature of a hypothesis", or "being assumed to exist as an immediate consequence of a hypothesis", can refer to any of these meanings of the term "hypothesis". In its ancient usage, hypothesis referred to a summary of the plot of a classical drama . The English word hypothesis comes from

417-429: A helical structure (i.e., shaped like a corkscrew). Their double-helix model had two strands of DNA with the nucleotides pointing inward, each matching a complementary nucleotide on the other strand to form what look like rungs on a twisted ladder. This structure showed that genetic information exists in the sequence of nucleotides on each strand of DNA. The structure also suggested a simple method for replication : if

556-534: A sexual process for transferring DNA from one cell to another cell (usually of the same species). Transformation requires the action of numerous bacterial gene products , and its primary adaptive function appears to be repair of DNA damages in the recipient cell. The diploid nature of chromosomes allows for genes on different chromosomes to assort independently or be separated from their homologous pair during sexual reproduction wherein haploid gametes are formed. In this way new combinations of genes can occur in

695-582: A DNA molecule. In 1983, Kary Banks Mullis developed the polymerase chain reaction , providing a quick way to isolate and amplify a specific section of DNA from a mixture. The efforts of the Human Genome Project , Department of Energy, NIH, and parallel private efforts by Celera Genomics led to the sequencing of the human genome in 2003. At its most fundamental level, inheritance in organisms occurs by passing discrete heritable units, called genes , from parents to offspring. This property

834-493: A complex trait is called heritability . Measurement of the heritability of a trait is relative—in a more variable environment, the environment has a bigger influence on the total variation of the trait. For example, human height is a trait with complex causes. It has a heritability of 89% in the United States. In Nigeria, however, where people experience a more variable access to good nutrition and health care , height has

973-576: A consistent, coherent whole that could begin to be quantitatively modeled. In parallel to this overall development, the pioneering work of D'Arcy Thompson in On Growth and Form also helped to add quantitative discipline to biological study. Despite the fundamental importance and frequent necessity of statistical reasoning, there may nonetheless have been a tendency among biologists to distrust or deprecate results which are not qualitatively apparent. One anecdote describes Thomas Hunt Morgan banning

1112-479: A convenient mathematical approach that simplifies cumbersome calculations . Cardinal Bellarmine gave a famous example of this usage in the warning issued to Galileo in the early 17th century: that he must not treat the motion of the Earth as a reality, but merely as a hypothesis. In common usage in the 21st century, a hypothesis refers to a provisional idea whose merit requires evaluation. For proper evaluation,

1251-483: A different parent. Many species have so-called sex chromosomes that determine the sex of each organism. In humans and many other animals, the Y chromosome contains the gene that triggers the development of the specifically male characteristics. In evolution, this chromosome has lost most of its content and also most of its genes, while the X chromosome is similar to the other chromosomes and contains many genes. This being said, Mary Frances Lyon discovered that there

1390-546: A diploid cell with paired chromosomes. Diploid organisms form haploids by dividing, without replicating their DNA, to create daughter cells that randomly inherit one of each pair of chromosomes. Most animals and many plants are diploid for most of their lifespan, with the haploid form reduced to single cell gametes such as sperm or eggs . Although they do not use the haploid/diploid method of sexual reproduction, bacteria have many methods of acquiring new genetic information. Some bacteria can undergo conjugation , transferring

1529-523: A formative phase. In recent years, philosophers of science have tried to integrate the various approaches to evaluating hypotheses, and the scientific method in general, to form a more complete system that integrates the individual concerns of each approach. Notably, Imre Lakatos and Paul Feyerabend , Karl Popper's colleague and student, respectively, have produced novel attempts at such a synthesis. Concepts in Hempel's deductive-nomological model play

SECTION 10

#1732791702439

1668-429: A gene is used to produce a specific amino acid sequence . This process begins with the production of an RNA molecule with a sequence matching the gene's DNA sequence, a process called transcription . This messenger RNA molecule then serves to produce a corresponding amino acid sequence through a process called translation . Each group of three nucleotides in the sequence, called a codon , corresponds either to one of

1807-482: A heritability of only 62%. The molecular basis for genes is deoxyribonucleic acid (DNA). DNA is composed of deoxyribose (sugar molecule), a phosphate group, and a base (amine group). There are four types of bases: adenine (A), cytosine (C), guanine (G), and thymine (T). The phosphates make phosphodiester bonds with the sugars to make long phosphate-sugar backbones. Bases specifically pair together (T&A, C&G) between two backbones and make like rungs on

1946-435: A higher body temperature. In a low-temperature environment, however, the protein's structure is stable and produces dark-hair pigment normally. The protein remains functional in areas of skin that are colder—such as its legs, ears, tail, and face—so the cat has dark hair at its extremities. Environment plays a major role in effects of the human genetic disease phenylketonuria . The mutation that causes phenylketonuria disrupts

2085-436: A human-based only method for data collection. Finally, all data collected of interest must be stored in an organized data frame for further analysis. Data can be represented through tables or graphical representation, such as line charts, bar charts, histograms, scatter plot. Also, measures of central tendency and variability can be very useful to describe an overview of the data. Follow some examples: One type of table

2224-430: A hypothesis must be falsifiable , and that one cannot regard a proposition or theory as scientific if it does not admit the possibility of being shown to be false. Other philosophers of science have rejected the criterion of falsifiability or supplemented it with other criteria, such as verifiability (e.g., verificationism ) or coherence (e.g., confirmation holism ). The scientific method involves experimentation to test

2363-461: A key role in the development and testing of hypotheses. Most formal hypotheses connect concepts by specifying the expected relationships between propositions . When a set of hypotheses are grouped together, they become a type of conceptual framework . When a conceptual framework is complex and incorporates causality or explanation, it is generally referred to as a theory. According to noted philosopher of science Carl Gustav Hempel , Hempel provides

2502-506: A ladder. The bases, phosphates, and sugars together make a nucleotide that connects to make long chains of DNA. Genetic information exists in the sequence of these nucleotides, and genes exist as stretches of sequence along the DNA chain. These chains coil into a double a-helix structure and wrap around proteins called Histones which provide the structural support. DNA wrapped around these histones are called chromosomes. Viruses sometimes use

2641-505: A living cell or organism may increase or decrease gene transcription. A classic example is two seeds of genetically identical corn, one placed in a temperate climate and one in an arid climate (lacking sufficient waterfall or rain). While the average height the two corn stalks could grow to is genetically determined, the one in the arid climate only grows to half the height of the one in the temperate climate due to lack of water and nutrients in its environment. The word genetics stems from

2780-401: A mistaken alignment; this makes some regions in genomes more prone to mutating in this way. These errors create large structural changes in DNA sequence— duplications , inversions , deletions of entire regions—or the accidental exchange of whole parts of sequences between different chromosomes, chromosomal translocation . Scientific question A hypothesis ( pl. : hypotheses )

2919-456: A phenotype involves studying identical and fraternal twins , or other siblings of multiple births . Identical siblings are genetically the same since they come from the same zygote. Meanwhile, fraternal twins are as genetically different from one another as normal siblings. By comparing how often a certain disorder occurs in a pair of identical twins to how often it occurs in a pair of fraternal twins, scientists can determine whether that disorder

SECTION 20

#1732791702439

3058-560: A proposed new law of nature. In such an investigation, if the tested remedy shows no effect in a few cases, these do not necessarily falsify the hypothesis. Instead, statistical tests are used to determine how likely it is that the overall effect would be observed if the hypothesized relation does not exist. If that likelihood is sufficiently small (e.g., less than 1%), the existence of a relation may be assumed. Otherwise, any observed effect may be due to pure chance. In statistical hypothesis testing, two hypotheses are compared. These are called

3197-403: A series of genes can be combined to form a linear linkage map that roughly describes the arrangement of the genes along the chromosome. Genes express their functional effect through the production of proteins, which are molecules responsible for most functions in the cell. Proteins are made up of one or more polypeptide chains, each composed of a sequence of amino acids . The DNA sequence of

3336-457: A single parent. Offspring that are genetically identical to their parents are called clones . Eukaryotic organisms often use sexual reproduction to generate offspring that contain a mixture of genetic material inherited from two different parents. The process of sexual reproduction alternates between forms that contain single copies of the genome ( haploid ) and double copies ( diploid ). Haploid cells fuse and combine genetic material to create

3475-448: A small circular piece of DNA to another bacterium. Bacteria can also take up raw DNA fragments found in the environment and integrate them into their genomes, a phenomenon known as transformation . These processes result in horizontal gene transfer , transmitting fragments of genetic information between organisms that would be otherwise unrelated. Natural bacterial transformation occurs in many bacterial species, and can be regarded as

3614-400: A smooth blend of traits from their parents. Mendel's work provided examples where traits were definitely not blended after hybridization, showing that traits are produced by combinations of distinct genes rather than a continuous blend. Blending of traits in the progeny is now explained by the action of multiple genes with quantitative effects . Another theory that had some support at that time

3753-423: A study aims to understand an effect of a phenomenon over a population . In biology , a population is defined as all the individuals of a given species , in a specific area at a given time. In biostatistics, this concept is extended to a variety of collections possible of study. Although, in biostatistics, a population is not only the individuals, but the total of one specific component of their organisms , as

3892-468: A sum, a subtraction must be applied. When testing a hypothesis, there are two types of statistic errors possible: Type I error and Type II error . The significance level denoted by α is the type I error rate and should be chosen before performing the test. The type II error rate is denoted by β and statistical power of the test is 1 − β. The p-value is the probability of obtaining results as extreme as or more extreme than those observed, assuming

4031-452: A transition of heredity from its status as myth to that of a scientific discipline, by providing a fundamental theoretical basis for genetics in the twentieth century. Other theories of inheritance preceded Mendel's work. A popular theory during the 19th century, and implied by Charles Darwin 's 1859 On the Origin of Species , was blending inheritance : the idea that individuals inherit

4170-412: A unique three-dimensional structure for that protein, and the three-dimensional structures of proteins are related to their functions. Some are simple structural molecules, like the fibers formed by the protein collagen . Proteins can bind to other proteins and simple molecules, sometimes acting as enzymes by facilitating chemical reactions within the bound molecules (without changing the structure of

4309-411: A useful metaphor that describes the relationship between a conceptual framework and the framework as it is observed and perhaps tested (interpreted framework). "The whole system floats, as it were, above the plane of observation and is anchored to it by rules of interpretation. These might be viewed as strings which are not part of the network but link certain points of the latter with specific places in

Biostatistics - Misplaced Pages Continue

4448-400: A variety of hereditary characteristics that replicate and remain active throughout generations. While haploid organisms have only one copy of each chromosome, most animals and many plants are diploid , containing two of each chromosome and thus two copies of every gene. The two alleles for a gene are located on identical loci of the two homologous chromosomes , each allele inherited from

4587-424: A working hypothesis is constructed as a statement of expectations, which can be linked to the exploratory research purpose in empirical investigation. Working hypotheses are often used as a conceptual framework in qualitative research. The provisional nature of working hypotheses makes them useful as an organizing device in applied research. Here they act like a useful guide to address problems that are still in

4726-488: Is X-chromosome inactivation during reproduction to avoid passing on twice as many genes to the offspring. Lyon's discovery led to the discovery of X-linked diseases. When cells divide, their full genome is copied and each daughter cell inherits one copy. This process, called mitosis , is the simplest form of reproduction and is the basis for asexual reproduction. Asexual reproduction can also occur in multicellular organisms, producing offspring that inherit their genome from

4865-417: Is a proposed explanation for a phenomenon . For a hypothesis to be a scientific hypothesis , the scientific method requires that one can test it. Scientists generally base scientific hypotheses on previous observations that cannot satisfactorily be explained with the available scientific theories. Even though the words "hypothesis" and " theory " are often used interchangeably, a scientific hypothesis

5004-412: Is a range of values that can contain the true real parameter value in given a certain level of confidence. The first step is to estimate the best-unbiased estimate of the population parameter. The upper value of the interval is obtained by the sum of this estimate with the multiplication between the standard error of the mean and the confidence level. The calculation of lower value is similar, but instead of

5143-462: Is an accepted version of this page Genetics is the study of genes , genetic variation , and heredity in organisms . It is an important branch in biology because heredity is vital to organisms' evolution . Gregor Mendel , a Moravian Augustinian friar working in the 19th century in Brno , was the first to study genetics scientifically. Mendel studied "trait inheritance", patterns in

5282-482: Is caused by genetic or postnatal environmental factors. One famous example involved the study of the Genain quadruplets , who were identical quadruplets all diagnosed with schizophrenia . The genome of a given organism contains thousands of genes, but not all these genes need to be active at any given moment. A gene is expressed when it is being transcribed into mRNA and there exist many cellular methods of controlling

5421-589: Is common to use randomized controlled clinical trials , where results are usually compared with observational study designs such as case–control or cohort . Data collection methods must be considered in research planning, because it highly influences the sample size and experimental design. Data collection varies according to type of data. For qualitative data , collection can be done with structured questionnaires or by observation, considering presence or intensity of disease, using score criterion to categorize levels of occurrence. For quantitative data , collection

5560-477: Is commonly achieved by using a more stringent threshold to reject null hypotheses. The Bonferroni correction defines an acceptable global significance level, denoted by α* and each test is individually compared with a value of α = α*/m. This ensures that the familywise error rate in all m tests, is less than or equal to α*. When m is large, the Bonferroni correction may be overly conservative. An alternative to

5699-558: Is done by measuring numerical information using instruments. In agriculture and biology studies, yield data and its components can be obtained by metric measures . However, pest and disease injuries in plats are obtained by observation, considering score scales for levels of damage. Especially, in genetic studies, modern methods for data collection in field and laboratory should be considered, as high-throughput platforms for phenotyping and genotyping. These tools allow bigger experiments, while turn possible evaluate many plots in lower time than

Biostatistics - Misplaced Pages Continue

5838-408: Is essential to carry the study based on the three basic principles of experimental statistics: randomization , replication , and local control. The research question will define the objective of a study. The research will be headed by the question, so it needs to be concise, at the same time it is focused on interesting and novel topics that may improve science and knowledge and that field. To define

5977-423: Is not the same as a scientific theory . A working hypothesis is a provisionally accepted hypothesis proposed for further research in a process beginning with an educated guess or thought. A different meaning of the term hypothesis is used in formal logic , to denote the antecedent of a proposition ; thus in the proposition "If P , then Q ", P denotes the hypothesis (or antecedent); Q can be called

6116-436: Is often accompanied by other technical assumptions (e.g., about the form of the probability distribution of the outcomes) that are also part of the null hypothesis. When the technical assumptions are violated in practice, then the null may be frequently rejected even if the main hypothesis is true. Such rejections are said to be due to model mis-specification. Verifying whether the outcome of a statistical test does not change when

6255-469: Is proposed to answer a scientific question we might have. To answer this question with a high certainty, we need accurate results. The correct definition of the main hypothesis and the research plan will reduce errors while taking a decision in understanding a phenomenon. The research plan might include the research question, the hypothesis to be tested, the experimental design , data collection methods, data analysis perspectives and costs involved. It

6394-421: Is required to separate the signal from the noise. For example, a microarray could be used to measure many thousands of genes simultaneously, determining which of them have different expression in diseased cells compared to normal cells. However, only a fraction of genes will be differentially expressed. Multicollinearity often occurs in high-throughput biostatistical settings. Due to high intercorrelation between

6533-441: Is responsible for the development of structures within multicellular organisms, these patterns arise from the complex interactions between many cells. Within eukaryotes , there exist structural features of chromatin that influence the transcription of genes, often in the form of modifications to DNA and chromatin that are stably inherited by daughter cells. These features are called " epigenetic " because they exist "on top" of

6672-501: Is that it is more robust: It is more likely that a single gene is found to be falsely perturbed than it is that a whole pathway is falsely perturbed. Furthermore, one can integrate the accumulated knowledge about biochemical pathways (like the JAK-STAT signaling pathway ) using this approach. The development of biological databases enables storage and management of biological data with the possibility of ensuring access for users around

6811-659: Is the Arabidopsis thaliana genetic and molecular database – TAIR. Phytozome, in turn, stores the assemblies and annotation files of dozen of plant genomes, also containing visualization and analysis tools. Moreover, there is an interconnection between some databases in the information exchange/sharing and a major initiative was the International Nucleotide Sequence Database Collaboration (INSDC) which relates data from DDBJ, EMBL-EBI, and NCBI. Genetics This

6950-460: Is the frequency table, which consists of data arranged in rows and columns, where the frequency is the number of occurrences or repetitions of data. Frequency can be: Absolute : represents the number of times that a determined value appear; N = f 1 + f 2 + f 3 + . . . + f n {\displaystyle N=f_{1}+f_{2}+f_{3}+...+f_{n}} Relative : obtained by

7089-497: Is the physical basis for inheritance: DNA replication duplicates the genetic information by splitting the strands and using each strand as a template for synthesis of a new partner strand. Genes are arranged linearly along long chains of DNA base-pair sequences. In bacteria , each cell usually contains a single circular genophore , while eukaryotic organisms (such as plants and animals) have their DNA arranged in multiple linear chromosomes. These DNA strands are often extremely long;

SECTION 50

#1732791702439

7228-694: Is the same as that which Mendel published. In his third law, he developed the basic principles of mutation (he can be considered a forerunner of Hugo de Vries ). Festetics argued that changes observed in the generation of farm animals, plants, and humans are the result of scientific laws. Festetics empirically deduced that organisms inherit their characteristics, not acquire them. He recognized recessive traits and inherent variation by postulating that traits of past generations could reappear later, and organisms could produce progeny with different attributes. These observations represent an important prelude to Mendel's theory of particulate inheritance insofar as it features

7367-486: The Blue-eyed Mary ( Omphalodes verna ), for example, there exists a gene with alleles that determine the color of flowers: blue or magenta. Another gene, however, controls whether the flowers have color at all or are white. When a plant has two copies of this white allele, its flowers are white—regardless of whether the first gene has blue or magenta alleles. This interaction between genes is called epistasis , with

7506-517: The Friden calculator from his department at Caltech , saying "Well, I am like a guy who is prospecting for gold along the banks of the Sacramento River in 1849. With a little intelligence, I can reach down and pick up big nuggets of gold. And as long as I can do that, I'm not going to let any people in my department waste scarce resources in placer mining ." Any research in life sciences

7645-413: The ancient Greek γενετικός genetikos meaning "genitive"/"generative", which in turn derives from γένεσις genesis meaning "origin". The observation that living things inherit traits from their parents has been used since prehistoric times to improve crop plants and animals through selective breeding . The modern science of genetics, seeking to understand this process, began with

7784-401: The ancient Greek word ὑπόθεσις hypothesis whose literal or etymological sense is "putting or placing under" and hence in extended use has many other meanings including "supposition". In Plato 's Meno (86e–87b), Socrates dissects virtue with a method used by mathematicians, that of "investigating from a hypothesis". In this sense, 'hypothesis' refers to a clever idea or to

7923-452: The experiment . They are completely randomized design , randomized block design , and factorial designs . Treatments can be arranged in many ways inside the experiment. In agriculture , the correct experimental design is the root of a good study and the arrangement of treatments within the study is essential because environment largely affects the plots ( plants , livestock , microorganisms ). These main arrangements can be found in

8062-415: The neutral theory of molecular evolution through publishing the nearly neutral theory of molecular evolution . In this theory, Ohta stressed the importance of natural selection and the environment to the rate at which genetic evolution occurs. One important development was chain-termination DNA sequencing in 1977 by Frederick Sanger . This technology allows scientists to read the nucleotide sequence of

8201-484: The null hypothesis (H 0 ) is true. It is also called the calculated probability. It is common to confuse the p-value with the significance level (α) , but, the α is a predefined threshold for calling significant results. If p is less than α, the null hypothesis (H 0 ) is rejected. In multiple tests of the same hypothesis, the probability of the occurrence of falses positives (familywise error rate) increase and some strategy are used to control this occurrence. This

8340-463: The null hypothesis and the alternative hypothesis . The null hypothesis is the hypothesis that states that there is no relation between the phenomena whose relation is under investigation, or at least not of the form given by the alternative hypothesis. The alternative hypothesis, as the name suggests, is the alternative to the null hypothesis: it states that there is some kind of relation. The alternative hypothesis may take several forms, depending on

8479-602: The 1930s, models built on statistical reasoning had helped to resolve these differences and to produce the neo-Darwinian modern evolutionary synthesis . Solving these differences also allowed to define the concept of population genetics and brought together genetics and evolution. The three leading figures in the establishment of population genetics and this synthesis all relied on statistics and developed its use in biology. These and other biostatisticians, mathematical biologists , and statistically inclined geneticists helped bring together evolutionary biology and genetics into

SECTION 60

#1732791702439

8618-570: The Bonferroni correction is to control the false discovery rate (FDR) . The FDR controls the expected proportion of the rejected null hypotheses (the so-called discoveries) that are false (incorrect rejections). This procedure ensures that, for independent tests, the false discovery rate is at most q*. Thus, the FDR is less conservative than the Bonferroni correction and have more power, at the cost of more false positives. The main hypothesis being tested (e.g., no association between treatments and outcomes)

8757-421: The DNA sequence and retain inheritance from one cell generation to the next. Because of epigenetic features, different cell types grown within the same medium can retain very different properties. Although epigenetic features are generally dynamic over the course of development, some, like the phenomenon of paramutation , have multigenerational inheritance and exist as rare exceptions to the general rule of DNA as

8896-632: The F1 offspring mate with each other, the offspring are called the "F2" (second filial) generation. One of the common diagrams used to predict the result of cross-breeding is the Punnett square . When studying human genetic diseases, geneticists often use pedigree charts to represent the inheritance of traits. These charts map the inheritance of a trait in a family tree. Organisms have thousands of genes, and in sexually reproducing organisms these genes generally assort independently of each other. This means that

9035-504: The Greek word genesis —γένεσις, "origin", predates the noun and was first used in a biological sense in 1860. Bateson both acted as a mentor and was aided significantly by the work of other scientists from Newnham College at Cambridge, specifically the work of Becky Saunders , Nora Darwin Barlow , and Muriel Wheldale Onslow . Bateson popularized the usage of the word genetics to describe

9174-405: The ability of some hypothesis to adequately answer the question under investigation. In contrast, unfettered observation is not as likely to raise unexplained issues or open questions in science, as would the formulation of a crucial experiment to test the hypothesis. A thought experiment might also be used to test the hypothesis. In framing a hypothesis, the investigator must not currently know

9313-448: The ability of the body to break down the amino acid phenylalanine , causing a toxic build-up of an intermediate molecule that, in turn, causes severe symptoms of progressive intellectual disability and seizures. However, if someone with the phenylketonuria mutation follows a strict diet that avoids this amino acid, they remain normal and healthy. A common method for determining how genes and environment ("nature and nurture") contribute to

9452-559: The ability to collect data on a high-throughput scale, and the ability to perform much more complex analysis using computational techniques. This comes from the development in areas as sequencing technologies, Bioinformatics and Machine learning ( Machine learning in bioinformatics ). New biomedical technologies like microarrays , next-generation sequencers (for genomics) and mass spectrometry (for proteomics) generate enormous amounts of data, allowing many tests to be performed simultaneously. Careful analysis with biostatistical methods

9591-444: The adaptive function of repair of DNA damages. The first cytological demonstration of crossing over was performed by Harriet Creighton and Barbara McClintock in 1931. Their research and experiments on corn provided cytological evidence for the genetic theory that linked genes on paired chromosomes do in fact exchange places from one homolog to the other. The probability of chromosomal crossover occurring between two given points on

9730-440: The basis for inheritance. During the process of DNA replication, errors occasionally occur in the polymerization of the second strand. These errors, called mutations, can affect the phenotype of an organism, especially if they occur within the protein coding sequence of a gene. Error rates are usually very low—1 error in every 10–100 million bases—due to the "proofreading" ability of DNA polymerases . Processes that increase

9869-404: The cat plays the role of the environment. The cat's genes code for dark hair, thus the hair-producing cells in the cat make cellular proteins resulting in dark hair. But these dark hair-producing proteins are sensitive to temperature (i.e. have a mutation causing temperature-sensitivity) and denature in higher-temperature environments, failing to produce dark-hair pigment in areas where the cat has

10008-429: The cell, these genes for tryptophan synthesis are no longer needed. The presence of tryptophan directly affects the activity of the genes—tryptophan molecules bind to the tryptophan repressor (a transcription factor), changing the repressor's structure such that the repressor binds to the genes. The tryptophan repressor blocks the transcription and expression of the genes, thereby creating negative feedback regulation of

10147-421: The chromosome is related to the distance between the points. For an arbitrarily long distance, the probability of crossover is high enough that the inheritance of the genes is effectively uncorrelated. For genes that are closer together, however, the lower probability of crossover means that the genes demonstrate genetic linkage; alleles for the two genes tend to be inherited together. The amounts of linkage between

10286-566: The collected data. In the early 1900s, after the rediscovery of Mendel's Mendelian inheritance work, there were gaps in understanding between genetics and evolutionary Darwinism. Francis Galton tried to expand Mendel's discoveries with human data and proposed a different model with fractions of the heredity coming from each ancestral composing an infinite series. He called this the theory of " Law of Ancestral Heredity ". His ideas were strongly disagreed by William Bateson , who followed Mendel's conclusions, that genetic inheritance were exclusively from

10425-422: The combined DNA sequences of all chromosomes) is called the genome . DNA is most often found in the nucleus of cells, but Ruth Sager helped in the discovery of nonchromosomal genes found outside of the nucleus. In plants, these are often found in the chloroplasts and in other organisms, in the mitochondria. These nonchromosomal genes can still be passed on by either partner in sexual reproduction and they control

10564-462: The corresponding residual sum of squares (RSS) and R of the validation test set, not those of the training set. Often, it is useful to pool information from multiple predictors together. For example, Gene Set Enrichment Analysis (GSEA) considers the perturbation of whole (functionally related) gene sets rather than of single genes. These gene sets might be known biochemical pathways or otherwise functionally related genes. The advantage of this approach

10703-527: The data is limited, it is necessary to make use of a representative sample in order to estimate them. With that, it is possible to test previously defined hypotheses and apply the conclusions to the entire population. The standard error of the mean is a measure of variability that is crucial to do inferences. Hypothesis testing is essential to make inferences about populations aiming to answer research questions, as settled in "Research planning" section. Authors defined four steps to be set: A confidence interval

10842-504: The data. Outliers may be plotted as circles. Although correlations between two different kinds of data could be inferred by graphs, such as scatter plot, it is necessary validate this though numerical information. For this reason, correlation coefficients are required. They provide a numerical value that reflects the strength of an association. Pearson correlation coefficient is a measure of association between two variables, X and Y. This coefficient, usually represented by ρ (rho) for

10981-417: The description of gene function classifying it by cellular component, molecular function and biological process ( Gene Ontology ). In addition to databases that contain specific molecular information, there are others that are ample in the sense that they store information about an organism or group of organisms. As an example of a database directed towards just one organism, but that contains much data about it,

11120-405: The diets have different effects over animals metabolism (H 1 : μ 1 ≠ μ 2 ). The hypothesis is defined by the researcher, according to his/her interests in answering the main question. Besides that, the alternative hypothesis can be more than one hypothesis. It can assume not only differences across observed parameters, but their degree of differences ( i.e. higher or shorter). Usually,

11259-418: The division of the absolute frequency by the total number; n i = f i N {\displaystyle n_{i}={\frac {f_{i}}{N}}} In the next example, we have the number of genes in ten operons of the same organism. Line graphs represent the variation of a value over another metric, such as time. In general, values are represented in the vertical axis, while

11398-417: The expression of genes such that proteins are produced only when needed by the cell. Transcription factors are regulatory proteins that bind to DNA, either promoting or inhibiting the transcription of a gene. Within the genome of Escherichia coli bacteria, for example, there exists a series of genes necessary for the synthesis of the amino acid tryptophan . However, when tryptophan is already available to

11537-484: The framer of a hypothesis needs to define specifics in operational terms. A hypothesis requires more work by the researcher in order to either confirm or disprove it. In due course, a confirmed hypothesis may become part of a theory or occasionally may grow to become a theory itself. Normally, scientific hypotheses have the form of a mathematical model . Sometimes, but not always, one can also formulate them as existential statements , stating that some particular instance of

11676-669: The function and behavior of genes. Gene structure and function, variation, and distribution are studied within the context of the cell , the organism (e.g. dominance ), and within the context of a population. Genetics has given rise to a number of subfields, including molecular genetics , epigenetics , and population genetics . Organisms studied within the broad field span the domains of life ( archaea , bacteria , and eukarya ). Genetic processes work in combination with an organism's environment and experiences to influence development and behavior , often referred to as nature versus nurture . The intracellular or extracellular environment of

11815-475: The hypothesis is proven to be either "true" or "false" through a verifiability - or falsifiability -oriented experiment . Any useful hypothesis will enable predictions by reasoning (including deductive reasoning ). It might predict the outcome of an experiment in a laboratory setting or the observation of a phenomenon in nature . The prediction may also invoke statistics and only talk about probabilities. Karl Popper , following others, has argued that

11954-424: The hypothesis is sustained by question research and its expected and unexpected answers. As an example, consider groups of similar animals (mice, for example) under two different diet systems. The research question would be: what is the best diet? In this case, H 0 would be that there is no difference between the two diets in mice metabolism (H 0 : μ 1 = μ 2 ) and the alternative hypothesis would be that

12093-469: The information an organism uses to function, the environment plays an important role in determining the ultimate phenotypes an organism displays. The phrase " nature and nurture " refers to this complementary relationship. The phenotype of an organism depends on the interaction of genes and the environment. An interesting example is the coat coloration of the Siamese cat . In this case, the body temperature of

12232-406: The inheritance of an allele for yellow or green pea color is unrelated to the inheritance of alleles for white or purple flowers. This phenomenon, known as " Mendel's second law " or the "law of independent assortment," means that the alleles of different genes get shuffled between parents to form offspring with many different combinations. Different genes often interact to influence the same trait. In

12371-427: The largest human chromosome, for example, is about 247 million base pairs in length. The DNA of a chromosome is associated with structural proteins that organize, compact, and control access to the DNA, forming a material called chromatin ; in eukaryotes, chromatin is usually composed of nucleosomes , segments of DNA wound around cores of histone proteins. The full set of hereditary material in an organism (usually

12510-425: The literature under the names of " lattices ", "incomplete blocks", " split plot ", "augmented blocks", and many others. All of the designs might include control plots , determined by the researcher, to provide an error estimation during inference . In clinical studies , the samples are usually smaller than in other biological studies, and in most cases, the environment effect can be controlled or measured. It

12649-571: The nature of inheritance in plants. In his paper " Versuche über Pflanzenhybriden " (" Experiments on Plant Hybridization "), presented in 1865 to the Naturforschender Verein (Society for Research in Nature) in Brno , Mendel traced the inheritance patterns of certain traits in pea plants and described them mathematically. Although this pattern of inheritance could only be observed for a few traits, Mendel's work suggested that heredity

12788-440: The nature of the hypothesized relation; in particular, it can be two-sided (for example: there is some effect, in a yet unknown direction) or one-sided (the direction of the hypothesized relation, positive or negative, is fixed in advance). Conventional significance levels for testing hypotheses (acceptable probabilities of wrongly rejecting a true null hypothesis) are .10, .05, and .01. The significance level for deciding whether

12927-430: The null hypothesis is rejected and the alternative hypothesis is accepted must be determined in advance, before the observations are collected or inspected. If these criteria are determined later, when the data to be tested are already known, the test is invalid. The above procedure is actually dependent on the number of the participants (units or sample size ) that are included in the study. For instance, to avoid having

13066-409: The number of items of this collection ( n {\displaystyle {n}} ). The median is the value in the middle of a dataset. The mode is the value of a set of data that appears most often. Box plot is a method for graphically depicting groups of numerical data. The maximum and minimum values are represented by the lines, and the interquartile range (IQR) represent 25–75% of

13205-531: The number of observations n is smaller than the number of features or predictors p: n < p). As a matter of fact, one can get quite high R-values despite very low predictive power of the statistical model. These classical statistical techniques (esp. least squares linear regression) were developed for low dimensional data (i.e. where the number of observations n is much larger than the number of predictors p: n >> p). In cases of high dimensionality, one should always consider an independent validation test set and

13344-500: The offspring of a mating pair. Genes on the same chromosome would theoretically never recombine. However, they do, via the cellular process of chromosomal crossover . During crossover, chromosomes exchange stretches of DNA, effectively shuffling the gene alleles between the chromosomes. This process of chromosomal crossover generally occurs during meiosis , a series of cell divisions that creates haploid cells. Meiotic recombination , particularly in microbial eukaryotes , appears to serve

13483-435: The original sequence. A particularly important source of DNA damages appears to be reactive oxygen species produced by cellular aerobic respiration , and these can lead to mutations. In organisms that use chromosomal crossover to exchange DNA and recombine genes, errors in alignment during meiosis can also cause mutations. Errors in crossover are especially likely when similar sequences cause partner chromosomes to adopt

13622-480: The outbreak of Zika virus in the birth rate in Brazil. The histogram (or frequency distribution) is a graphical representation of a dataset tabulated and divided into uniform or non-uniform classes. It was first introduced by Karl Pearson . A scatter plot is a mathematical diagram that uses Cartesian coordinates to display values of a dataset. A scatter plot shows the data as a set of points, each one presenting

13761-400: The outcome of a test or that it remains reasonably under continuing investigation. Only in such cases does the experiment, test or study potentially increase the probability of showing the truth of a hypothesis. If the researcher already knows the outcome, it counts as a "consequence" — and the researcher should have already considered this while formulating the hypothesis. If one cannot assess

13900-429: The parents, half from each of them. This led to a vigorous debate between the biometricians, who supported Galton's ideas, as Raphael Weldon , Arthur Dukinfield Darbishire and Karl Pearson , and Mendelians, who supported Bateson's (and Mendel's) ideas, such as Charles Davenport and Wilhelm Johannsen . Later, biometricians could not reproduce Galton conclusions in different experiments, and Mendel's ideas prevailed. By

14039-402: The phenomenon under examination has some characteristic and causal explanations, which have the general form of universal statements , stating that every instance of the phenomenon has a particular characteristic. In entrepreneurial setting, a hypothesis is used to formulate provisional ideas about the attributes of products or business models. The formulated hypothesis is then evaluated, where

14178-470: The phenotype of the organism, while the other allele is called recessive as its qualities recede and are not observed. Some alleles do not have complete dominance and instead have incomplete dominance by expressing an intermediate phenotype, or codominance by expressing both alleles at once. When a pair of organisms reproduce sexually , their offspring randomly inherit one of the two alleles from each parent. These observations of discrete inheritance and

14317-414: The plane of observation. By virtue of those interpretative connections, the network can function as a scientific theory." Hypotheses with concepts anchored in the plane of observation are ready to be tested. In "actual scientific practice the process of framing a theoretical structure and of interpreting it are not always sharply separated, since the intended interpretation usually guides the construction of

14456-426: The population and r for the sample, assumes values between −1 and 1, where ρ = 1 represents a perfect positive correlation, ρ = −1 represents a perfect negative correlation, and ρ = 0 is no linear correlation. It is used to make inferences about an unknown population, by estimation and/or hypothesis testing. In other words, it is desirable to obtain parameters to describe the population of interest, but since

14595-510: The population. So, the sample might catch the most variability across a population. The sample size is determined by several things, since the scope of the research to the resources available. In clinical research , the trial type, as inferiority , equivalence , and superiority is a key in determining sample size . Experimental designs sustain those basic principles of experimental statistics . There are three basic experimental designs to randomly allocate treatments in all plots of

14734-410: The predictions by observation or by experience , the hypothesis needs to be tested by others providing observations. For example, a new technology or theory might make the necessary experiments feasible. A trial solution to a problem is commonly referred to as a hypothesis—or, often, as an " educated guess " —because it provides a suggested outcome based on the evidence. However, some scientists reject

14873-512: The predictors (such as gene expression levels), the information of one predictor might be contained in another one. It could be that only 5% of the predictors are responsible for 90% of the variability of the response. In such a case, one could apply the biostatistical technique of dimension reduction (for example via principal component analysis). Classical statistical techniques like linear or logistic regression and linear discriminant analysis do not work well for high dimensional data (i.e. when

15012-543: The process of protein production . It was discovered that the cell uses DNA as a template to create matching messenger RNA , molecules with nucleotides very similar to DNA. The nucleotide sequence of a messenger RNA is used to create an amino acid sequence in protein; this translation between nucleotide sequences and amino acid sequences is known as the genetic code . With the newfound molecular understanding of inheritance came an explosion of research. A notable theory arose from Tomoko Ohta in 1973 with her amendment to

15151-435: The product rule, the sum rule, and more. Geneticists use diagrams and symbols to describe inheritance. A gene is represented by one or a few letters. Often a "+" symbol is used to mark the usual, non-mutant allele for a gene. In fertilization and breeding experiments (and especially when discussing Mendel's laws) the parents are referred to as the "P" generation and the offspring as the "F1" (first filial) generation. When

15290-519: The properties of a protein by destabilizing the structure or changing the surface of the protein in a way that changes its interaction with other proteins and molecules. For example, sickle-cell anemia is a human genetic disease that results from a single base difference within the coding region for the β-globin section of hemoglobin, causing a single amino acid change that changes hemoglobin's physical properties. Sickle-cell versions of hemoglobin stick to themselves, stacking to form fibers that distort

15429-426: The protein itself). Protein structure is dynamic; the protein hemoglobin bends into slightly different forms as it facilitates the capture, transport, and release of oxygen molecules within mammalian blood. A single nucleotide difference within DNA can cause a change in the amino acid sequence of a protein. Because protein structures are the result of their amino acid sequences, some changes can dramatically change

15568-406: The rate of changes in DNA are called mutagenic : mutagenic chemicals promote errors in DNA replication, often by interfering with the structure of base-pairing, while UV radiation induces mutations by causing damage to the DNA structure. Chemical damage to DNA occurs naturally as well and cells use DNA repair mechanisms to repair mismatches and breaks. The repair does not, however, always restore

15707-408: The same allele of a given gene are called homozygous at that gene locus , while organisms with two different alleles of a given gene are called heterozygous . The set of alleles for a given organism is called its genotype , while the observable traits of the organism are called its phenotype . When organisms are heterozygous at a gene, often one allele is called dominant as its qualities dominate

15846-576: The sample size be too small to reject a null hypothesis, it is recommended that one specify a sufficient sample size from the beginning. It is advisable to define a small, medium and large effect size for each of a number of important statistical tests which are used to test the hypotheses. Mount Hypothesis in Antarctica is named in appreciation of the role of hypothesis in scientific research. Several hypotheses have been put forth, in different subject areas: hypothesis [...]— Working hypothesis ,

15985-401: The second gene epistatic to the first. Many traits are not discrete features (e.g. purple or white flowers) but are instead continuous features (e.g. human height and skin color ). These complex traits are products of many genes. The influence of these genes is mediated, to varying degrees, by the environment an organism has experienced. The degree to which an organism's genes contribute to

16124-509: The segregation of alleles are collectively known as Mendel's first law or the Law of Segregation. However, the probability of getting one gene over the other can change due to dominant, recessive, homozygous, or heterozygous genes. For example, Mendel found that if you cross heterozygous organisms your odds of getting the dominant trait is 3:1. Real geneticist study and calculate probabilities by using theoretical probabilities, empirical probabilities,

16263-653: The shape of red blood cells carrying the protein. These sickle-shaped cells no longer flow smoothly through blood vessels , having a tendency to clog or degrade, causing the medical problems associated with this disease. Some DNA sequences are transcribed into RNA but are not translated into protein products—such RNA molecules are called non-coding RNA . In some cases, these products fold into structures which are involved in critical cell functions (e.g. ribosomal RNA and transfer RNA ). RNA can also have regulatory effects through hybridization interactions with other RNA molecules (such as microRNA ). Although genes contain all

16402-446: The similar molecule RNA instead of DNA as their genetic material. DNA normally exists as a double-stranded molecule, coiled into the shape of a double helix . Each nucleotide in DNA preferentially pairs with its partner nucleotide on the opposite strand: A pairs with T, and C pairs with G. Thus, in its two-stranded form, each strand effectively contains all necessary information, redundant with its partner strand. This structure of DNA

16541-500: The single celled alga Acetabularia . The Hershey–Chase experiment in 1952 confirmed that DNA (rather than protein) is the genetic material of the viruses that infect bacteria, providing further evidence that DNA is the molecule responsible for inheritance. James Watson and Francis Crick determined the structure of DNA in 1953, using the X-ray crystallography work of Rosalind Franklin and Maurice Wilkins that indicated DNA has

16680-441: The strands are separated, new partner strands can be reconstructed for each based on the sequence of the old strand. This property is what gives DNA its semi-conservative nature where one strand of new DNA is from an original parent strand. Although the structure of DNA showed how inheritance works, it was still not known how DNA influences the behavior of cells. In the following years, scientists tried to understand how DNA controls

16819-580: The study of inheritance in his inaugural address to the Third International Conference on Plant Hybridization in London in 1906. After the rediscovery of Mendel's work, scientists tried to determine which molecules in the cell were responsible for inheritance. In 1900, Nettie Stevens began studying the mealworm. Over the next 11 years, she discovered that females only had the X chromosome and males had both X and Y chromosomes. She

16958-446: The technical assumptions are slightly altered (so-called robustness checks) is the main way of combating mis-specification. Model criteria selection will select or model that more approximate true model. The Akaike's Information Criterion (AIC) and The Bayesian Information Criterion (BIC) are examples of asymptotically efficient criteria. Recent developments have made a large impact on biostatistics. Two important changes have been

17097-451: The term "educated guess" as incorrect. Experimenters may test and reject several hypotheses before solving the problem. According to Schick and Vaughn, researchers weighing up alternative hypotheses may take into consideration: A working hypothesis is a hypothesis that is provisionally accepted as a basis for further research in the hope that a tenable theory will be produced, even if the hypothesis ultimately fails. Like all hypotheses,

17236-399: The theoretician". It is, however, "possible and indeed desirable, for the purposes of logical clarification, to separate the two steps conceptually". When a possible correlation or similar relation between phenomena is investigated, such as whether a proposed remedy is effective in treating a disease, the hypothesis that a relation exists cannot be examined the same way one might examine

17375-496: The time variation is represented in the horizontal axis. A bar chart is a graph that shows categorical data as bars presenting heights (vertical bar) or widths (horizontal bar) proportional to represent values. Bar charts provide an image that could also be represented in a tabular format. In the bar chart example, we have the birth rate in Brazil for the December months from 2010 to 2016. The sharp fall in December 2016 reflects

17514-403: The topic or an obvious occurrence of the phenomena, sustained by a deep literature review. We can say it is the standard expected answer for the data under the situation in test . In general, H O assumes no association between treatments. On the other hand, the alternative hypothesis is the denial of H O . It assumes some degree of association between the treatment and the outcome. Although,

17653-536: The tryptophan synthesis process. Differences in gene expression are especially clear within multicellular organisms , where cells all contain the same genome but have very different structures and behaviors due to the expression of different sets of genes. All the cells in a multicellular organism derive from a single cell, differentiating into variant cell types in response to external and intercellular signals and gradually establishing different patterns of gene expression to create different behaviors. As no single gene

17792-482: The twenty possible amino acids in a protein or an instruction to end the amino acid sequence ; this correspondence is called the genetic code . The flow of information is unidirectional: information is transferred from nucleotide sequences into the amino acid sequence of proteins, but it never transfers from protein back into the sequence of DNA—a phenomenon Francis Crick called the central dogma of molecular biology . The specific sequence of amino acids results in

17931-545: The two is responsible for inheritance. In 1928 , Frederick Griffith discovered the phenomenon of transformation : dead bacteria could transfer genetic material to "transform" other still-living bacteria. Sixteen years later, in 1944, the Avery–MacLeod–McCarty experiment identified DNA as the molecule responsible for transformation. The role of the nucleus as the repository of genetic information in eukaryotes had been established by Hämmerling in 1943 in his work on

18070-464: The value of one variable determining the position on the horizontal axis and another variable on the vertical axis. They are also called scatter graph , scatter chart , scattergram , or scatter diagram . The arithmetic mean is the sum of a collection of values ( x 1 + x 2 + x 3 + ⋯ + x n {\displaystyle {x_{1}+x_{2}+x_{3}+\cdots +x_{n}}} ) divided by

18209-426: The way to ask the scientific question , an exhaustive literature review might be necessary. So the research can be useful to add value to the scientific community . Once the aim of the study is defined, the possible answers to the research question can be proposed, transforming this question into a hypothesis . The main propose is called null hypothesis (H 0 ) and is usually based on a permanent knowledge about

18348-437: The way traits are handed down from parents to offspring over time. He observed that organisms (pea plants) inherit traits by way of discrete "units of inheritance". This term, still used today, is a somewhat ambiguous definition of what is referred to as a gene. Trait inheritance and molecular inheritance mechanisms of genes are still primary principles of genetics in the 21st century, but modern genetics has expanded to study

18487-404: The whole genome , or all the sperm cells , for animals, or the total leaf area, for a plant, for example. It is not possible to take the measures from all the elements of a population . Because of that, the sampling process is very important for statistical inference . Sampling is defined as to randomly get a representative part of the entire population, to make posterior inferences about

18626-538: The work of the Augustinian friar Gregor Mendel in the mid-19th century. Prior to Mendel, Imre Festetics , a Hungarian noble, who lived in Kőszeg before Mendel, was the first who used the word "genetic" in hereditarian context, and is considered the first geneticist. He described several rules of biological inheritance in his work The genetic laws of nature (Die genetischen Gesetze der Natur, 1819). His second law

18765-464: The world. They are useful for researchers depositing data, retrieve information and files (raw or processed) originated from other experiments or indexing scientific articles, as PubMed . Another possibility is search for the desired term (a gene, a protein, a disease, an organism, and so on) and check all results related to this search. There are databases dedicated to SNPs ( dbSNP ), the knowledge on genes characterization and their pathways ( KEGG ) and

18904-518: Was able to conclude that sex is a chromosomal factor and is determined by the male. In 1911, Thomas Hunt Morgan argued that genes are on chromosomes , based on observations of a sex-linked white eye mutation in fruit flies . In 1913, his student Alfred Sturtevant used the phenomenon of genetic linkage to show that genes are arranged linearly on the chromosome. Although genes were known to exist on chromosomes, chromosomes are composed of both protein and DNA, and scientists did not know which of

19043-591: Was first observed by Gregor Mendel, who studied the segregation of heritable traits in pea plants, showing for example that flowers on a single plant were either purple or white—but never an intermediate between the two colors. The discrete versions of the same gene controlling the inherited appearance (phenotypes) are called alleles . In the case of the pea, which is a diploid species, each individual plant has two copies of each gene, one copy inherited from each parent. Many species, including humans, have this pattern of inheritance. Diploid organisms with two copies of

19182-421: Was particulate, not acquired, and that the inheritance patterns of many traits could be explained through simple rules and ratios. The importance of Mendel's work did not gain wide understanding until 1900, after his death, when Hugo de Vries and other scientists rediscovered his research. William Bateson , a proponent of Mendel's work, coined the word genetics in 1905. The adjective genetic , derived from

19321-529: Was the inheritance of acquired characteristics : the belief that individuals inherit traits strengthened by their parents. This theory (commonly associated with Jean-Baptiste Lamarck ) is now known to be wrong—the experiences of individuals do not affect the genes they pass to their children. Other theories included Darwin's pangenesis (which had both acquired and inherited aspects) and Francis Galton 's reformulation of pangenesis as both particulate and inherited. Modern genetics started with Mendel's studies of

#438561