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Posted by motoman 03/29/2009 @ 08:13

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On May 12, the American Civil Liberties Union and Yeshiva University sued Myriad Genetics, a Utah-based company that holds the patents for BRCA1 and BRCA2, two genes known to cause hereditary breast and ovarian cancer. The ACLU argues that it is...
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McKelvey Tabbed For Clinical Genetics Chair at UAMS - Arkansas Business Online
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sembiosys Genetics Q1 Loss Narrows - RTT News
(rttnews) - Friday, manufacturer of high-value proteins and oils in plant seeds, sembiosys Genetics Inc. (SBS.TO: News ), reported a first-quarter net loss that narrowed from the year-ago period primarily due to higher revenue....
Response Genetics Inc. Reports Operating Results (10-Q) -
Response Genetics Inc. is engaged in the research and development of pharmacogenomic cancer diagnostic tests based on its proprietary and patented technologies which enable extraction and analysis of genetic information from genes derived from tumor...
Do-It-Yourself Genetic Sleuthing - Forensic
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The common fruit fly (Drosophila melanogaster) is a popular model organism in genetics research.

Genetics (from Ancient Greek γενετικός genetikos, “genitive” and that from γένεσις genesis, “origin”), a discipline of biology, is the science of heredity and variation in living organisms. The fact that living things inherit traits from their parents has been used since prehistoric times to improve crop plants and animals through selective breeding. However, the modern science of genetics, which seeks to understand the process of inheritance, only began with the work of Gregor Mendel in the mid-nineteenth century. Although he did not know the physical basis for heredity, Mendel observed that organisms inherit traits in a discrete manner—these basic units of inheritance are now called genes.

Genes correspond to regions within DNA, a molecule composed of a chain of four different types of nucleotides—the sequence of these nucleotides is the genetic information organisms inherit. DNA naturally occurs in a double stranded form, with nucleotides on each strand complementary to each other. Each strand can act as a template for creating a new partner strand—this is the physical method for making copies of genes that can be inherited.

The sequence of nucleotides in a gene is translated by cells to produce a chain of amino acids, creating proteins—the order of amino acids in a protein corresponds to the order of nucleotides in the gene. This is known as the genetic code. The amino acids in a protein determine how it folds into a three-dimensional shape; this structure is, in turn, responsible for the protein's function. Proteins carry out almost all the functions needed for cells to live. A change to the DNA in a gene can change a protein's amino acids, changing its shape and function: this can have a dramatic effect in the cell and on the organism as a whole.

Although genetics plays a large role in the appearance and behavior of organisms, it is the combination of genetics with what an organism experiences that determines the ultimate outcome. For example, while genes play a role in determining a person's height, the nutrition and health that person experiences in childhood also have a large effect.

Although the science of genetics began with the applied and theoretical work of Gregor Mendel in the mid-1800s, other theories of inheritance preceded Mendel. A popular theory during Mendel's time was the concept of blending inheritance: the idea that individuals inherit a smooth blend of traits from their parents. Mendel's work disproved this, showing that traits are composed of combinations of distinct genes rather than a continuous blend. Another theory that had some support at that time 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 the pangenesis of Charles Darwin (which had both acquired and inherited aspects) and Francis Galton's reformulation of pangenesis as both particulate and inherited.

The modern science of genetics traces its roots to Gregor Johann Mendel, a German-Czech Augustinian monk and scientist who studied 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 Brünn, 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 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 the 1890s, after his death, when other scientists working on similar problems re-discovered his research. William Bateson, a proponent of Mendel's work, coined the word genetics in 1905. (The adjective genetic, derived from the Greek word genesis - γένεσις, "origin" and that from the word genno - γεννώ, "to give birth", predates the noun and was first used in a biological sense in 1860.) Bateson popularized the usage of the word genetics to describe the study of inheritance in his inaugural address to the Third International Conference on Plant Hybridization in London, England, in 1906.

After the rediscovery of Mendel's work, scientists tried to determine which molecules in the cell were responsible for inheritance. In 1910, 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—scientists did not know which of these is responsible for inheritance. In 1928, Frederick Griffith discovered the phenomenon of transformation (see Griffith's experiment): dead bacteria could transfer genetic material to "transform" other still-living bacteria. Sixteen years later, in 1944, Oswald Theodore Avery, Colin McLeod and Maclyn McCarty identified the molecule responsible for transformation as DNA. The Hershey-Chase experiment in 1952 also showed 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 D. Watson and Francis Crick determined the structure of DNA in 1953, using the X-ray crystallography work of Rosalind Franklin that indicated DNA had 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 looks 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 duplication: if the strands are separated, new partner strands can be reconstructed for each based on the sequence of the old 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 the process of protein production. It was discovered that the cell uses DNA as a template to create matching messenger RNA (a molecule 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 and amino acid sequences is known as the genetic code.

With this molecular understanding of inheritance, an explosion of research became possible. One important development was chain-termination DNA sequencing in 1977 by Frederick Sanger: This technology allows scientists to read the nucleotide sequence of 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 a DNA from a mixture. Through the pooled efforts of the Human Genome Project and the parallel private effort by Celera Genomics, these and other techniques culminated in the sequencing of the human genome in 2003.

At its most fundamental level, inheritance in organisms occurs by means of discrete traits, called genes. This property was first observed by Gregor Mendel, who studied the segregation of heritable traits in pea plants. In his experiments studying the trait for flower color, Mendel observed that the flowers of each pea plant were either purple or white - and never an intermediate between the two colors. These different, discrete versions of the same gene are called alleles.

In the case of pea plants, each organism has two alleles of each gene, and the plants inherit one allele from each parent. Many organisms, including humans, have this pattern of inheritance. Organisms with two copies of the same allele of a given gene are called homozygous at that gene, while organisms with two different alleles of a given gene are called heterozygous at that gene.

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 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 the segregation of alleles are collectively known as Mendel's first law or the Law of Segregation.

Geneticists use diagrams and symbols to describe inheritance. A gene is represented by a letter (or letters)—the capitalized letter represents the dominant allele and the recessive is represented by lowercase. 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 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.

Often different genes can interact in a way that influences the same trait. In 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: color or 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 the second gene epistatic to the first.

Many traits are not discrete features (eg. purple or white flowers) but are instead continuous features (eg. human height and skin color). These complex traits are the product 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 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 complex trait with 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 a heritability of only 62%.

The molecular basis for genes is deoxyribonucleic acid (DNA). DNA is composed of a chain of nucleotides, of which there are four types: adenine (A), cytosine (C), guanine (G), and thymine (T). Genetic information exists in the sequence of these nucleotides, and genes exist as stretches of sequence along the DNA chain. Viruses are the only exception to this rule—sometimes viruses use the very 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 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 sequence, called chromosomes. In bacteria, each cell has a single circular chromosome, while eukaryotic organisms (which includes plants and animals) have their DNA arranged in multiple linear chromosomes. These DNA strands are often extremely long; 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, repeating units of DNA wound around a core of histone proteins. The full set of hereditary material in an organism (usually the combined DNA sequences of all chromosomes) is called the genome.

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 sister chromatids, each allele inherited from a different parent.

An exception exists in the sex chromosomes, specialized chromosomes many animals have evolved that play a role in determining the sex of an organism. In humans and other mammals, the Y chromosome has very few genes and triggers the development of male sexual characteristics, while the X chromosome is similar to the other chromosomes and contains many genes unrelated to sex determination. Females have two copies of the X chromosome, but males have one Y and only one X chromosome - this difference in X chromosome copy numbers leads to the unusual inheritance patterns of sex-linked disorders.

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 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 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.

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 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 genome, a phenomenon known as transformation. These processes result in horizontal gene transfer, transmitting fragments of genetic information between organisms that would be otherwise unrelated.

The diploid nature of chromosomes allows for genes on different chromosomes to assort independently during sexual reproduction, recombining to form new combinations of genes. Genes on the same chromosome would theoretically never recombine, however, were it not for the 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.

The probability of chromosomal crossover occurring between two given points on 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 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 generally express their functional effect through the production of proteins, which are complex molecules responsible for most functions in the cell. Proteins are chains of amino acids, and the DNA sequence of a gene (through RNA intermediate) is used to produce a specific protein 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 is then used to produce a corresponding amino acid sequence through a process called translation. Each group of three nucleotides in the sequence, called a codon, corresponds to one of the twenty possible amino acids in protein - 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 a unique three-dimensional structure for that protein, and the three-dimensional structures of protein are related to their function. 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 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 single 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 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 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 genes are transcribed into RNA but are not translated into protein products - these are called non-coding RNA molecules. In some cases, these products fold into structures which are involved in critical cell functions (eg. ribosomal RNA and transfer RNA). RNA can also have regulatory effect through hybridization interactions with other RNA molecules (eg. microRNA).

Although genes contain all the information an organism uses to function, the environment plays an important role in determining the ultimate phenotype—a dichotomy often referred to as "nature vs. nurture." The phenotype of an organism depends on the interaction of genetics with the environment. One example of this is the case of temperature-sensitive mutations. Often, a single amino acid change within the sequence of a protein does not change its behavior and interactions with other molecules, but it does destabilize the structure. In a high temperature environment, where molecules are moving more quickly and hitting each other, this results in the protein losing its structure and failing to function. In a low temperature environment, however, the protein's structure is stable and functions normally. This type of mutation is visible in the coat coloration of Siamese cats, where a mutation in an enzyme responsible for pigment production causes it to destabilize and lose function at high temperatures. The protein remains functional in areas of skin that are colder—legs, ears, tail, and face—and so the cat has dark fur at its extremities.

Environment also plays a dramatic role in effects of the human genetic disease phenylketonuria. The mutation that causes phenylketonuria disrupts 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 mental retardation and seizures. If someone with the phenylketonuria mutation follows a strict diet that avoids this amino acid, however, they remain normal and healthy.

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 translated into protein), and there exist many cellular methods of controlling the expression of genes such that proteins are produced only when needed by the cell. Transcription factors are regulatory proteins that bind to the start of genes, either promoting or inhibiting the transcription of the 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 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 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 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 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 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 have an impact on 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. (Without proofreading error rates are a thousand-fold higher; because many viruses rely on DNA and RNA polymerases that lack proofreading ability, they experience higher mutation rates.) Processes that increase 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 in DNA—nevertheless, the repair sometimes fails to return the DNA to its original sequence.

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 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 or deletions of entire regions, or the accidental exchanging of whole parts between different chromosomes (called translocation).

Mutations produce organisms with different genotypes, and those differences can result in different phenotypes. Many mutations have little effect on an organism's phenotype, health, and reproductive fitness. Mutations that do have an effect are often deleterious, but occasionally mutations are beneficial. Studies in the fly Drosophila melanogaster suggest that if a mutation changes a protein produced by a gene, this will probably be harmful, with about 70 percent of these mutations having damaging effects, and the remainder being either neutral or weakly beneficial.

Population genetics research studies the distributions of these genetic differences within populations and how the distributions change over time. Changes in the frequency of an allele in a population can be influenced by natural selection, where a given allele's higher rate of survival and reproduction causes it to become more frequent in the population over time. Genetic drift can also occur, where chance events lead to random changes in allele frequency.

Over many generations, the genomes of organisms can change, resulting in the phenomenon of evolution. Mutations and the selection for beneficial mutations can cause a species to evolve into forms that better survive their environment, a process called adaptation. New species are formed through the process of speciation, a process often caused by geographical separations that allow different populations to genetically diverge. The application of genetic principles to the study of population biology and evolution is referred to as the modern synthesis.

As sequences diverge and change during the process of evolution, these differences between sequences can be used as a molecular clock to calculate the evolutionary distance between them. Genetic comparisons are generally considered the most accurate method of characterizing the relatedness between species, an improvement over the sometimes deceptive comparison of phenotypic characteristics. The evolutionary distances between species can be combined to form evolutionary trees - these trees represent the common descent and divergence of species over time, although they cannot represent the transfer of genetic material between unrelated species (known as horizontal gene transfer and most common in bacteria).

Although geneticists originally studied inheritance in a wide range of organisms, researchers began to specialize in studying the genetics of a particular subset of organisms. The fact that significant research already existed for a given organism would encourage new researchers to choose it for further study, and so eventually a few model organisms became the basis for most genetics research. Common research topics in model organism genetics include the study of gene regulation and the involvement of genes in development and cancer.

Organisms were chosen, in part, for convenience—short generation times and easy genetic manipulation made some organisms popular genetics research tools. Widely used model organisms include the gut bacterium Escherichia coli, the plant Arabidopsis thaliana, baker's yeast (Saccharomyces cerevisiae), the nematode Caenorhabditis elegans, the common fruit fly (Drosophila melanogaster), and the common house mouse (Mus musculus).

Medical genetics seeks to understand how genetic variation relates to human health and disease. When searching for an unknown gene that may be involved in a disease, researchers commonly use genetic linkage and genetic pedigree charts to find the location on the genome associated with the disease. At the population level, researchers take advantage of Mendelian randomization to look for locations in the genome that are associated with diseases, a technique especially useful for multigenic traits not clearly defined by a single gene. Once a candidate gene is found, further research is often done on the same gene (called an orthologous gene) in model organisms. In addition to studying genetic diseases, the increased availability of genotyping techniques has led to the field of pharmacogenetics—studying how genotype can affect drug responses.

Although it is not an inherited disease, cancer is also considered a genetic disease. The process of cancer development in the body is a combination of events. Mutations occasionally occur within cells in the body as they divide. While these mutations will not be inherited by any offspring, they can affect the behavior of cells, sometimes causing them to grow and divide more frequently. There are biological mechanisms that attempt to stop this process; signals are given to inappropriately dividing cells that should trigger cell death, but sometimes additional mutations occur that cause cells to ignore these messages. An internal process of natural selection occurs within the body and eventually mutations accumulate within cells to promote their own growth, creating a cancerous tumor that grows and invades various tissues of the body.

DNA can also be amplified using a procedure called the polymerase chain reaction (PCR). By using specific short sequences of DNA, PCR can isolate and exponentially amplify a targeted region of DNA. Because it can amplify from extremely small amounts of DNA, PCR is also often used to detect the presence of specific DNA sequences.

One of the most fundamental technologies developed to study genetics, DNA sequencing allows researchers to determine the sequence of nucleotides in DNA fragments. Developed in 1977 by Frederick Sanger and coworkers, chain-termination sequencing is now routinely used to sequence DNA fragments. With this technology, researchers have been able to study the molecular sequences associated with many human diseases.

As sequencing has become less expensive and with the aid of computational tools, researchers have sequenced the genomes of many organisms by stitching together the sequences of many different fragments (a process called genome assembly). These technologies were used to sequence the human genome, leading to the completion of the Human Genome Project in 2003. New high-throughput sequencing technologies are dramatically lowering the cost of DNA sequencing, with many researchers hoping to bring the cost of resequencing a human genome down to a thousand dollars.

The large amount of sequences available has created the field of genomics, research that uses computational tools to search for and analyze patterns in the full genomes of organisms. Genomics can also be considered a subfield of bioinformatics, which uses computational approaches to analyze large sets of biological data.

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Population genetics

Tree of life with genome size.svg

Population genetics is the study of the allele frequency distribution and change under the influence of the four evolutionary processes: natural selection, genetic drift, mutation and gene flow. It also takes account of population subdivision and population structure in space. As such, it attempts to explain such phenomena as adaptation and speciation. Population genetics was a vital ingredient in the modern evolutionary synthesis, its primary founders were Sewall Wright, J. B. S. Haldane and R. A. Fisher, who also laid the foundations for the related discipline of quantitative genetics.

Perhaps the most significant "formal" achievement of the modern evolutionary synthesis has been the framework of mathematical population genetics. Indeed some authors (Beatty 1986) would argue that it does define the core of the modern synthesis.

T1 represents the genetic and epigenetic laws, the aspects of functional biology, or development, that transform a genotype into phenotype. We will refer to this as the "genotype-phenotype map". T2 is the transformation due to natural selection, T3 are epigenetic relations that predict genotypes based on the selected phenotypes and finally T4 the rules of Mendelian genetics.

In practice, there are two bodies of evolutionary theory that exist in parallel, traditional population genetics operating in the genotype space and the biometric theory used in plant and animal breeding, operating in phenotype space. The missing part is the mapping between the genotype and phenotype space. This leads to a "sleight of hand" (as Lewontin terms it) whereby variables in the equations of one domain, are considered parameters or constants, where, in a full-treatment they would be transformed themselves by the evolutionary process and are in reality functions of the state variables in the other domain. The "sleight of hand" is assuming that we know this mapping. Proceeding as if we do understand it is enough to analyze many cases of interest. For example, if the phenotype is almost one-to-one with genotype (sickle-cell disease) or the time-scale is sufficiently short, the "constants" can be treated as such; however, there are many situations where it is inaccurate.

The three founders of population genetics were the Britons R.A. Fisher and J.B.S. Haldane and the American Sewall Wright. Fisher and Wright had some fundamental disagreements and a controversy about the relative roles of selection and drift continued for much of the century between the Americans and the British. The Frenchman Gustave Malécot was also important early in the development of the discipline. John Maynard Smith was Haldane's pupil, whilst W.D. Hamilton was heavily influenced by the writings of Fisher. The American George R. Price worked with both Hamilton and Maynard Smith. On the American side, Richard Lewontin and the Japanese Motoo Kimura were heavily influenced by Wright.

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Race and genetics

geographic distribution of blood group A

Notions of race based on Human genetic variation have replaced historical approaches such as craniology with the advent of human genetics in the 20th century.

Prior to the discovery of DNA as the hereditary material, scientists used blood proteins to study human genetic variation. Research by Ludwik and Hanka Herschfeld during World War I found that the frequencies of blood groups A and B differed greatly from region to region. For example, among Europeans, 15% were group B and 40% were group A. Eastern Europeans and Russians had higher frequencies of group B, with people from India having the highest proportion. The Herschfelds concluded that humans were made of two different "biochemical races," each with its own origin. It was hypothesized that these two pure races later became mixed, resulting in the complex pattern of groups A and B. This was one of the first theories of racial differences to include the idea that visible human variation did not necessarily correlate with invisible genetic variation.

It was expected that groups that had similar proportions of the blood groups would be more closely related in racial terms, but instead it was often found that groups separated by large distances, such as those from Madagascar and Russia, had similar frequencies. This confounded scientists who were attempting to learn more about human evolutionary history. The next big advance in biological description of human variation would come with the discovery of more blood groups and proteins.

Techniques based on molecular evolution principles were used in early studies of presupposed racial differences. One major technique in the field is to use mutations in individual proteins or genetic sequences as a molecular clock indicating the evolutionary relatedness of various species or groups.

Luigi Luca Cavalli-Sforza and Anthony Edwards would then incorporate these techniques into the field of population genetics. Using computer based statistical analysis to average across the several blood group systems, they were able to produce a phylogenetic relationship of the various populations around the world.

In 1972 Richard Lewontin performed a statistical analysis of the data available on blood proteins. His results showed that the majority of genetic differences between humans, about 85%, were found within a population. 7% of genetic differences were found between populations within a race. Only 8% on average was found to differentiate the various races.

Human to human total genetic variation is approximately 0.5%. Single-nucleotide polymorphisms (SNPs) are single base-pair DNA differences accounting for 0.1% variation. Of this 0.1% difference, 85% is found within any given population, 7% is found between populations within a continent and only 8% is found on average between the various continental populations. Based on this observation, Richard Lewontin has claimed that accurate classification of humans is therefore impossible and can have no taxonomic utility. However, this view has been rejected by A. W. F. Edwards in his paper entitled Human Genetic Diversity: Lewontin's Fallacy, Edwards shows that accurate classification of humans is possible because most of the data that distinguishes populations occurs in correlations between allele frequencies, although these classifications vary depending on a number of criteria, such as sampling strategy, type of locus, distribution of loci around the genome and number of loci. On the other hand Witherspoon et al. (2007) have shown that even when accurate classification of human populations is achieved, often individuals classified into different groups are more genetically similar to each other than to members of their own group. This seems to be due to the fact that multi-locus clustering does not take into account the genetic similarities between individuals, and only uses population level traits for comparison. Witherspoon et al. conclude that accurate classification of individuals drawn from a continuously varying human population may be impossible. Compared with other species the amount of genetic diversity among humans is relatively small. For example two random chimpanzee are expected to differ by about 1 in 500 DNA base pairs, equivalent to double the diversity amongst humans. This may indicate that chimpanzees have existed as a species much longer than humans.

Ancestry-informative marker are stretches of DNA which have several polymorphisms that exhibit substantially different frequencies between the different populations. Using these AIMs scientists can determine a person's continent of origin based solely on their DNA. AIMs can also be used to determine someone's admixture proportions.

There are several methods used to model human genetic variation. Genetic distance is a measure used to quantify the genetic differences between two populations. It is based on the principle that two populations that share similar frequencies of a trait are more closely related than populations that have more divergent frequencies of a trait. In its simplest form it is the difference in frequencies of a particular trait between two populations. For example the frequency of RH negative individuals is 50.4% among Basques, is 41.2% in France and 41.1 in England. Thus the genetic difference between the Basques and French is 9.2% and the genetic difference between the French and the English is 0.1%for the RH negative trait.

When only one trait is considered it often results in two very distant populations having little or no genetic difference. For example the frequency of blood group B allele in Russia is the same as in Madagascar indicating zero value for genetic distance. To adjust for these instances it is thus necessary to average values over several genetic systems. As DNA of all humans is 99.9 percent the same the vast majority of traits show little genetic distance between the continents. However, for a few traits that are highly polymorphic genetic distances can be calculated and used to create phylogenetic relationships.

Historically people have chosen spouses from nearby villages. Hence genetic distance is largely related to geographic distance between populations. Genetic distance may also occur due to physical boundaries that restrict gene flow such as Islands cut off by rising seas.

The largest genetic distance between any two continents is between Africa and Oceania at 24.7. Based on physical appearance this may be counterintuitive, since Australians and New Guineans resemble Africans with dark skin and sometimes frizzy hair. This resemblance is probably an example of convergent evolution. This large figure for genetic distance reflects the relatively long Isolation of Australia and New Guinea since the end of the Last glacial maximum when the continent was further isolated from mainland Asia due to rising sea levels.

The next largest genetic distance is between Africa and the Americas at 22.6%. This is expected since the longest geographic distance by land is between Africa and South America. The shortest genetic distance at 8.9% is between Asia and the Americas indicating a more recent separation.

Africans are the most divergent continent with all other groups being more related to each other than to Africa. This is expected in accordance with the Recent single-origin hypothesis. The population most closely related to Africans are Europeans. However, this short distance indicates significant interaction and gene exchange between Africa and Europe in the not so distant past. Europe has a genetic variation in general about three times less than that of other continents. Even though Europeans are the non-African group closest to Africans, Europeans are most closely related to East Asians. As the genetic distance from Africa to Europe (16.6) is shorter than the genetic distance from Africa to East Asia (20.6) Cavalli-Sforza proposes that both Asian and African populations contributed to the settlement of Europe which began 40,000 years ago. The overall contributions from Asia and Africa were estimated to be around two-thirds and one-third, respectively.

Positive selection plays an important role in shaping genetic variation. Most notably is its role in influencing physical appearance. Dark skin appears to be under strong selection because the protein that causes it varies very little in African populations but is free to vary in populations found outside Africa. This indicates that dark skin was selected to protect against the harmful effects of UV radiation that cause birth defects due to destruction of vitamin b folate. UV radiation also causes sunburn and skin cancer. When people left the sun intensive regions of Africa the protein was free to vary as a result lighter skin color reemerged in populations around the world. Light skin color was probably an advantage in very cold and wet climates, for the manufacture of vitamin D by sun light, in the skin.

Immunoglobulins or antibodies are also under strong selection in response to local diseases. For example people who are duffy negative tend to have higher resistance to malaria. Most Africans are duffy negative and most non-Africans are duffy positive.

Native Americans are almost exclusively Blood group O at about 98%. Some scientists believe this widespread distribution indicates strong selection, possibly resistance to syphilis. During the European invasion of the Americas, millions of Native Americans were decimated because of diseases they were not immune to such as smallpox and influenza. Europeans had become resistant to these disease after suffering several series of deadly plagues (such as the Plague of Justinian and the Black death). In turn the Europeans contracted syphilis to which they had no immunity.

Genetic drift is the random change in gene frequencies between generations. By chance, a few individuals may leave behind more descendants and thus genes than other individuals. The genes of the next generation will be the genes of the “lucky” individuals, not necessarily the healthier or “better” individuals.

The founder effect is the establishment of a new population by a few original founders which carry only a small fraction of the total genetic variation of the parental population. As a result, the new population may be distinctively different, both genetically and phenotypically, from the parent population from which it is derived. Some scientists speculate that the ubiquity of Blood group O amongst native Americans is an example of a strong founder effect. They argue that a small band of Asian people who crossed the Bering strait into Alaska may have been predominantly Blood group O.

Founder effects are notable following the colonization of Islands. The crania of Indigenous Australians is one of the most differentiated from other populations and is the most easily identified due to more prominent brow ridges. Since the crania shows little variability amongst Australians some scientists believe it arose from a founding effect.

Gene flow is the exchange of genes from one population to another. Gene flow has the effect of reducing the genetic distance between two populations. Since genes are exchanged between neighboring populations many traits are distributed along clines. The boundaries of the major continents may in some cases restrict gene flow, allowing for genetic differentiation.

However many of the political divisions of today are not naturally occurring and in the past have not restricted gene flow. Europe and Asia are in fact the single continent of Eurasia. This would explain the relatively small genetic distance of 9.7% as calculated by Cavalli-Sforza.

North Africa is sometimes included as part of Eurasia. Northeast Africa is adjacent to Saudi Arabia and thus Africans have a long history of interaction with the middle east. Populations in the horn of Africa have significant Arab admixture. African mitochondrial DNA haplotypes are also frequent in the Middle east. Across the Sahara from Sudan to Senegal interactions between blacks and Arabs have resulted in significant gene exchange between the populations. In North Africa, in a study by Rando et al. 1998, levels of sub-Saharan mtDNA (excluding L3 lineage, which may be of ancient introduction and so remains ambiguous) ran from 2% in Moroccan Berbers, 9% in Algerian Berbers and in non-Berber Moroccans to 40% in Saharans and Mauritanians, and 56% in Tuareg. During the 8th century the Moors from North Africa conquered the Iberian peninsula, in the process they would have brought African admixture to Europe. This is clinically distributed across Europe from southwest to North east with Northern Europe showing no presence. On the other hand, Northern Europe, especially some parts of Scandinavia and the Baltic states have the highest Asian lineage-related genetic markers in Europe, represented mainly by haplogroup N..

Africa is the most genetically divergent continent. However, the most closely related population to Africa based on genetic distance is Europe at 16.6%. This may be counterintuitive based on different skin colors. Independent evolution on the different continents would result in equal genetic distances between Africa and the other continents. However, this low figure of 16.6(relative to Australia 24.7, and America 22.6%) indicates that there has been substantial interaction and exchange of genes between Africa and Europe. Cavalli-Sforza estimates that Europeans are mixed race population, one third African and two thirds Asian.

Joseph Greenberg classified American languages into three large families. He proposed that these families represent three separate migrations that filled the Americas in the order they arrived. These separate migrations across the Bering strait would have continued to bring new genes from Asia thus reducing the genetic distance between Asia and America.

Australasia is largely considered to be the most isolated continent. It was occupied at least 40,000 years ago when sea levels were much lower and the shortest distance between Indonesia and Australia was a 90 km sea voyage. 20,000 years ago at the end of the last Glacial Maximum, sea levels rose due to melting ice sheets flooding much of Australia's coastline and increasing its geographic isolation from Asia. Tasmania was cut off from Australia 10,000 years ago making it the most isolated region. These obstacles significantly restricted gene flow to indigenous Australasians. Second to Africa, Australasia is the most genetically divergent continent by genetic distance; however evidence suggests that even with Australasia gene flow has been taking place. Fossils of the Dingo in Australia have been dated to only 3500 years ago indicating that it was recently introduced. The dingo is native to India. Some Y chromosomal studies indicate a recent influx of y chromosomes from the Indian subcontinent. More recently fisherman from Makassar in Indonesia regularly made contact with Indigenous Australians from possibly as early as 1000 AD.

Genetic techniques have been used to study racial admixture in America.

The 0.1% genetic difference that differentiates any two random humans is still the subject of much debate. The discovery that only 8% of this difference separates the major races led some scientists to proclaim that race is biologically meaningless. They argue that since genetic distance increases in a continuous manner any threshold or definitions would be arbitrary. Any two neighboring villages or towns will show some genetic differentiation from each other and thus could be defined as a race. Thus any attempt to classify races would be imposing an artificial discontinuity on what is otherwise a naturally occurring continuous phenomenon.

However, other scientists disagree by claiming that the assertion that race is biologically meaningless is politically motivated and that genetic differences are significant. Neil Risch states that numerous studies over past decades have documented biological differences among the races with regard to susceptibility and natural history of a chronic disease, though acknowledges that these differences do not constitute any major subdivisions of the human species: '...These conclusions seem consistent with the claim that "there is no biological basis for 'race'" and that "the myth of major genetic differences across 'races' is nonetheless worth dismissing with genetic evidence". Of course, the use of the term "major" leaves the door open for possible differences but a priori limits any potential significance of such differences.' Effectively Neil Risch is attempting to redefine "race" for human populations to represent that small proportion of variation that is known to vary between continental populations. It is well established, that the level of differentiation between the continental human groups, as measured by the statistic FST is about 0.06-0.1 (6-10%), with about 5-10% of variation at the population level (that is between different populations occupying the same continent) and about 75-85% of variation within populations.(Risch et al., 2002; Templeton, 1998; Ossorio and Duster, 2005; Lewontin, 2005). Tempeton (1998) states that in biology a level of 0.25-0.3 (20-30%) of differentiation normally accepted in biological literature for a population to be considered a race or subspecies.

When we want to assign an individual to one of these populations using this single locus we will assign any + to population I because the probability (p) of this allele belonging to Population I is p=0.7, the probability (q) of incorrectly assigning this allele to Population I is q=1-p, or 0.3. This amounts to a Bernoulli trial because the answer to the question "is this the correct population?" is a simple yes or no. This makes the test Binomially distributed but with a single trial.

But when three loci per individual are taken into account, each with p=0.7 for a + allele in Population I the average number of + alleles per individual becomes kp=2.1 (number of trials (k=3) x probability for each allele (p=0.7)) and 0.9 (3 x 0.3) + alleles per individual in Population II. This is sometimes referred to as the population trait value. Because alleles are discrete entities we can only assign an individual to a population based on the number of whole + alleles it contains. Therefore we will assign any individual with three or two + alleles to Population I, and any individual with one or fewer + alleles to population II.

The binomial distribution with three trials and a probability of 0.7 shows that the probability of and individual from this population having a single + allele is 0.189 and for zero + alleles it is 0.027, which gives a misclassification rate of 0.189 + 0.027 = 0.216, which is a smaller chance of misclassification than for a single allele. Misclassification becomes much smaller as we use more alleles. When more loci are taken into account, each new locus adds an extra independent test to the binomial distribution, decreasing the chance of misclassification.

Though the authors of the study do not equate the clusters with race there are some who view the studies on clusters as evidence of the existence of biological races. Hence these studies have attracted considerable controversy. Critics argue that using genetic information to determine an individual's continent of origin is not a new concept. Using the ABO, RH and MNS blood groups, scientists in the 1950s could already determine continent of origin based on known frequencies of these traits.

Critics argue that any attempt to divide humanity will always produce artificial results. They point to the fact that in the study when six clusters were used an additional cluster (race) appeared which consisted solely of the Kalash of Pakistan. Several groups in the study also appeared in two races such as Ethiopians, Hazara of Pakistan, and Uyghur from Pakistan and western China. Joseph Graves argues that in the study the people sampled were from regions separated by large distances such as South African Bantu and Russians. He argues that if more people came from the regions that bridge the continents results may have been different. Examples such as Armenians would cluster both with Asia and Europe. Somalians or Yemenites may cluster both with Africa and Europe.

Others say the bulk of human variation is continuously distributed and, as a result, any categorization schema attempting to meaningfully partition that variation will necessarily create artificial truncations. It is for this reason, they argue, that attempts to allocate individuals into ancestry groupings based on genetic information have yielded varying results that are highly dependent on methodological design.

Nicholas Wade, who often cites the work of clusters in articles for the New York Times, says that even if individuals can be assigned to continent of origin based on their genotype (genes), this is not an indication of phenotype. This is because the SNPs used in the clustering study are selectively neutral i.e. stretches of Junk DNA that have no known function. Since they do not code for any protein or have regulatory function, mutations can occur without interfering in normal cell function. Over time these mutations can accumulate much quicker in local populations and thus they can be used to identify continent of origin. Therefore these SNPS that can be used to differentiate continental populations are not known to influence intelligence, behavior, susceptibility to disease or ability in sports. Wade argues that it is possible that even though the sites used are nonworking sections of DNA, mutations in them may serve as a proxy for mutations in genes that influence intelligence and behaviour. However, he admits that at the moment there is no known relationship between mutations in junk DNA and mutations in genes.

Many human phenotypes are polygenic, meaning that they depend on the interaction among many genes. Polygeneity makes the study of individual phenotypic differences more difficult. Additionally, phenotypes may be influenced by environment as well as by genetics. The measure of the genetic role in phenotypes is heritability.

Different genes may also produce the same phenotype. For example the gene that causes light skin color in Europeans is different from the gene that causes light skin in East Asians. Europeans have a different version of the SLC24A5 than East Asians possibly indicating that they evolved light skin independently. A recent asthma study found that genes that defined susceptibility to asthma in blacks were different from the genes defined susceptibility in whites which were again different for the genes that defined susceptibility to asthma in Hispanics.

Epigenetic inheritance describes a phenomenon where traits are passed on to the next generation based on environmental effects or experience. These traits are inherited without being written into the DNA sequence. In some cases traits are passed on to the next generation by the switching off or on of various genes that are already present. The implication of this is that having the same genotype at a locus does not necessarily mean having the same phenotype.

In his book Guns, Germs, and Steel, Jared Diamond argues that European explorers believed that differences between European societies and American societies could be explained by differences in innate biological ability. Darwinian evolution viewed the "primitive societies" to be vestiges of human descent from apelike ancestors.

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History of genetics

James Watson and colleagues discovered the structure of DNA

The history of genetics is generally held to have started with the work of an Augustinian monk, Gregor Mendel. His work on pea plants, published in 1866, described what came to be known as Mendelian Inheritance. In the centuries before—and for several decades after—Mendel's work, a wide variety of theories of heredity proliferated (see below). 1900 marked the "rediscovery of Mendel" by Hugo de Vries, Carl Correns and Erich von Tschermak, and by 1915 the basic principles of Mendelian genetics had been applied to a wide variety of organisms—most notably the fruit fly Drosophila melanogaster. Led by Thomas Hunt Morgan and his fellow "drosophilists", geneticists developed the Mendelian-chromosome theory of heredity, which was widely accepted by 1925. Alongside experimental work, mathematicians developed the statistical framework of population genetics, bring genetical explanations into the study of evolution.

With the basic patterns of genetic inheritance established, many biologists turned to investigations of the physical nature of the gene. In the 1940s and early 1950s, experiments pointed to DNA as the portion of chromosomes (and perhaps other nucleoproteins) that held genes. A focus on new model organisms such as viruses and bacteria, along with the discovery of the double helical structure of DNA in 1953, marked the transition to the era of molecular genetics. In the following years, chemists developed techniques for sequencing both nucleic acids and proteins, while others worked out the relationship between the two forms of biological molecules: the genetic code. The regulation of gene expression became a central issue in the 1960s; by the 1970s gene expression could be controlled and manipulated through genetic engineering. In the last decades of the 20th century, many biologists focused on large-scale genetics projects, sequencing entire genomes.

The most influential early theories of heredity were that of Hippocrates and Aristotle. Hippocrates' theory (possibly based on the teachings of Anaxagoras) was similar to Darwin's later ideas on pangenesis, involving heredity material that collects from throughout the body. Aristotle suggested instead that the (nonphysical) form-giving principle of an organism was transmitted through semen (which he considered to be a purified form of blood) and the mother's menstrual blood, which interacted in the womb to direct an organism's early development. For both Hippocrates and Aristotle—and nearly all Western scholars through to the late 19th century—the inheritance of acquired characters was a supposedly well-established fact that any adequate theory of heredity had to explain. At the same time, individual species were taken to have a fixed essence; such inherited changes were merely superficial.

In 1000 CE, the Arab physician, Abu al-Qasim al-Zahrawi (known as Albucasis in the West), wrote the first clear description of haemophilia, a hereditary genetic disorder, in his Al-Tasrif. In this work, he wrote of an Andalusian family whose males died of bleeding after minor injuries.

In the 18th century, with increased knowledge of plant and animal diversity and the accompanying increased focus on taxonomy, new ideas about heredity began to appear. Linnaeus and others (among them Joseph Gottlieb Kölreuter, Carl Friedrich von Gärtner, and Charles Naudin) conducted extensive experiments with hybridization, especially species hybrids. Species hybridizers described a wide variety of inheritance phenomena, include hybrid sterility and the high variability of back-crosses.

Plant breeders were also developing an array of stable varieties in many important plant species. In the early 19th century, Augustin Sageret established the concept of dominance, recognizing that when some plant varieties are crossed, certain characters (present in one parent) usually appear in the offspring; he also found that some ancestral characters found in neither parent may appear in offspring. However, plant breeders made little attempt to establish a theoretical foundation for their work or to share their knowledge with current work of physiology.

In breeding experiments between 1856 and 1865, Gregor Mendel first traced inheritance patterns of certain traits in pea plants and showed that they obeyed simple statistical rules. Although not all features show these patterns of Mendelian inheritance, his work acted as a proof that application of statistics to inheritance could be highly useful. Since that time many more complex forms of inheritance have been demonstrated.

From his statistical analysis Mendel defined a concept that he described as an allele, which was the fundamental unit of heredity. The term allele as Mendel used it is nearly synonymous with the term gene, and now means a specific variant of a particular gene.

Mendel's work was published in 1866 as "Versuche über Pflanzen-Hybriden" (Experiments on Plant Hybridization) in the Verhandlungen des Naturforschenden Vereins zu Brünn (Proceedings of the Natural History Society of Brünn), following two lectures he gave on the work in early 1865.

Mendel's work was published in a relatively obscure scientific journal, and it was not given any attention in the scientific community. Instead, discussions about modes of heredity were galvanized by Darwin's theory of evolution by natural selection, in which mechanisms of non-Lamarckian heredity seemed to be required. Darwin's own theory of heredity, pangenesis, did not meet with any large degree of acceptance. A more mathematical version of pangenesis, one which dropped much of Darwin's Lamarckian holdovers, was developed as the "biometrical" school of heredity by Darwin's cousin, Francis Galton. Under Galton and his successor Karl Pearson, the biometrical school attempted to build statistical models for heredity and evolution, with some limited but real success, though the exact methods of heredity were unknown and largely unquestioned.

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Source : Wikipedia