Draft:Original research/Genetics

Genetics involves the expression, transmission, and variation of inherited characteristics.

Genetics studies how living organisms inherit features from their ancestors; for example, children often look like their parents. Genetics seeks to identify which features are inherited, and explain how these features are passed from generation to generation.

In genetics, a feature of an organism is called a "trait". Some traits are features of an organism's morphology or physical appearance; for example, a person's eye-color, height or weight. There are many other trait types, and these range from aspects of behavior to resistance to disease. Traits are often inherited, for example tall and thin people tend to have tall and thin children. Other traits come from the interaction between inherited features and the environment. For example a child might inherit the tendency to be tall, but if little food is available and the child is poorly nourished, it will still be short. The way genetics and environment interact to produce a trait can be complicated: for example, the chances of somebody dying of cancer or heart disease seem to depend on both their family history and their lifestyle.

Genetic information is carried by a long molecule called DNA which is copied and inherited across generations. Traits are carried in DNA as instructions for constructing and operating an organism. These instructions are contained in segments of DNA called genes. DNA is made of a sequence of simple units, with the order of these units spelling out instructions in the genetic code. This is similar to the order of letters spelling out words. The organism "reads" the sequence of these units and decodes the instruction.

Not all the genes for a particular instruction are exactly the same. Different forms of one type of gene are called different alleles of that gene. As an example, one allele of a gene for hair color could carry the instruction to produce a lot of the pigment in black hair, while a different allele could give a garbled version of this instruction, so that no pigment is produced and the hair is white. Mutations are random events that change the sequence of a gene and therefore create a new allele. Mutations can produce a new trait, such as turning an allele for black hair into an allele for white hair. The appearance of new traits is important in evolution.

Heredity
Def. gene "transmission of the physical and [genetic] qualities of parents to their offspring; the biological law by which living beings tend to repeat their characteristics in their descendants" is called heredity.

In humans, eye color is an example of an inherited characteristic: an individual might inherit the "brown-eye trait" from one of the parents. Inherited traits are controlled by genes and the complete set of genes within an organism's genome is called its genotype.

The complete set of observable traits (phenotype) arise from the interaction of its genotype with the environment. As a result, many aspects of an organism's phenotype are not inherited. For example, suntanned skin comes from the interaction between a person's phenotype and sunlight; thus, suntans are not passed on to people's children. However, some people tan more easily than others, due to differences in their genotype: a striking example is people with the inherited trait of albinism, who do not tan at all and are very sensitive to sunburn.

Heritable traits are known to be passed from one generation to the next via DNA. The sequence of bases along a particular DNA molecule specifies the genetic information: this is comparable to a sequence of letters spelling out a passage of text.

If a mutation occurs within a gene, the new allele may affect the trait that the gene controls, altering the phenotype of the organism.

While this simple correspondence between an allele and a trait works in some cases, most traits are more complex and are controlled by a quantitative trait locus (multiple interacting genes) within and among organisms. Developmental biologists suggest that complex interactions in genetic networks and communication among cells can lead to heritable variations that may underlie some of the mechanics in developmental plasticity and canalization.

Recent findings have confirmed important examples of heritable changes that cannot be explained by direct agency of the DNA molecule.

DNA methylation marking chromatin, self-sustaining metabolic loops, gene silencing by RNA interference, and the three dimensional conformation of proteins (such as prions) are areas where epigenetic inheritance systems have been discovered at the organismic level.

Heritability may also occur at even larger scales such as ecological inheritance through the process of niche construction is defined by the regular and repeated activities of organisms in their environment. This generates a legacy of effect that modifies and feeds back into the selection regime of subsequent generations. Descendants inherit genes plus environmental characteristics generated by the ecological actions of ancestors. Other examples of heritability in evolution that are not under the direct control of genes include the inheritance of cultural traits, group heritability, and symbiogenesis. These examples of heritability that operate above the gene are covered broadly under the title of multilevel or hierarchical selection, which has been a subject of intense debate in the history of evolutionary science.

Phenotypes
Def. the "appearance of an organism based on a multifactorial combination of genetic traits and environmental factors, especially used in pedigrees" is called a phenotype.

Theory of genetics
Def. a "branch of biology that deals with the transmission and variation of inherited characteristics, in particular chromosomes and DNA" is called genetics.

Molecular genetics
Def. a "field of biology which studies the structure and function of genes at a molecular level" is called molecular genetics.

Optogenetics
Def. a "science that combines optics and genetics to probe neural circuits" is called optogenetics.

Population genetics
Def. 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" is called population genetics.

Epigenetics
Epigenetics is the study of genome or epigenome changes resulting from external rather than genetic influences.

Inside each eukaryote nucleus is genetic material (DNA) surrounded by protective and regulatory proteins. These protective and regulatory proteins and the dynamic changes to them that occur during the course of a eukaryote's existence are the epigenome.

Changes to the epigenome can result in changes to the structure of chromatin and changes to the function of the genome.

There are "nearly 50,000 acetylated sites [punctate sites of modified histones] in the human genome that correlate with active transcription start sites and CpG islands and tend to cluster within gene-rich loci."

Cytogenetics
Cytogenetics is a study of structure, function, behavior and pathology of chromosomes.

Reverse genetics
Reverse genetics is an approach to discovering the function of a gene by analyzing the phenotypic effects of specific gene sequences obtained by DNA sequencing. This investigative process proceeds in the opposite direction of so-called forward genetic screens of classical genetics. Simply put, while forward genetics seeks to find the genetic basis of a phenotype or trait, reverse genetics seeks to find what phenotypes arise as a result of particular genes.

Automated DNA sequencing generates large volumes of genomic sequence data relatively rapidly. Many genetic sequences are discovered in advance of other, less easily obtained, biological information. Reverse genetics attempts to connect a given genetic sequence with specific effects on the organism.

Hypotheses

 * 1) Individual breeding preferences coupled with geographical isolation may produce new species.
 * 2) Cavia porcellus may be derived from Cavia tschudii.