What is the difference between geno and phenotype

Incomplete dominance removed some of the ambiguities in using phenotypes to distinguish genotypes, but the combination of the four phenomena and linkage for multiple loci meant that Mendelian researchers had to distinguish among multiple hypotheses about the genotypes consistent with observed patterns of traits in the offspring of crosses.

Background levels of mutation, including mutations in non-germ cells during the lifetime, ensure that even genotypes-as-classes consisting of clones or of identical or monozygotic twins are not made up of strictly identical members. Nevertheless, with suitable organisms and for certain traits, and under the inbreeding and control of conditions typical of Mendelian experiments, the painstaking work of inferring genotypes as pairs of genes from phenotypes could bear fruit.

Not all aspects of the study of heredity could be made an experimental endeavor through Mendelian methods. There were many traits for which the continuous variation could not be subdivided into discrete phenotypes, let alone linked to genotypes, especially for traits in agriculture of economic interest such as yield of plant and animal varieties or breeds.

By the end of the s Ronald Fisher and Sewall Wright had begun to address the need to reconcile the discreteness of genotypes with continuous variation in many observable traits. In the mathematical models of a field that came to be known as quantitative genetics , differences between unobserved theoretical genotypes in the sense of pairs of genes at each of a large number of loci contribute to differences in the trait, modulated by degrees of correspondingly theoretical dominance and epistasis.

Under the reasonable assumption that more of the genes are shared among relatives than in the population as a whole, data on a given trait as it varies across genealogically defined lines or groups of specified relatedness could be analyzed so as to provide predictions of changes in the average value of the trait in the population under selective breeding.

Of course, the trait values and thus the predictions depended on the conditions in which the organisms developed, but in the laboratory and, to varying degrees, in agricultural breeding, conditions could be replicated. For the breeder, the focus of the quantitative genetic data analysis on differences in the trait makes practical sense; it is not necessary to know the mechanisms through which the traits developed as organisms reacted to conditions.

In other words, the meanings of genotype, phenotype, and their distinction again make sense as an abstraction through practices of control over biological materials and conditions in agricultural and laboratory breeding and the allied use of models and analysis of data. It should also be noted that, in agricultural breeding, the lines or other genealogically defined groups became called genotypes as well. Genotypes in this sense are classes of individuals related by genealogy from a common ancestor or set of ancestors.

The relatedness takes a variety of forms—not only pure inbred or cloned lines, but also offspring of a given pair of parents or a set of ancestors or an open pollinated plant variety in which the genes vary within replicable bounds among the generations of individuals in the class. The corresponding phenotype is then the range of values of the trait or set of traits as they are observed to vary for the genealogically defined line or group in the given location s or situation s.

Quantitative genetics extended to humans does not involve controlled breeding, but does rely on relatedness that differs between, say, monozygotic and dizygotic i. Even though a twin pair is not conventionally referred to as a genotype, human quantitative genetics has followed the same idea for data analysis as used in agricultural breeding. The mathematical models of quantitative genetics could be readily extended from selective breeding to evolutionary change by having theoretical genotypes from a large number of loci each contribute to parameters for surviving and leaving offspring—so-called selection coefficients.

Data on the variation for a trait in a specific group or population could be analyzed so as to estimate the parameters in the model that would generate the observed changes in the average value of the trait over time. Notice, again the separate theoretical genotypes and their contributions, this time to selection coefficients, remain unobserved; the focus of the data analysis could be on differences in the trait, not the mechanisms of trait development.

The complexity of developmental mechanisms, which involve interactions with the environment, was collapsed in the models into the selection coefficients modulated by parameters for dominance between alleles i. A parallel development, initiated again by Fisher and Wright, as well as by J. Haldane, involved mathematical models of theoretical genotypes at one or a few loci each contributing to the parameters for surviving and leaving offspring.

In this field, which came to be known as Population Genetics, estimation of selection coefficients of genotypes inferred from distinct phenotypes was possible, albeit more readily when the populations were subject to artificial selection in the laboratory than when frequencies or changes over time were observed in the wild which was studied in the new field of ecological genetics.

Just as in quantitative genetics, the focus in population genetics was on difference in traits; complexities of development in its ecological context were typically collapsed into the parameters of the models. Some Mendelian researchers extended the investigation of the material basis for genes to their role in developmental processes.

For example, the eyes of fruit flies, normally red, are sometimes white. Geneticists identified the location on the chromosomes that corresponds to the white-eye mutation Morgan and later investigated the pigment-formation metabolic pathway and the enzymes proteins that modulate biochemical interactions involved as fruit fly eyes develop the normal or mutant color e.

Research since World War II that came to be known as molecular genetics or molecular biology went on to identify DNA as the chemical basis of genes and the mechanisms of DNA replication, mutation, transcription to RNA, and translation to polypeptides components of proteins.

Researchers probed the feedback networks that regulate these mechanisms, first in viruses and bacteria, then in complex, multicellular organisms; mapped and modified the specific DNA sequence of organisms; compared sequences among taxonomic groups i. Such research, which now occupies the center of biology, renders it plausible to many researchers and commentators that development of traits will eventually be understood in terms of a composite of the influences on the organism over time of identified DNA variants see entry on gene.

Johannsen, as noted earlier and conveyed in the contrast between the method of figure 2 and the theory of figure 1 , provided no method to divide a natural varying population into phenotypes as classes of organisms, let alone to use these classes to identify genotypes as classes within such populations.

What would be required then in order to apply his terms and distinction in the study of heredity for natural varying populations? A number of pathways can be delineated:. As a sociological, not a logical matter, success in engineering may underwrite theoretical generalizing and both may, in turn, make more plausible any assumed extension to naturally varying populations.

Together with further experiments, these pathways may eventually lead to success in re-integration. It could be imagined that the processes exposed in controlled conditions would eventually explain heredity in naturally varying populations. However, there is no guarantee that the original experimental basis for the genotype-phenotype distinction or subsequent developments must lead to effective engineering, theoretical generalization, or likening that clarifies. Indeed, as a sociological not logical matter, pursuing such steps may distract attention from the project of re-integration.

Section 5 reviews what would be entailed in reintegration, doing so in order to problematize the status of the original experimentally based distinction as a basis for the study of heredity for natural varying populations.

The rest of section 4 points to several areas of philosophical discussions brought into play and extended by experiments followed by the pathways and steps above. As noted earlier section 2 , attention is also warranted to the ways that an area of biology, such as the study of heredity, becomes experimental in the first place. Experiments in biology may lead to the engineering of new phenomena or objects, such as knockout mice i.

To continue the knockout example: does the effect of a gene knocked out in a highly inbred line of mice extrapolate to its effects in naturally variable populations of mice, let alone other species? In other words, the demonstration of genes in knockout lines that have defined effects could be a textbook case of something represented—the DNA sequence as gene—warranting the status real given the reliable effect of its absence.

Yet antirealists could point to what has not yet been observed given the special experimental conditions of Mendelian research and subsequent molecular biology see entry on scientific realism. Such an objection notwithstanding, if there is a method that is productive of results, there will be scientists who apply it even if the results do not address questions that once motivated their line of inquiry as evident, for example, when, as noted earlier, the study of heredity came to focus on differences not similarity and development.

How is any such pragmatism to be viewed? Or is it a pragmatism highlighted more in sociology than philosophy of science, in which the researcher or the interpreter of science considers how difficult it is in practice to modify what has been established as knowledge Latour ? It should be noted, however, that this form of abstraction centers on objects that are concrete, not therefore conforming to the contrast abstract versus concrete see entry on abstract objects.

The interrelated issues concerning pragmatism, scientific realism, and abstraction become even more pertinent when the theory and models that inform experiments, such as the genotype-phenotype distinction in Mendelian research, are extended to less-controlled situations, such as agricultural breeding trials, and to analysis of data derived from them. As noted earlier, quantitative genetics relies on models of contributions from unobserved, theoretical genotypes.

Analyses of data using those models allow breeders to decide which traits to enhance through selection even though they have no evidence independent of the data to confirm the assumption in their models about theoretical genotypes and their contributions Lloyd Yet, as publications, careers, release of varieties, software packages, and so on get built on such a foundation, it becomes ever more difficult in practical terms for researchers to promote alternatives that do not rest on the unobserved and unconfirmed entities and properties.

Indeed, unconceived alternatives , the possibility that Stanford highlights, may well include theories that entail methods that are, for various reasons, impractical. The pragmatic issue of needing a practical method applies in turn to philosophy: When philosophers make distinctions or otherwise point to issues that scientists have left unclear or under-examined, by what means do they envisage influencing the scientists to change their views or practices?

That question is left open by this entry. The genotype-phenotype distinction has been positioned in this entry in relation to control of biological materials and conditions, thus drawing attention to the challenge of reintegrating what had been de-emphasized through that control. Yet, no method is provided for philosophers to get the challenge taken up beyond the implication that the description—the framing—would be a helpful starting point.

In other words, the entry has positioned the genotype-phenotype distinction in line with the descriptive emphasis in the New Experimentalism on scientific practice, a prescriptive possibility of reintegration, and an open question about the method needed to shift actual practice.

The description versus prescription contrast also comes into play in relation to the different kinds of meaning given to the genotype-phenotype distinction. Should philosophers descriptively trace the shifts in meaning from Johannsen to the current day, or should they prescriptively disambiguate different meanings that may coexist among the work of different groups of researchers or even within a given group see entry on ambiguity?

Descriptively, philosophers could tease out the different, sometimes incommensurable, interests and purposes that make a line of inquiry rational. However, two other possibilities remain, namely, ambiguity in the use of the genotype-phenotype distinction obscures shortcomings in theories and methods and allows the advances in one field e.

Sections 2 and 3 described how the original genotype-phenotype distinction was operationalized under special, controlled conditions, namely, the growing and crossing of inbred lines raised under uniform conditions. Section 4 laid out pathways from the experimentally based distinction: reintegrate, engineer, generalize theoretically, liken, and experiment more. Yet biology and philosophy of biology have not emphasized the need to reintegrate what has been abstracted away as a necessary step if the genotype-conception of heredity is to be extended beyond those special conditions Figures 2 and 3 and applied to the study of heredity for natural varying populations Figure 1.

Therefore, to highlight the implications of basing the genotype-phenotype distinction in controlled conditions, this section considers what control and possible reintegration might entail in the different realms reviewed so far. For inbred lines, in contrast to the realm of natural varying populations, the phenotype-as-class is not used to identify the genotype-as-class; indeed it is recognized as a phenotype because the genotype, which is the inbred line, is given.

Such a program had proponents, especially in the first half of the twentieth century, but came to be eclipsed by Mendelian genetics and discounted by historians and philosophers of heredity Sapp Mendelian experiments require further control than for inbred lines, because the lines have to be raised in uniform conditions, crossed, and self-pollinated.

The relevant part of the genotype was shown to be pairs of genes located along chromosomes as long as, given the control entailed by Mendelian experiments, the focus lay on differences in traits, not on how an offspring develops to have the trait at all. Recall, as Johannsen noted, that Mendelian experiments are limited in examining the species-typical aspects of the germ cells and subsequent development. Again, a program for reintegrating what is abstracted away through experimental control can be imagined: researchers identify the material constituents of the genotype and then trace how all these constituents influence the development over time of the species-typical traits.

From the composite of these influences the organism as a structured whole might emerge. Two emerging features of the study of heredity, however, work against such a reintegration program: Heredity, as mentioned earlier, has become equated with the transmission of and cross-generational patterns in the differences.

That means development became a separate and secondary matter Sapp ; analysis of the dynamics of species-typical development of morphological structure was eclipsed by genetics. It is not strictly correct to assert that Mendelian experiments are unable to examine species-typical traits. For example, all individuals of all species of the fruit-fly genus Drosophila have exactly three simple light receptors, ocelli , arranged in a symmetrical triangle on the midline of the top of their heads.

The simplest assumption is that there is no variation in genotypes in the sense of material constituents that influence this trait and its development is resistant to normal environmental disturbance. However, if the development of the fly is sufficiently disturbed, some flies with two or fewer ocelli are observed. If those with fewer than three ocelli are used as parents for the next generation, they produced more abnormal flies than the parental generation. Any investigation of how the diverse genotypes result in the development of the typical three-ocelli pattern now has to explain the occurrence of the aberrant pattern as well.

Yet, Mendelian experiments seemed to show that the discrete-particles idea was justified. Much progress in restoring what was abstracted away has come through the productive research program of molecular genetics as summarized at the end of section 3.

Nevertheless, with ever-improving knowledge about genetics at the molecular level and technologies to manipulate DNA, the field of genetics is now involved, not only in accounting for how one organism differs in a trait from another, but also in illuminating the networks of gene activity and feedback gene regulation and the major branch-points of development of the organized structures—biochemical, physiological, and behavioral, as well as morphological—which phenotypes-as-traits are variants of.

Whether this progress eventually leads to an account of the operation of the genotype as a whole or even of some delimited parts of the genotype , and then to the species-typical development of structure, remains to be seen Robert , entry on developmental biology. The need for such reintegration is, however, often discounted. This is evident when, for example, it is assumed that genes descended from a common ancestor orthologs should have the same function and influence the same traits across taxonomic groups descended from that ancestor e.

What that assumption overlooks is the possibility that traits depend on the genotype as a whole in the development of the organism as a whole and the possibility that a gene may be conserved through roles that shift in the evolving lineages. Notwithstanding the advances of molecular genetics, its methods involve another significant form of control. Yet, again, the need for reintegration of these aspects of naturally variable situations may readily get discounted.

Consider animal experiments viewed as models for human medicine. Questions are routinely raised about the validity of, say, mice as a model for humans. If, instead, the variation were paid attention to, the first step would be to note that highly selected strains of laboratory mice are less variable than undomesticated populations Rader and experiments made on such mice involve tightly controlled situations.

To what extent, it could then be asked, do experimental observations hold for individuals from undomesticated populations raised in varied and far more complex situations? If mechanisms have been exposed using laboratory mice Tabery , to what extent do they depend on the controlled value of factors that are not typically enumerated when describing the mechanism? Of course, this line of questioning is preempted when biotechnology expands its capacity to control conditions and harness genetically engineered organisms to produce desired products.

Biotechnology can be seen as the industrial manifestation of analytic biology , the program that seeks to understand organisms by cutting them up into some appropriate small parts.

Relevant here are the politics, economics, and cultural dimensions of the rise of biotechnology and, before that, genetics itself in the areas of agriculture, health, food science, the legal system, and more. The use of models in quantitative genetics and population genetics is also based on control of biological materials and conditions.

For these fields, as indicated in this section, it is more difficult to formulate programs that reintegrate what had been de-emphasized. Mendelian experiments crossing inbred lines met the goal of Johannsen and biologists following him of giving repeatable outcomes and exposing hidden processes, but quantitative genetics, designed to analyze continuous traits see sections 3.

Models allowed breeders to predict outcomes under different mating designs; the outcomes were not strictly repeatable given that what was actually achieved typically varies from what was predicted. Moreover, while researchers could imagine that the hidden processes were like the theoretical ones in the models, the theoretical genotypes forming the basis for quantitative genetic models were unobservable see entry on scientific realism.

It appears. As genetic material inside the body. As physical appearance outside the body. During reproduction, the genotype is partly inherited from an individual to the offspring as one of the two alleles. These characters are not inherited.

Determined by. To find the kind of genes on the allele, scientific methods like polymerase chain are used. By observation. Factors Affecting Genotype And Phenotype. The genotype of a person can be affected by the environment in which the person lives and the internal environment of a person's body such as hormones and metabolism. Phenotype is affected by the genotype of a person.

Genotype In Biology. Genotype helps to determine the heredity potentials and limitations of an individual from the embryonic stage through adulthood. Among sexually reproducing organisms, a genotype contains the entire complex of genes inherited from both parents. Examples of Genotype. Example 1. In the pea plant, the possible genotypes for the flower- color gene was red - red, red- white, and white- white. Example 2. Considering the genotype for height in a species of a pea plant, T is for tall variety and s small variety.

It is considered that pure breed of plants is TT and ss, then the probability of offspring being short is 1 in 4. Phenotype In Biology. The two terms are often used at the same time to describe the same organism, but there is a difference between genotype and phenotype:. For example, two mice that look virtually identical could have different genotypes.

But if they have visibly different traits - say, one has white fur and the other has black fur - then they have different phenotypes. How does genotype affect phenotype? Genotype is the collection of genes responsible for the various genetic traits of a given organism. Genotype is determined by the makeup of alleles , pairs of genes responsible for particular traits. An allele can be made up of two dominant genes, a dominant and a recessive gene, or two recessive genes.

The combination of the two, and which one is dominant, determines what trait the allele will express. However, having certain genes does have observable results.