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The Genie and the Bottle; When a Genotype is not a Genotype

Discussion of everything related to the Theory of Evolution.

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The Genie and the Bottle; When a Genotype is not a Genotype

Postby Crucible » Sun Oct 23, 2011 3:29 am

I've just lined up some definitions in order to play with them. First to compare definitions for "genotype" and for "genome".

http://www.biology-online.org/dictionary/Genotype
Genotype

Definition

noun, plural: genotypes

noun

(genetics)

(1) The entire set of genes in an organism.

(2) A set of alleles that determines the expression of a particular characteristic or trait (phenotype).

(zoology)

The genetic makeup of an individual or taxon.


Supplement

The genotype refers to the entire set of genes in a cell, an organism, or an individual. A gene for a particular character or trait may exist in two allelic forms; one is dominant (e.g. A) and the other is recessive (e.g. a). Based on this, there could be three possible genotypes for a particular character: AA (homozygous dominant), Aa (heterozygous), and aa (homozygous recessive).

Word origin: Greek genos, race + Latin typus, type.

Related forms: genotypic (adjective), genotypically (adverb).
Related phrases: genotype frequency.

Compare: phenotype.

http://www.biology-online.org/dictionary/Genome
Genome

Definition

noun, plural: genomes

(1) The complete set of genes in an organism.

(2) The total genetic content in one set of chromosomes.


Supplement

The genome of eukaryotes is contained in a single, haploid set of chromosomes. The genome of bacteria is contained in a single chromosome whereas the genome of viruses is in the DNA or RNA.

The human genome is made up of approximately 35000 genes, or three billion chemical base pairs.

Word origin: a portmanteau of the words gene and chromosome.
Related forms: genomic (adjective), genomics (noun), genomewide (adjective).
Related phrases: Human Genome Project, mitochondrial genome.
Compare: proteome.
See also: genes, DNA.





Definitions (1) are the same, for "genotype' and for "genome". Genotype definitions given first, genome second.

(1) The entire set of genes in an organism.
(1) The complete set of genes in an organism.


Definitions (2) look like this:

2) A set of alleles that determines the expression of a particular characteristic or trait (phenotype).
(2) The total genetic content in one set of chromosomes.

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Postby Crucible » Sun Oct 23, 2011 4:07 am

Since one thing leads to another, these terms need definition now:
    trait
    characteristic
    character
    gene
    phenotype
    phenome
    haploid
The mention of "haploid" throws a twist, considering the (1) definitions are the same for "genotype" and "genome".
"Characteristic", "character", and "trait" add some fun..and "phenotype" can mean lots of things it seems
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Re: The Genie and the Bottle; When a Genotype is not a Genotype

Postby Crucible » Sun Oct 23, 2011 9:41 pm

Trait:
trait

A qualitative characteristic; a discrete attribute as contrasted with metrical character. A trait is amenable to segregation rather than quantitative analysis; it is an attribute of phenotype, not of genotype.

Origin: Fr. From L. Tractus, a drawing out, extension
http://www.biology-online.org/dictionary/Segregation

Characteristic


Characteristic

Definition

noun, plural: characteristics

(1) A distinguishing quality, trait or feature of an individual, thing, disorder, etc.

(2) A distinctive mark, feature, attribute, or property of an individual or thing.


adjective

Being a feature or trait that helps identify an individual, thing, etc.


Supplement

For instance, a living thing is considered alive when it shows the following general characteristics:

It is made up of cell(s).
It is capable of growth and development.
It obtains energy and utilizes it.
It can reproduce.
It responds to its environment.
It is capable of adapting to its environment.


Word origin: Greek charaktēristikós (to designate, characterize)
Related forms: characteristically (adverb)

Related terms:

Characteristic curve
Characteristic radiation





A trait is a qualitative characteristic.
A characteristic is a distinguishing quality, trait or feature
Therefore:
A trait is a qualitative distinguishing quality. Or, a trait is a qualitative distinguishing trait.
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Postby Cat » Mon Oct 24, 2011 1:31 am

The definitions you refer to are somewhat erroneous. Please, compare these:

http://en.wikipedia.org/wiki/Genome

http://en.wikipedia.org/wiki/Genotype

These are more accurate.
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Re:

Postby Crucible » Mon Oct 24, 2011 11:29 am

Cat wrote:The definitions you refer to are somewhat erroneous. Please, compare these:

http://en.wikipedia.org/wiki/Genome

http://en.wikipedia.org/wiki/Genotype

These are more accurate.


OK. I'll have to stay with just one source at a time.
From wiki:

The genotype is the genetic makeup of a cell, an organism, or an individual (i.e. the specific allele makeup of the individual) usually with reference to a specific character under consideration.[1] For instance, the human CFTR gene, which encodes a protein that transports chloride ions across cell membranes, can be dominant (A) as the normal version of the gene, or recessive (a) as a mutated version of the gene. Individuals receiving two recessive alleles will be diagnosed with cystic fibrosis. It is generally accepted that inherited genotype, transmitted epigenetic factors, and non-hereditary environmental variation contribute to the phenotype of an individual.

Non-hereditary DNA mutations are not classically understood as representing the individual's genotype. Hence, scientists and physicians sometimes talk for example about the (geno)type of a particular cancer, that is the genotype of the disease as distinct from the diseased.
In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA.[1]


So wiki suggests that "genotype" is about "character" differences i.e. "traits" ..one might suppose ?

And "genome" is about commonalities ?

Genome on commonalities
Does "genome" include epigenetic factors and RNA and everything to do with inheritance ? or not ?

How does wiki define "character" and "trait" ? Let's see.
A trait is a distinct variant of a phenotypic character of an organism that may be inherited, environmentally determined or be a combination of the two.[1] For example, eye color is a character or abstraction of an attribute, while blue, brown and hazel are traits.

A phenotypic trait is an obvious and observable trait; it is the expression of genes in an observable way. An example of a phenotypic trait is hair color, there are underlying genes that control the hair color, which make up the genotype, but the actual hair color, the part we see, is the phenotype. The phenotype is the physical characteristics of the organism. The phenotype is controlled by the genetic make-up of the organism and the environmental pressures the organism is subject to. [2]

A trait may be any single feature or quantifiable measurement of an organism. However, the most useful traits for genetic analysis are present in different forms in different individuals.

A visible trait is the final product of many molecular and biochemical processes. In most cases, information starts with DNA traveling to RNA and finally to protein (ultimately affecting organism structure and function). This is the central dogma of molecular biology as stated by Francis Crick.

This information flow may also be followed through the cell as it travels from the DNA in the nucleus, to the cytoplasm, to the ribosomes and the endoplasmic reticulum, and finally to the Golgi apparatus, which may package the final products for export outside the cell.

Cell products are released into the tissue, and organs of an organism, to finally affect the physiology in a way that produces a trait.
[edit] Genetic origin of traits in diploid organisms
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Re: The Genie and the Bottle; When a Genotype is not a Genotype

Postby Crucible » Mon Oct 24, 2011 11:49 am

A phenotypic trait is an obvious and observable trait; it is the expression of genes in an observable way.
This is incorrect. A phenotypic trait that which one may observe; nothing to do with assigning genetic cause or not. The wiki definition presupposes information that is most often not even available. I'll bet this definition works out to be inconsistent with other wiki definitions.

The "expression of genes" might be said to be the character being looked at ( hair colour ).
The phenotypic trait might be "white" from age or from bleach. It's still observably "white" no matter what the genetics for the character.
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Re: The Genie and the Bottle; When a Genotype is not a Genotype

Postby Crucible » Mon Oct 24, 2011 12:30 pm

wiki on "Phenotype"
A phenotype is an organism's observable characteristics or traits: such as its morphology, development, biochemical or physiological properties, behavior, and products of behavior (such as a bird's nest). Phenotypes result from the expression of an organism's genes as well as the influence of environmental factors and the interactions between the two.

The genotype of an organism is the inherited instructions it carries within its genetic code. Not all organisms with the same genotype look or act the same way because appearance and behavior are modified by environmental and developmental conditions. Similarly, not all organisms that look alike necessarily have the same genotype.

This genotype-phenotype distinction was proposed by Wilhelm Johannsen in 1911 to make clear the difference between an organism's heredity and what that heredity produces.[1][2] The distinction is similar to that proposed by August Weismann, who distinguished between germ plasm (heredity) and somatic cells (the body). The Genotype-Phenotype concept should not be confused with Francis Crick's central dogma of molecular biology which is a statement about the directionality of molecular sequential information flowing from DNA to protein (but which cannot become transferred from proteins).



wiki on "Phenotypic Trait"
A visible trait is the final product of many molecular and biochemical processes. In most cases, information starts with DNA traveling to RNA and finally to protein (ultimately affecting organism structure and function). This is the central dogma of molecular biology as stated by Francis Crick.


So wiki says not to confuse the concepts
The Genotype-Phenotype concept should not be confused with Francis Crick's central dogma of molecular biology which is a statement about the directionality of molecular sequential information flowing...
, and then confuses the concepts in precisely that way.
A phenotypic trait is an obvious and observable trait; it is the expression of genes in an observable way.
In most cases, information starts with DNA traveling to RNA and finally to protein (ultimately affecting organism structure and function). This is the central dogma of molecular biology as stated by Francis Crick.
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