The genotype and the environment influences the resulting phenotype, and it is often mistakenly thought that the genotype never changes. However, the field of molecular mutations has shown that phenotypic abnormalities sometimes alter the sequence of the genetic code. Chemical mutations cause substitutions and deletions in base pairs and frameshift mutations that generate gaps in DNA during replication. Other types of mutations can cause the spontaneous loss in nitrogenous bases (lesions) in the intact double-helical DNA molecule before replication, thus altering the organisms genetic code. The following are examples of the effect of the environment on both the phenotype and the genotype:

Ultraviolet and high energy radiation (X-rays, gamma rays, and cosmic irradiation) and chemo-toxins penetrate the phenotype that in turn cause genetic mutations. Pathological viruses enter the phenotype causing a nucleotide change in the host's DNA that is then responsible for mutations within the genome: viruses are often the "precore mutants" that disrupt the base pair in the pregenome.

Many studies have indicated that aging phenotypes produce degraded gametes. In other words, increased birth defects are associated with older couples having children due to the resulting degradation in both the egg and the sperm.

Another good example is mercury poisoning. Among other abnormalities, it causes purine and pyrimidine metabolism errors and mitochondrial disturbances that lead to autism. There then occurs a "90% concordance in monozygotic twins and a 3-5% risk of autism in siblings of affected probands, a rate 50 to 100 times higher than would be expected in the general population." http://www.autismwebsite.com/ari/vaccine/mercurylong.htm
http://www.cqs.com/autismmercury.htm

Biochemical phenotype deficiencies in phenylaline (phenylalanine hydroxylase -PAH) causes lower IQ and is then genetically transmitted causing further mutations. This disorder is referred to as maternal phenylketonuria (PKU): "Phenotypic variability of PAH deficiency is correlated directly with allelic heterogeneity at the PAH locus." http://pediatrics.aappublications.org/cgi/content/full/104/2/258

Levels in certain enzymes can also lead to mutations by degenerating proteins. For example, abnormal levels in angiotensin converting enzyme (ACE) affects polymerized nucleotides before polymerase.

Warning:

All casual readers of this post with an interest in, but limited knowledge of, genetics, please note that vallich's undertanding of what constitutes a phenotype, and its realtionship to genotype, is flawed. As a result his observations above range from misleading to wrong. You would be advised to consult a good textbook, or reliable on-line source for clarification of these issues.

Isn't a phenotype simply an arbitrary definition of the outward appearance of things caused by genotypes, such as hair colour?

Warning:

All casual readers of this post with an interest in, but limited knowledge of, genetics, please note that vallich's undertanding of what constitutes a phenotype, and its realtionship to genotype, is flawed. As a result his observations above range from misleading to wrong. You would be advised to consult a good textbook, or reliable on-line source for clarification of these issues.

You know, I saw the title of the thread and just had to peep in. :)

What are they teaching in school these days?

The genotype and the environment influences the resulting phenotype, and it is often mistakenly thought that the genotype never changes.

Who thought this? when? give me a source

However, the field of molecular mutations Molecules do not mutate; there is no such field. Genes mutate.

What is mutation? There are 2 major steps in the formation of chromosomes (which are made up of genes).

DNA-------->genes-------->chromosomes------>phenotype

http://upload.wikimedia.org/wikipedia/en/0/07/Gene.png

1. Synthesis of DNA
2. Packaging of the chromosomes

DNA is synthesised by copying information from RNA. If there are copying errors, due to natural or unnatural causes ( radiation, viruses) these copying errors lead to change in genetic material. This is a MUTATION.

There are 2 types of mutations:

germ line mutations : which are inherited
somatic mutations: which are not inherited
( which has shown that phenotypic abnormalities sometimes alter the sequence of the genetic code. WRONG see above Chemical mutations cause substitutions and deletions in base pairs and frameshift mutations that generate gaps in DNA during replication. Other types of mutations can cause the spontaneous loss in nitrogenous bases (lesions) in the intact double-helical DNA molecule before replication, thus altering the organisms genetic code. This is what I just told you.The following are examples of the effect of the environment on both the phenotype and the genotype:

Ultraviolet and high energy radiation (X-rays, gamma rays, and cosmic irradiation) and chemo-toxins penetrate the phenotype that in turn cause genetic mutations.look at the figure above and you will see that phenotype cannot affect the gene; it is a one way process. If the gene is damaged by mutation it can cause changes in phenotype e.g. cancer not vice versa Pathological viruses enter the phenotype causing a nucleotide change in the host's DNA that is then responsible for mutations within the genome: viruses are often the "precore mutants" that disrupt the base pair in the pregenome. WRONG viruses disrupt DNA synthesis or repair

Many studies have indicated that aging phenotypes produce degraded gametes.because the genes have had a longer time to be exposed to radiation, viruses, carcinogens In other words, increased birth defects are associated with older couples having children due to the resulting degradation in both the egg and the sperm.eggs are degraded because a female is born with ALL her eggs and by the time she reaches 40 years each and every one of her eggs is 40 years and has been exposed for 40 years to radiations, viruses etc. Sperm are produced in lower quantities(not always true) due to aging of the machinery which produces them

Another good example is mercury poisoning. Among other abnormalities, it causes purine and pyrimidine purine and pyrimidine are the bases of the nucleotides which make up the DNA which makes up the gene which makes up the chromosomes. They all ultimately mean the same thing. DNA SYNTHESIS IS IMPAIRED metabolism errors and mitochondrial disturbances that lead to autism. There then occurs a "90% concordance in monozygotic twins and a 3-5% risk of autism in siblings of affected probands, a rate 50 to 100 times higher than would be expected in the general population." http://www.autismwebsite.com/ari/vaccine/mercurylong.htmif the affected parties are related it is a germ line mutation.i.e. they got ot from their parents.

Obviously all DNA is subject to mutation. Also the germline. Indeed the Germline DNA can be affected by environmental mutagenic agencies and by internal mutagenic agencies (errors in duplication that are not corrected).

The germline doesn't contribute to the phenotype. And hence Valich is wrong.

Old age is not a phenotype. Old age for the germline is just the accumulation of errors over time.

If I hold a stick of plutonium near Valich nutsack I certainly am going to change his genotype and phenotype locally. I will probably cause great cellular damage, killing off millions of cells. Some might give rise to cancer if valich survives the original radiation dose long enough. A local phenotypic change caused by a local change in phenotype. This new genotype will not be transfered to the germline though. The germline is full of its own original errors that have absolutely NOTHING in common with the genotypic change that resulted in the phenotypic change.

Valich is just being anal. He thinks he is on to something. But he just reinvented the wheel.

An intellectual fart of the third order.

Someone open a window.

how old is he?

Easy questions that boggle me:

Where is 'germline' DNA stored? How often is it replicated/backed-up, i.e. how long do those cells live for / how long before they must divide?

Having been told many of the ailments ot old age are due to genetic degredation - I wonder why children do not start where their parents had left off!? (In terms of genetic damage, obviously).

DNA is synthesised by copying information from RNA. If there are copying errors, due to natural or unnatural causes ( radiation, viruses) these copying errors lead to change in genetic material. This is a MUTATION.

Hmm I have to add that DNA is copied from DNA and also RNA is synthsesized from DNA. I assume it was not intentional to put it that way, but since it was a critique on the nonsense posted in the OP I thought it may be important to point that out.

Also viruses are able to change the genotype (although they do not "enter the phenotype" or any such nonsense), by integrating themselves into the genome. As such viruses (or e.g. transposons for that matter) can be counted as mutagenic agents, but of course it stands in no relation to Valich's posts.
Valich, in case you are wondering why people respond to your posts in a "disruptive" way, the answer is quite simple. Garbage in garbage out. You really should try reading the basics of any topic you blunder in. At least get the basic definitions right.

how old is he?He has been vague on this, but I think has claimed, or implied he is at least in his forties. (Yes, I know, he should know better by now.) He also claims a number of advanced degrees, but again is vague on the specifics.
We should also distinguish between his chronological age and his mental age. ;)

Vallich, if you find this discussion of your shortcomings in public in anyway distressing, all I can recommend is that you cease exposing those shortcomings in public with such single minded alacrity.

He has been vague on this, but I think has claimed, or implied he is at least in his forties. (Yes, I know, he should know better by now.) He also claims a number of advanced degrees, but again is vague on the specifics.
We should also distinguish between his chronological age and his mental age. ;)

Vallich, if you find this discussion of your shortcomings in public in anyway distressing, all I can recommend is that you cease exposing those shortcomings in public with such single minded alacrity.


I do not believe he is in his forties. NO WAY!

What type of mutations occurs by ionizing radiation widely used to produce new cultivated varieties cultivars of plants--genotype, phenotype or anyone effecting other?

I am not familiar with this process, but as you describe it, it is the genotype of the germ cells which is changed by the ionisation. The genotype that arises from these mutated cells will generate a new phenotype.

What type of mutations occurs by ionizing radiation widely used to produce new cultivated varieties cultivars of plants--genotype, phenotype or anyone effecting other?


I think the idea is that the mutations are random. They obviously are always genotypical (otherwise they wouldn't be mutations), which sometimes result in phenotypical changes. Sometimes not. It's a lottery.

I think the idea is that the mutations are random. They obviously are always genotypical (otherwise they wouldn't be mutations), which sometimes result in phenotypical changes. Sometimes not. It's a lottery.

"The germline doesn't contribute to the phenotype. And hence Valich is wrong. "


Sorry but, How then above is correct?

Originally Posted by Kumar
Sorry but, How then above is correct?

The germline cells are the cells from which gametes are created. Mutations in these cells could affect phenotype in the offspring, but will not affect phenotype in the individual that those cells belong to.

We now know that environmental influences on development, and not mutation, are the first order cause of design. If the genotype is not accomodated by the environment, then it cannot survive. Yet it does and it evolves accordingly.

As stated in review of Mary Jane West-Eberhard's book "Developmental Plasticity and Evolution": "The hypothesis of genetic accommodation can be understood as beginning when the environment induces a phenotypic change. This change imposes a new selective regime onto pre-existing polygenic variation. In this way, we are encouraged to understand genes as "followers", as opposed to "leaders" in evolution. The variants can be inherited in subsequent generations if the environmental conditions inducing them are recurrent, and if there is genetic variation underlying the population in the developmental capacity to produce them. Natural selection will favor the spread of a particular environmentally-induced variant when it has positive effects on individual fitness. Although both mutation and environmental induction are considered important modes of initiation of new phenotypic variation, West-Eberhard's argument is that environmental induction is in fact more important."

So tell us what that means valich. ........ In your own words.

The environment inducing a phenotypic change?

I suppose the cast of various insects can be altered by the presence/absence of chemcials its the environment.

The environment routinely induces phenotypic changes, since the phenotype is the product of the environment acting on a specific genotype. That still has nothing to do with valich's spurious claims of the phenotype changing the genotype.
All he is doing with his ignorance is muddying the waters for a serious discussion of epigenetics.
[Warning: Expect a rash of quotations based on vallich's trawling of the internet for this term, which he claim to be in support of his opening remarks .]

ummm... can i speak a little? thanks.

i think i kind of get valich's drift here. he just, i /think/ got confused and forgot what phenotype and genotype meant.

genotype is the genetic makeup/code for a certain trait, correct? meaning, it is found in the dna, and is subject to mutation. phenotype, on the other hand, is the MANIFESTATION or the 'decoded' form of this code. so, most of you guys are correct--mutation does not occur due to phenotypic changes because phenotypes are simply manifestations. it's comparable to a webpage: the phenotype is the page viewed from a browser while the genotype is the html that makes it appear that way. so even if you click ang type in between the text in page, it doesn't change unless you change the coding. correct?

what valich, i think, is trying to say here, is that environmental changes on an organism may possible induce mutation or adaptation. however, valich has mistaken the phenotype for... i don't know, the organism itself? this is probably due to the fact that the phenotypical change caused by the mutation is more easily observable than its corresponding genotypical change, which frankly, can be a pain in the butt to find. but then again, environment inducing mutation is not a new area here, so i don't see the point of me trying to make sense out of it again.

...

(heeeeadache....)

An organism's genotype is the largest influencing factor in the development of its phenotype, but it is not the only one. Even two organisms with identical genotypes normally differ in their phenotypes. One experiences this in everyday life with monozygous (i.e. identical) twins. Identical twins share the same genotype, since their genomes are identical; but they never have the same phenotype, although their phenotypes may be very similar. This is apparent in the fact that their mothers and close friends can always tell them apart, even though others might not be able to see the subtle differences. Further, identical twins can be distinguished by their fingerprints, which are never completely identical.


The concept of phenotypic plasticity describes the degree to which an organism's phenotype is determined by its genotype. A high level of plasticity means that environmental factors have a strong influence on the particular phenotype that develops.
http://en.wikipedia.org/wiki/Genotype-phenotype_distinction

Conclusions: Cold outdoor temperature at birth is associated with increased coronary heart disease, insulin resistance, dyslipidaemia, and poor lung function. Further research is needed to determine whether this finding reflects events occurring late in the third trimester of intrauterine growth or early in the postnatal period.

http://heart.bmjjournals.com/cgi/content/abstract/90/4/381

Results Birth rates of people who later kill themselves show disproportionate excess for April, May and June compared with the other months.
http://bjp.rcpsych.org/cgi/content/abstract/188/5/416

The interaction between genotype and phenotype has often been described using a simple equation:

genotype + environment → phenotype
A slightly more nuanced version of the equation is:

genotype + environment + random-variation → phenotype
An example of the importance of random variation in phenotypic expression is Drosophila flies in which number of eyes may vary (randomly) between left and right sides in a single individual as much as they do between different genotypes overall, or between clones raised in different environments.

A phenotype is any detectable characteristic of an organism (i.e., structural, biochemical, physiological and behavioral) determined by an interaction between its genotype and environment
http://en.wikipedia.org/wiki/Phenotype

Gene-environment interaction is a term used to describe any phenotypic effects that are due to interactions between the environment and genes. Naive nature versus nurture debates assume that variation in a given trait is primarily due to either genes, or the individual's experiences. The current scientific view is that neither genetics nor environment are solely responsible for producing individual variation, and that virtually all traits show gene-environment interaction.
http://en.wikipedia.org/wiki/Gene-environment_interaction

Above may be some of your interest? :)