Yes, in certain cases. For example if a protein quantity is control by ubiquitin tagging for destruction and a mutation to one of the proteins involved in this path disable the path this would be a loss of gene regulation due to a loss of function.
What about gene regulation at the transcriptional level? Is any change in RNA transcription a loss in function?
Not necessarily if I understand your question. The cell is able to make changes base on needs. Change in regulation is different then regulation that is broken.
The cell is not able to specifically mutate DNA based on needs.
I could be wrong, but it seems that any mutation that causes a change in gene regulation is going to be categorized as a loss in function simply because it is no longer the same.
Gene regulation changes are not caused by mutation they are part of the make up of the cell. Certain genes have very different expression levels in embryo development then it they do when an animal is mature.
So sorry @colewd, but that is not how it works. There are whole gigantic databases of example after example showing how mutations change gene expression. Do you know what an eQTL is? Back in 2013 they had few thousands of examples in humans alone (Expression quantitative trait loci: present and future - PMC ). How much more do you think it has increased in five years? This one study finds more than 14,000 (http://eqtl.rc.fas.harvard.edu/eqtlbrowser/about.html). Iām not even sure if we have a large aggregation database yet.
@colewd it is okay to have a lot to learn about biology. However, perhaps stop trying to make arguments for ID till you learn the basics. Maybe you donāt the information you need to effectively make the case.
Josh with all due respect I understanding how mutations can change gene expression as I mentioned to T in a previous post.
Here I am talking about normal gene expression changes in the same organisms life cycle. These are not normally mutation based but part of normal cellular changes through the animals life. For example if a cell is in a condition of hypoxia ( low oxygen) the expression level of vegf will be increased to create blood vessels for increased oxygen. This change in expression is independent of mutation.
Thanks for the papers you cited. The first is quite interesting.
I am talking about mutations that change gene expression. For example, the mutations in the promoter region of the lactase gene in humans allows for the gene to be active into adulthood.
2 Likes
Mutation simply means change in DNA. In the case where I say it is a loss of information is where a cellular function is disabled and normal regulation is lost. I donāt think that is the case here.
No such thing as āloss of informationā when discussion mutations. They all require information to specify.
Normal regulation is lost due to the mutation in the human lactase gene. Normally, the gene isnāt expressed past weening age. However, the mutation causes expression into adulthood. That is a loss of normal regulation, and it is beneficial for humans living in an environment where dairy products are available.
So is this a loss in information?
2 Likes
Very possibly true depending on definitions. I hope we can drive this discussion to consensus 
This is the sort of thing I find frustrating in our debates. I mathematically demonstrated in our ASC discussion that misestimating P does not automatically result in an ASC value that is too high. It might, it might not. It probably does not if we are only looking at a subset of samples, which absolutely everyone does. No one scientifically examines every single atom in the universe.
But then you go on as if our discussion had not happened. Itād be great that if you decided I was wrong you could show my error.