Genetics & Molecular Biology

After earning the ire of computational biologists and network theorists last week, it's time to get to the positive side of networks and systems biology. If you hadn't guessed it before, the name of this blog reflects my interest in complex biological systems. When I rant about networks and comp. bio., it's tough love, and I really have the best interests of the field at heart.

Every week you probably see papers ( here and elsewhere) reporting the discovery of new genetic variants that affect the risk of coronary artery disease and heart attacks.

It's an exciting time and the findings will undoubtedly lead to new biological insights into the mechanisms that cause heart attacks, which in turn may result in new types of treatments, but how much value is there to it individually now?   Is 'personalized medicine' for heart attacks on the way?

In 1935 one of the founders of modern genetics, J. B. S. Haldane, studied men in London with the blood disease hemophilia and estimated that there would be a one in 50,000 incidence of mutations causing hemophilia in the gene affected – the equivalent of a mutation rate of perhaps one in 25 million nucleotides across the genome. Others have measured rates at a few further specific genes or compared DNA from humans and chimpanzees to produce general estimates of the mutation rate expressed more directly in nucleotides of DNA. 16 scientists report today the first direct measurement of the general rate of genetic mutation at individual DNA letters in humans and show that those early estimates were spot on.
For the past few days I've been fiddling with a set of data that measure the effects of single nucleotide changes on an organism's phenotype across a variety of environments and genetic backgrounds. Any good statistics manual will tell you the best way to analyze the type of data I have is through logistic regression with a generalized linear model.  So, I tried that.  Here are the results: 

> logistic <- glm(y~full_model, family=binomial(link="logit"))
> summary(logistical)
Null deviance: 20650253  on 860  degrees of freedom
Residual deviance:   118972  on 573  degrees of freedom
AIC: 128316
I've been mean to computational/network/systems biologists recently (twice). Real soon here I'm going to get into some positive aspects of these fields, but before that, I have to slam systems biology one more time.

Guess which blurb was written within the last 5 years, and which one was written more than 30 years ago:

UC Santa Barbara scientists have revealed what they call a potential new drug delivery system - a biological mechanism for delivery of nanoparticles into tissue.

They developed a peptide, a small piece of protein that can carry "cargo" for delivery into the cell, whose cargo could be a nanoparticle, or even a cell.

Riding on the peptide, the cargo gets out of the blood vessel and penetrates the tissue.
The so-called SHOX gene (short stature homeobox gene) is responsible for the normal growth of bones and is often mutated in short-stature patients. Short stature is considered when final height of an individual is no more than 160 cm (men) or 150 cm (women).

Researchers in Heidelberg have now discovered that sequences of genetic material on the X and Y chromosome that regulate this gene are also crucial for growth in children.
This research paper attempts to investigate the influence of N, P &K on chlorophyll, carbohydrate, proteins and sapogenin contents of Asparagus racemosus (Willd.). The treatment consisted different concentrations of Nitrogen (N 20, N 40, N 80 and
Craig Venter says that in a few months, his team will have created the first genuine artificial life form. As you may recall, Venter's team did the first whole genome transplant a few years back, which involved taking the genome of one species of bacteria and putting it into the genome-free cell of another closely related species. The new hybrid species was able to reboot with the new genome. According to The Times:

Artificial life will be created within four months, a controversial scientist has predicted. Craig Venter, who led a private project to sequence the human genome, told The Times that his team had cleared a critical hurdle to creating man-made organisms in a laboratory.
Seriously, if you have to ask, then you should probably just keep your mouth shut. Because nothing good is going to come of asking.

The question? Whether or not 18-year-old South African runner Caster Semenya, who won the 800-meter race at the World Athletics Championship in Berlin, is a chick or a dude.

Imagine crossing the finish line to thunderous applause, accolades, etc. Job well done after pouring so much effort into this race. And then, some insensitive prick says, wait, are you actually a girl?