Genetic Network Modelling

The bench biologist is in a continual search mode for some new gene interaction. What new gene can be a, not the, cause of say prostate cancer. At the other extreme is the systems biologists who use their mathematical models to propose reactions. The intersection of these two is not that fruitful as of yet.

In Science the authors conclude:

Models are simplified (but not simplistic) representations of real systems, and this is precisely the property that makes them attractive to explore the consequences of our assumptions, and to identify where we lack understanding of the principles governing a biological system. Models are tools to uncover mechanisms that cannot be directly observed, akin to microscopes or nuclear magnetic resonance machines. Used and interpreted appropriately, with due attention paid to inherent uncertainties, the mathematical and computational modeling of biological systems allows the exploration of hypotheses. But the relevance of these models depends on the ability to assess, communicate, and, ultimately, understand their uncertainties. 

 The process is iterative. Models are built, tested, found lacking, and then reiterated. The challenge is that these are quite complex and of massive dimensions. Perhaps methods akin to 19th Century thermodynamics may play a role, gross constructs like enthalpy and Gibbs free energy, but perhaps not.

It will take time to get these models to work properly, but they are needed as a cornerstone of true science.

The Government Again

I like Amazon, I mean I really like Amazon. If you have a problem they solve it near instantaneously and you are happy. Maybe we should have them take over the Government. They get things right, get them inexpensively, get them on time, and give customers satisfaction.

Now their only Achilles heel is that in the New York area they rely upon the USPS. Yes, the Post Office, yes the Government. During the winter the good old mailman just drops packages off on the snow pile, and I had better get there before the snow plows, yes again Town Government, gets to try and knock them off and crush them to bits. All too often the USPS looses packages but reports them delivered, and then when asked never responds. They are"tracking" the package but most likely it went to package heaven some where. The result is Amazon immediately sends a replacement. Good for Amazon and bad for the USPS.

You can tell the Government they messed up but you might just as well try and reach another galaxy. No one there and frankly they just don't care. Well why should they? They can't get fired, remember the Army balloon, they have great pensions, and in New Jersey they have multiple ones, and they get life long health care etc. And of course our taxes go up to keep them all happy.

So as we start off this campaign season, perhaps we could put a cardboard Amazon box up on the stage to remind us that someone does get it right and does think of us.

The Army and the Balloon

Government keeps giving and giving. If things seem down, just look to our Government for a good chuckle. Back to the Balloon. As ArsTechnica notes:

The wayward JLENS aerostat, which left a trail of power outages caused by the 6,000 feet of cable it dragged for over 160 miles on Wednesday, was hit by a barrage of shotgun fire to remove its remaining helium. Approximately 100 shotgun blasts were fired at the balloon by Pennsylvania State Police, according to US Army Captain Matthew Villa, an Army spokesperson, who said that firing on the balloon was the easiest way to remove the remaining helium gas in the grounded radar aerostat. The Army still has not determined how the JLENS aerostat broke loose. But the military has labeled the incident as a Class A mishap, an aviation accident classification for events that took no human life but caused over $2 million in property damage or caused injury. Anyone who suffered property damage from the JLENS' tether will have to file claims with the Army.

 Class A indeed. And try to ever collect from the Army. But it did show how to attack the Grid, just get a big balloon.

The key question is who will be held to account? This should be a career breaker for some gree suit.

Viral Attack on Melanoma

Several years ago we started following TVEC a viral attack approach on melanoma. According to Nature:

An engineered herpesvirus that provokes an immune response against cancer has become the first treatment of its kind to be approved for use in the United States, paving the way for a long-awaited class of therapies. On 27 October, the US Food and Drug Administration (FDA) approved a genetically engineered virus called talimogene laherparepvec (T-VEC) to treat advanced melanoma. Four days earlier, advisers to the European Medicines Agency had endorsed the drug. With dozens of ongoing clinical trials of similar ‘oncolytic’ viruses, researchers hope that the approval will generate the enthusiasm and cash needed to spur further development of the approach. “The era of the oncolytic virus is probably here,” says Stephen Russell, a cancer researcher and haematologist at the Mayo Clinic in Rochester, Minnesota. “I expect to see a great deal happening over the next few years.”

We expected this back in 2012 and have been following closely. We now have a three prong attack on melanoma:

1. Pathway
2. Immunological
3. Viral

One suspects that we shall see all three being used in some form of cocktail. Nature continues:

Administering T-VEC in combination with cancer immunotherapy could prove particularly effective, notes Stephen Hodi, an oncologist at the Dana-Farber Cancer Institute in Boston, Massachusetts. In June 2014, a small clinical trial by Amgen suggested that this combination may boost effectiveness over that of the immunotherapies alone. And researchers continue to look for ways to improve T-VEC. In particular, they would like to be able to deliver the therapy systemically, so that the virus could target tumours in organs that are difficult to reach with an injection. This would require a technique to prevent the body from mounting an immune response to the virus prematurely, which would disable it before it could reach and kill tumour cells, says Howard Kaufman, a cancer researcher at Rutgers Cancer Institute of New Jersey.

The progress continues now that we understand some of the cause.

Remember the Hindenburg

When we go to Seaside Park, at least what little is left of it, we pass by Lakehurst the site of the Hindenburg explosion. I guess the Navy got the idea that big balloons can be a bit difficult to deal with. Now perhaps the Army did not get the message. On the loose is a power grid killing monster. We don't need a George Will to tell us of the threat, we have developed and now deployed out own such weapon, and it is slowly drifting across central Pennsylvania wiping out the grid.

Perhaps we need some hunters out there, perhaps that was the reason for the Second Amendment, to get those white whales down and stop the power outages!

As ArsTechnica reports:

One of the two tethered aerostats that make up the Joint Land Attack Cruise Missile Defense Elevated Netted Sensor System (JLENS), has broken loose from its moorings and is now drifting over Pennsylvania. Two Air National Guard F-16 fighters are monitoring its movements, but the trailing tether has already taken out power lines in Pennsylvania, causing blackouts in Bloomsberg as it got closer to the ground. JLENS' twin aerostats are (or were) supposed to provide airborne early warning and targeting of low-flying airborne threats coming in from the Atlantic, covering a radius of 300 miles with their look down search and targeting radar. They have been the subject of much controversy because of the cost of the program; a recent Los Angeles Times report called the $2.7 billion dollar project delivered by Raytheon a "zombie" program: "costly, ineffectual and seemingly impossible to kill."

Yes indeed, just in time for Halloween, a Zombie Project! Let's see who get reassigned, any guesses.

Oh and yes, I think there is another debate tonight. Any guess who will focus on this?

Oh yes and one more thing! CNN keeps bemoaning that it may explode. It is Helium stupid, a Noble Gas, inert, not Hydrogen! The worst that will happen is a few folks will talk like Donald Duck for a short while! What has happened to our educational system. And also, not radio like with the balloon, even amateur aircraft fliers have such a link to get control. Even the drones on Amazon! They put $200 M of electronics and no "phone home". Is this just a Halloween joke or for real?

Hurricanes and Staten Island

Three years ago, before Sandy hit, I remarked in this Blog that Staten Island was a prime location for its wrath. Why? It has been before and things have just gotten worse. In the early 1950s there were several massive Hurricanes and flooding went from the shore to Hylan Blvd. From Hylan in it was 2-3' underwater. Of course then there homes were at best summer shacks and the City had not improved anything.

Then in the late 50s and early 60s I was the NY City Lieutenant Lifeguard in charge of Ocean Breeze section. Every day, for almost 5 years, I watched as the Verazzano was built on one side and as people moved into the swamps that had been the buffer in the last Hurricanes on the other side. Sooner or later they too would be under water again.

Then in the 80s they moved Staten Island Hospital and a Mental Health clinic to the middle of the very same swamps. Worse yet, the road along the beach was raised so that if water even came across it, the water would then stay in this swamp land, now several yards below what was sea level. It became a natural pond, and when the next hurricane came it would become a veritable salt water swimming pool, unfortunately filled with homes. And the homes were filled with people who would not leave.

So along comes Sandy. We sadly know what happened; death and destruction.

Now the New Republic bemoans the situation. They state:

Of the nine buyout committees that sprung up on Staten Island after Sandy, three—Oakwood Beach, Ocean Breeze, and Graham Beach—would successfully organize a state-managed, federal buyout. In April of last year, Barbara Brancaccio, the press representative for the Governor's Office of Storm Recovery, said that the State had no intention of purchasing the entirety of Staten Island's eastern shore, limiting the eligible communities to those already selected. For those left out of the buyout the only sure thing is that their homes are worth less than they were before the storm made residents and policymakers aware of the true cost of living beside a rising sea. Here on the damp fringes of what was once the most powerful city in the world, Staten Islanders are retreating from the coast because they have recognized the limits of the built environment's ability to buffer them from a changing natural environment, and the limits of the government's ability to buffer them from unfair and inequitable development.

The problem is that no one should ever have been allowed to build there, especially the hospital.  I had seen the destruction to sea grass in the 50s, water knee deep on Hylan Blvd, and God knows how deep in the salt marshes.

So who is at fault? Most likely the City, whoever that may mean, who frankly should have known better. It had happened before, it happened in Sandy, and yes it will most likely occur again. The outer harbor is a dangerous body of water as tides come and go and as the winds can raise the water even higher. Midland Beach is a wonderful recreation area.

The ocean is a risky place to put anything at sea level. Sea level just is not reliable. People should question why building permits were even give for such locations, at least that is my opinion. This is not a first, it not the beginning of the end, it is an ongoing well-known process.