Saturday, October 31, 2015

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.

Friday, October 30, 2015

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.

Wednesday, October 28, 2015

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?

Sunday, October 25, 2015

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.

Undersea Cables

Some seventeen years ago I presented a paper to Members of the Russian Duma regarding a Russian Transit Cable system. I had said:

This Business Proposal articulates the strategy on how to implement the concept of taking transit traffic from the Atlantic to the Pacific across Russia. Apparently, others, like RosTeleCom, GTS and at least  one other team seeking to use National Rail and National Electric Utility fiber optic infrastructure are also working on a similar approach. A special opportunity to break ahead of them all has been distilled. The Consortium of companies represented herein, has the ability, facilities, contacts, and skills necessary to accomplish this task.

Then some three years ago we considered a trans Arctic system parallelling the systems to the south in the Indian Ocean and allowing for improved East-West transport. Unfortunately Ukraine and other steps intervened. The Arctic is a powerful opportunity to combine communications with environmental monitoring. It also provides for a back-up of the Indian and Pacific routes. Canada and the US could do likewise.

However as reported today in the NY Times the Russians, according t US sources, may be creating a threat to these systems. They report:

Russian submarines and spy ships are aggressively operating near the vital undersea cables that carry almost all global Internet communications, raising concerns among some American military and intelligence officials that the Russians might be planning to attack those lines in times of conflict.

Well frankly we do have a multiplicity of satellites as well as wireless systems, many real time deployable. Any such "cuts", which happen all the time, would at worst disrupt iPhones in Mumbai. Not an earth shattering event. Perhaps they could do the same in New York and it would make pedestrian traffic safer from collisions.

The key question is that of survivable strategic links. Collapse of Commerce might disrupt Russia a bit but it would be devastating to China. We have to my knowledge no items in Walmart from Russia but thousands from China. Thus in a strange way China may be more concerned that the US.

Then again setting cables across China may make for secure land based commercial assets. Just a thought.

Agincourt, Leyte and Charge of the Light Brigade

We few, we happy few, we band of brothers;
For he today that sheds his blood with me
Shall be my brother; be he ne’er so vile,
This day shall gentle his condition.
And gentlemen in England, now abed,
Shall think themselves accursed they were not here;
And hold their manhoods cheap whiles any speaks
That fought with us upon Saint Crispin’s day.

Today, October 25th marks the anniversary of these three battles. Agincourt, where Henry V defeated the French and its Nobles and thus changing France forever, in 1415, The Charge of the Light Brigade  led by Lord Cardigan against Russian forces during the Battle of Balaclava on 25 October 1854 in the Crimean War leading to a massive loss of life for no gain, and October 25th 1944 the Battle of Leyte Gulf in which my father and his shipmates defeated the last remnants of the Japanese Navy, leading to the final defeat of Japan.

Saturday, October 24, 2015

The Value of Research

Universities perform a great deal of research and much of it is funded by Government money. What value do we apply to these results? The WSJ has an interesting article which alleges it has little value. Generally I would agree. Much of University research is "training", namely training students to do research if ever they get the chance.

The author, Matt Ridley, first states:

linear model of how science drives innovation and prosperity goes right back to Francis Bacon, the early 17th-century philosopher and statesman who urged England to catch up with the Portuguese in their use of science to drive discovery and commercial gain. Supposedly Prince Henry the Navigator in the 15th century had invested heavily in mapmaking, nautical skills and navigation, which resulted in the exploration of Africa and great gains from trade. That is what Bacon wanted to copy. Yet recent scholarship has exposed this tale as a myth, or rather a piece of Prince Henry’s propaganda. Like most innovation, Portugal’s navigational advances came about by trial and error among sailors, not by speculation among astronomers and cartographers. If anything, the scientists were driven by the needs of the explorers rather than the other way around.

Most everything comes about by trial and error. Just look at Watson and Crick, at least as Watson states it.

They continue:

When you examine the history of innovation, you find, again and again, that scientific breakthroughs are the effect, not the cause, of technological change. It is no accident that astronomy blossomed in the wake of the age of exploration. The steam engine owed almost nothing to the science of thermodynamics, but the science of thermodynamics owed almost everything to the steam engine. The discovery of the structure of DNA depended heavily on X-ray crystallography of biological molecules, a technique developed in the wool industry to try to improve textiles. 

Indeed, being able to measure something leads to change. Suddenly having an X ray crystallography of DNA tells one that it is a helix, and a double not triple helix. Then go play with the stick model.

Finally they state:

In 2003, the Organization for Economic Cooperation and Development published a paper on the “sources of economic growth in OECD countries” between 1971 and 1998 and found, to its surprise, that whereas privately funded research and development stimulated economic growth, publicly funded research had no economic impact whatsoever. None. This earthshaking result has never been challenged or debunked. It is so inconvenient to the argument that science needs public funding that it is ignored. In 2007, the economist Leo Sveikauskas of the U.S. Bureau of Labor Statistics concluded that returns from many forms of publicly financed R&D are near zero and that “many elements of university and government research have very low returns, overwhelmingly contribute to economic growth only indirectly, if at all.”

My observations are somewhat upsetting but most likely correct:
1. That "organized r&d" is a total waste of time, I have been there. One needs a clear competitive product focus. I would argue that CRISPRs advances because of competition, not pure research.

2. Government funded research just sustains the Government funders not the results. All too often the funders have been assigned funds and they need boxes checked and paper written. No one ever rewards a Government employee for a breakthrough, also they never get fired for no results.

3. Publicly funded research such as NASA is almost all worthless to the economy, Tang and what else? I have been there. NASA results are at best good for NASA.

4. How do we judge or value research, by the economic advantage or by changing the way we think? I have been asked that question in prior lives. I never found anyone who had an answer. Take the Pharma world. Good research generates a profitable drug.

5. CRISPRs are now a hot topic, a tool for the genome tool kits which will have massive impact....lots of claims to parentage! Also lots of patent and start up actions. It is clear what the results could be.

6. Universities perform "research" which in reality is just "make busy work" to "train" students on how they should behave going forward, how many PhD theses really led to anything? They just allowed the faculty to see if the student would go through hoops

So for the Higgs particle, string theory, and the like, thay are training grounds to train future academics. Yet is there still a chance for some Patent Examiner in some obscure place to write three world shattering papers? Doubtful they would get published but there is now the Internet, so who cares about those Peer Reviewers anyhow!

The real question of good research is its ultimate value and that then begs the question of what do we mean by value. Consider the Human Genome Project. It was essentially a competitive venture between a Government and private entity. That worked and the result will have significant merit. I believe it speaks for itself. Then we have for example neuro research on how the brain works. That is really hard, and really hard stuff goes no where for decades and then as is often the case something pops. But it is impossible to predict just what that is.

Now consider Cancer research, namely looking for ways to stop its progression if not cure it. Pharmas do some here but they often build on what comes from others work, namely the risk takers who left Academia and started something. They may have been supported pre start up by Government post-doc work but they MUST leave that haven of sorts and start a real company. High risk and potential high return.

 The problem is that Government funding is all too often rant with political calculations. The funder wants to look good so they get someone who is already good. A cycle, But every so often we get sparks, again the genome or CRISPRs. These are real innovations, they are not Silicon Valley Apps, software that does nothing productive.

Thus somewhere between Government funding and Silicon Valley trend following is the world of real research, a game changing way to do something.

Beware of Correlations! They are NOT Causation!

In a recent Nature article the authors contend that "Global Warming" will result in drastic drops in certain national GDPs.

They state:

If societies continue to function as they have in the recent past, climate change is expected to reshape the global economy by substantially reducing global economic output and possibly amplifying existing global economic inequalities, relative to a world without climate change. Adaptations such as unprecedented innovation or defensive investments25 might reduce these effects, but social conflict or disrupted trade—either from political restrictions or correlated losses around the world—could exacerbate them.

As best as I can tell their analysis is predicate on the following chart:

Namely they plotted GDP versus average temperature for countries. They then contend that if say the US were to rise in temperature then we will look like Nigeria. Huh?

The also state:

Growing evidence demonstrates that climatic conditions can have a profound impact on the functioning of modern human societies, but effects on economic activity appear inconsistent. Fundamental productive elements of modern economies, such as workers and crops, exhibit highly non-linear responses to local temperature even in wealthy countries,. In contrast, aggregate macroeconomic productivity of entire wealthy countries is reported not to respond to temperature, while poor countries respond only linearly. Resolving this conflict between micro and macro observations is critical to understanding the role of wealth in coupled human–natural systems, and to anticipating the global impact of climate change, . Here we unify these seemingly contradictory results by accounting for non-linearity at the macro scale. We show that overall economic productivity is non-linear in temperature for all countries, with productivity peaking at an annual average temperature of 13 °C and declining strongly at higher temperatures.

But wait. They do not as far as I can tell demonstrate direct causation. Alabama is hotter than Maine but we have lots of factories in Alabama and few in Maine. Texas is hotter than North Dakota but there is a much higher GDP there than in North Dakota. There does not appear to be any causal relationship established.

This is pure abject conjecture in my opinion. I guess we shall see this paper referenced in the weeks and months to come. In my opinion it is at the very best abject conjecture and at the very worst poorly crafted propaganda.

Libraries and the Source of Knowledge

There still seems to be a lingering group who think the “Library” is still the old brick and mortar facility, controlled by a group of stodgy old lady librarians, and who keep tabs on all the “books” in “their” collection. The NY Times notes today[1]:

But today, the principal danger facing libraries comes not from threats like these but from ill-considered changes that may cause libraries to lose their defining triple role: as preservers of the memory of our society, as providers of the accounts of our experience and the tools to navigate them — and as symbols of our identity. Since the time of Alexandria, libraries have held a symbolic function. For the Ptolemaic kings, the library was an emblem of their power; eventually it became the encompassing symbol of an entire society, a numinous place where readers could learn the art of attention which, Hannah Arendt argued, is a definition of culture. But since the mid-20th century, libraries no longer seem to carry this symbolic meaning and, as mere storage rooms of a technology deemed defunct, are not considered worthy of proper preservation and funding.

With all due respect one should note that Libraries have managed to get an ever increasing piece of our tax dollars through mandated funding and no accountability. Take New Jersey as an example. The Stata mandates a percent of the gross Real Estate taxes go immediately to the Library. They state[2]:

The minimum funding statute for joint and municipal libraries (N.J.S.A. 40:54-8) sets the minimum funding rate at 33 cents on each $1,000 of equalized value of all assessable property in the town. This minimum funding amount is the total of what your local municipality must, at minimum, allocate in its budget, according to the law.

Thus consider a simple example:

Assume the home is assessed for $900,000. In our town that is the average assessment, they are done at market level.

Now for each such home the $0.33X900 or $300 of their property tax goes to the Library.

Now assume there are 5,000 HH in the town then the total to the Library is $1.5M. That is just the mandated “contribution”. Now add businesses etc and we get a hefty amount mandated and growing every year! This is for a library of some half dozen people loaded with old novels that are generally un-read.

The “Library” today is on the Internet, it is accessing primary sources, original documents, books themselves. It is “free” and knowledge is shared. Knowledge is consumed. One can tell a book has been “consumed” by it appearance. It looks devoured. Libraries do not have such books; one would be fined for such behavior.

The old brick and mortar library is an archaic establishment of the past. Free WiFi? You can get that anywhere; try the train station or any coffee shop. Need information on CRISPRs, try Google and definitely not some stodgy old librarian.

So what purposes do these old buggy whip Libraries serve? Meeting rooms, hang outs? It is not at all clear. I have been in our town for over 35 years and have never taken a book from the library. I use Amazon, ABE Books, or the used book shop in town! And yes, I use the Internet! Frankly the last place I would ever go would be the Library….It is Government controlled information….and they get paid by our taxes with no oversight.

Thus perhaps the writer from the Times should reconsider the facts of the 21st Century. As Alexandria was burned down by the advancing hordes from the sands of Arabia perhaps we should exult that it will be much more difficult for the hordes to burn down the Internet.

Friday, October 23, 2015

PostDocs and Productivity

I am continually surprised as to the size of the post doc world especially in engineering. In a recent Nature article they report a drop in the total post docs. They state:

From 1979 to 2010 the number of US postdocs in the biomedical sciences has risen steadily, from just over 10,000 to more than 40,000. But in the past three years, the tide has turned, according to official statistics. The population of US biomedical postdocs fell 5.5% between 2010 and 2013, to just under 38,000, with losses getting bigger each year, notes a study published on 6 October — although the number of new graduates with science PhDs continues to rise

The above is from Nature as referenced. What is interesting is the ratio of new PhDs to Post Docs, it appears to be dramatically different in Bio from Sci and Engr. That is a measure of the length of time as a post doc.

The true measure is that post docs are all too often used to replace technicians. The techs are employees and get paid more and have benefits. The post doc is at best a journeyman level position with no security.

Also there is a problem of lumping Science and Engineering. I would suspect that most PhDs in Engineering get jobs, for that is where one learns one's craft especially in engineering. Most Engineering Post docs seem to be foreign students being used as super techs. Then they return to wherever.

Thursday, October 22, 2015

Russians and Russian

The Guardian has a wonderful piece on Russian and the Russians. Perhaps Kennan and his kind would have appreciated the nuance but it is clear the US today is clueless. I recall my days in Russia, and when I heard "Nyet problemi" I knew we had a real problem. Russians unlike the Poles, who tell you what they think you want to hear, often speak in opposites. Namely they have a tendency to say just the opposite of what it is. Now if you are a Russian you can readily interpret it and respond accordingly.

The closest to this barrier of language is an Irishman telling a joke to a German. First German's have as best as I have experienced no sense of humor. The Irish, from firsthand personal existential experience, have a bit of a perverse sense. Thus a German doctor telling his patient that the biopsy was benign may hear an Irish patient remark, "And I was so much looking forward to a prostatectomy!". Humor dissonance at its best!

The Guardian recounts:

For example, in 1995 after a summit with President Bill Clinton, Boris Yeltsin poked gentle fun at reporters who had poured cold water on hopes for a successful meeting. He said: “You predicted our meeting today would fail”, which the interpreter translated (not knowing how Yeltsin was going to continue) as “You were writing that today’s meeting was going to be a disaster.” Yeltsin then went on: “I would say that it was you who failed.” The interpreter foolishly decided to stick with the ill-chosen word “disaster” and translated Yeltsin’s gentle rebuke as: “Well, now I can tell you that you’re a disaster,” – much stronger and more comical than Yeltsin had intended. Clinton was convulsed with laughter for a full minute, wiping tears from his eyes and hugging Yeltsin in appreciation of this witty joke – which in fact Yeltsin had not made. Yeltsin himself looked completely baffled, wondering why his wry comment had provoked such a wild reaction.

Now if one is speaking in Russian, albeit with my limited skills, one would even hear something else. I am reminded of my "I don't give a rat's ass!" comment and how my Russian friends tried to transliterate that one. It ended up with a few hours at the bar over vodka reminiscing over various similar senseless remarks in both languages.

But words mean something, but as Alice remarked, all too often they mean what we meant them to not what they are thought to have meant.

It would help that politicians who have really not spent time in other countries try to get better translators and not try to do it on the fly. This even applies to American English and that language spoken in Britain! Or parts of New Jersey.

MIT and Climate Change

MIT announced its "Plan" to deal with Climate Change. To that end they announced:

...MIT has developed a five-year plan to enhance its efforts in five areas of climate action, whose elements have consensus support within the MIT community:
  • research to further understand climate change and advance solutions to mitigate and adapt to it;
  • the acceleration of low-carbon energy technology via eight new research centers;
  • the development of enhanced educational programs on climate change;
  • new tools to share climate information globally; and
  • measures to reduce carbon use on the MIT campus.
The process is laudable but as one commentator noted:

You missed Step One...convince the skeptics of the validity of your conclusions. The non-believers are not bad people, they just do not understand the basis for your conclusions. To some the names of scientists and MIT itself are not convincing enough to get them to commit. They see MIT getting years of funding as self serving and therefore mistrust the conclusions.

Indeed the steps seems a bit self serving. MIT is already and has been at it for years examining alternative, ie non carbon based, energy, understanding the mechanisms behind various pollutants and carbon off shoots, as well as large scale networks and the like. Thus one wonders what is new here other than more overhead and possibly less research.

The comment indicating that the non-believers are not "bad people"  is quite valid and unlike those who attack anyone who thinks differently tends to use logic and facts and not vitriolic methods to communicate.

Unlike some who look at their political opposition as the "enemy" one must look at them as groups with whom they would engage in discussion.


The NIH has announced several new additions to the CRISPR world of slicing proteins. As they state:

An international team of CRISPR-Cas researchers has identified three new naturally-occurring systems that show potential for genome editing. The discovery and characterization of these systems is expected to further expand the genome editing toolbox, opening new avenues for biomedical research.  The research, published today in the journal Molecular Cell, was supported in part by the National Institutes of Health. “This work shows a path to discovery of novel CRISPR-Cas systems with diverse properties, which are demonstrated here in direct experiments,” said Eugene Koonin, Ph.D., senior investigator at the National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), part of the NIH. “The most remarkable aspect of the story is how evolution has achieved a broad repertoire of biological activities, a feat we can take advantage of for new genome manipulation tools.” Enzymes from the CRISPR system are revolutionizing the field of genomics, allowing researchers to target specific regions of the genome and edit DNA at precise locations.  

“CRISPR” stands for Clustered Regularly Interspaced Short Palindromic Repeats, which are key components of a system used by bacteria to defend against invading viruses. Cas9 — one of the enzymes produced by the CRISPR system — binds to the DNA in a highly sequence-specific manner and cuts it, allowing precise manipulation of a region of DNA. Enzymes such as Cas9 provide researchers with a gene editing tool that is faster, less expensive and more precise than previously developed methods. The three newly-characterized systems share some features with Cas9 and Cpf1, a recently characterized CRISPR enzyme, but have unique properties that could potentially be exploited for novel genome editing applications. This study highlights the diversity of CRISPR systems, which can be leveraged to develop more efficient, effective, and precise ways to edit DNA.

The "toolbox" for gene editing is expanding a an ever increasing rate. The original Cas9 enzyme which was the baseline for CRISPR work cut the gene at specific but opposite sites. That was good but the newer versions allow for "sticky" ends which dramatically reduce the chance of recombination errors.

We believe that this is but the beginning of an ever expanding set of such tools and well worth following.

Tuesday, October 20, 2015

Human Intelligence

In the spy game there are various means and methods to gather information. The US has been for several decades building a massive set of technical means, including the NSA and its collection of every bit of useless information. The other side of the spy game is human intel, namely stuff gathered by sitting in a bar or coffee shop, pretending to being someone else, or just looking around to see what is happening. The US under previous Spy Masters and Presidents has eschewed this human form, too messy, and requires certain types of people.

Now along comes the CIA DCI hack. In Wired is the tale, and you really can't make this up It is from the script of Three Days of the Condor. A group of sharp "kids" managed to elicit "secure" information from Verizon, surprise surprise, and then with that hacked the DCI's email account on AOL. Verizon should never have bought that but that is a tale for another day.

They state:

The hacker, who says he’s under 20 years old, told WIRED that he wasn’t working alone but that he and two other people worked on the breach. He says they first did a reverse lookup of Brennan’s mobile phone number to discover that he was a Verizon customer. Then one of them posed as a Verizon technician and called the company asking for details about Brennan’s account.“[W]e told them we work for Verizon and we have a customer on scheduled callback,” he told WIRED. The caller told Verizon that he was unable to access Verizon’s customer database on his own because “our tools were down.” After providing the Verizon employee with a fabricated employee Vcode—a unique code the he says Verizon assigns employees—they got the information they were seeking. This included Brennan’s account number, his four-digit PIN, the backup mobile number on the account, Brennan’s AOL email address and the last four digits on his bank card.

For those who do not remember, that is Human Intel, they did not need to have satellites or massive data centers.I wonder if this will change anything? Doubtful.....after all they are Government employees, perhaps Verizon should shake the tree a bit.

Broadband on Copper?

There is a lot of copper wire around which has provided the old telephone service we know and understand. I still have a classic old copper based phone, use it in the office all the time, good quality voice and secure, unless there is some Government tap. But that is another story.

Now people have been eschewing copper as being too slow but Shannon's Theorem really does not say that and I recall meetings at the old Bellcore some 30 years ago where they discussed Mbps speeds. Now BT in the UK has Gbps speeds.

Total Telecom reports:

BT on Tuesday came out fighting in favour of copper, revealing it has reached connection speeds topping 5 Gbps using technology. The tests were carried out in partnership with Alcatel-Lucent at the U.K. incumbent's Adastral Park R&D centre in Suffolk. It achieved aggregate speeds of 5.6 Gbps over 35 metres of BT cable, a new record for full-duplex data transmission over a standard single line, according to the telco. At more than 100 metres, the speed dropped substantially, albeit to a still impressive 1.8 Gbps. BT said this is significant because most U.K. homes are within 100 metres of their nearest distribution point.

 Theoretically one can use this existing infrastructure with a wireless backbone to get those Gbps speeds to homes out in the "no where" lands. You do not need the millions that New York is proposing, you can do it now with what is there. Just get the consumer to buy the modem!

Monday, October 19, 2015

How Long Will Microsoft Survive

One thing I learned in business was "If all else fails, listen to the customer." That apparently never occurs to Microsoft. Take a recent complaint about updates on W10.

As PCWorld notes:

If there's one Microsoft policy that has drawn the ire of IT managers over the course of its Windows 10 rollout, it's the company's decision to require that all users install cumulative updates without control over which packages a system receives. It's such a point of contention that a group of thousands of grumpy customers have petitioned company CEO Satya Nadella to change Windows 10 update practices. Customers want more control over what's added to their systems, but they're also concerned about what happens when they can't avoid installing an update that breaks key functionality. Cumulative updates include all the updates Microsoft has released for the branch of Windows 10 a customer is using. 

This is just another one of hundreds of "it's our way or the highway" attitude of Microsoft. I think I have finally disabled the never ending attempts to download and install W10 on perfectly fine systems. But on W10 apparently no chance!

Eliminating Cancer

Economists are often thought of as the broad thinkers who can provide out world with the best ideas on how to solve problems and improve our lives. Take Global Warming and carbon emissions. Their solution is a "free market" approach of taxing carbon. As noted in a recent Nature piece on an upcoming meeting:

A global carbon price — so far excluded from consideration in international negotiations — would be the ideal basis for a common commitment in our view. A price is easy to agree and handle, relatively fair, less vulnerable to gaming than global cap-and-trade systems, and consistent with climate policies already in place, such as fossil-fuel taxes and emissions cap-and-trade.

Now since this is considered the approach, not research and development, not engineering, but taxing, I thought we could do the same for Cancer. We know that cancer kills people, rather harshly at that, so why not have a Cancer Tax, stop all that R&D, close down the hospitals, eliminate the drugs; just tax it. It is a Jonathan Swift like solution. Swift suggested cooking Irish babies to eliminate the problem, a bit harsh but many English took his suggestion to heart, so we would just tax Cancer, not the victims, just the disease.

Then according to economists it should "clear the market", and with the tax money we could allow the Government to spend more, say on increasing Government salaries. With no hospitals, no doctors, no drugs, we drop health care burden to near zero, with people dying off real quickly, we reduce the demand for Social Security and Medicare, and with the added taxes, well we get a balanced budget!

Just think how smart these economists are! We don't need R&D, that just allows people to survive longer, with a cure, we need more people turnover. Thus the Cancer Tax, also a Carbon Tax, and yes we can most likely tax anything the Government folks think is bad for us.

I think there is the view that if all one has is a hammer then everything one sees looks like a nail. It may very well apply here.

Sunday, October 18, 2015


Most of us have never seen bats. Bats are those rodents with wings that fly around at night allegedly eating insects. We are told the insects are bad for us and ipso facto the bats are good for us. Now bats carry rabies and one in ten bats in New Jersey are rabid. Rabies is a horrible disease, a viral infection, single stranded RNA virus, that slowly eats up the nervous system turning the victim into a drooling and neurologically deficient slime mold.

Now one must remember that the Government has declared the "little brown bat" a protected species. It may kill humans but we must not touch this carrier of deadly disease. It is akin to the Administration declaring ISIS a protected class and anything we do to them a "hate crime". Only Government can make such a logical nexus.

As the NJ Health Department states:

The 5 year average of bat rabies cases from 2010 - 2014 was 57 per year. In 2014, 78 bats (out of 1,385 submitted for testing) were diagnosed with rabies, representing the highest number of rabid bats documented in a calendar year. However, the percentage of confirmed rabid bats has stayed relatively constant at about 4 - 6% of the bats submitted for testing.

In 2013 there were 66 rabies cases from bats in New Jersey. Much more than ISIS attacks. Now NH PR, that left wing radio station in NH, in fact almost the only radio in Northern NH, which is why it is so conservative, states:

Obviously, bats are really important in our eco-system because they are the greatest predator of nighttime insects. As von Oettengen explained, NH hosts eight species of bats (among them: Little brown bat, Long-eared bat, Tri-colored bat, Small-footed bat, Big-brown bat), so that adds up to a lot of insects consumed.

Now what is so wrong with these insects? I like bees, I like wasps, I even like Lady Bugs. So these vultures go out at night and consume all the insects pollinating my plants! These folks must be plant haters. No nocturnal plants get pollinated!

The NHPR continues:

There are small things we can do to help. If you’re comfortable living with bats in your attic, eaves or barn, leave them be. Or you could put up a bat house. Preston put one up in her yard in a hot, sunny place and had nineteen bats living there by the end of the summer.

Yeah, try and sell a house with bat fecal matter all in the attic infested with rabies!  Are you out of your mind! Well now let me tell you what I really think of bats......

Friday, October 16, 2015

Microsoft and Windows 10

Microsoft has tried over 40 times to download W10 to one of my computers, about the same for the other 8. That means 320 possible attempts. I think I finally shut it out by finding solutions of Google. But hour after hour of wasted time and my bandwidth. I have one new laptop with W10, it is OK, but I guess I will soon be seeing pop up ads from Microsoft. I would never buy anything from them nor would I consider buying from anyone who uses them to advertise. But alas the company in my opinion is going to the dogs.

I want an OS, so sell me one, don't make my life horrible with its attempts to monetize a relationship that does not exist. I really dislike Microsoft, but I also dislike colonoscopies and understand that they may be beneficial, in a limited amount.

I wonder if some smart lawyer will find a way to file a massive class action suit. The time wasted avoiding W10 and the time and productivity lost if perchance you download it and your drivers all die off. I assume the Microsoft lawyers have thought of this, perhaps not. This could make for a very wealth law firm. Perhaps...not being a lawyer...I seen many in action...but this smells like it could have legs. Watch for the shorts on Microsoft...time will tell.

Medicare and Who Pays?

Over the past few years I have analyzed the falacy that Medicare is a "gift" to those getting it. In the NY Times today there is a piece on the increased costs of Medicare. They state:

Even some affluent beneficiaries could struggle with the higher costs. For those with incomes of more than $214,000 a year, Medicare actuaries say, premiums next year could exceed $500 a month, up from about $335, if Congress does not change the law. Financially struggling state governments are expressing concern because they are responsible for many low-income beneficiaries.

 Now this means that a family making $214,000 in New York or New Jersey is paying the highest income tax for Federal and State and in addition is paying 3% (actually 2.9%) on the $214,000, or about $6,000 per person, plus a MediGap plan of about $4,000 per person, so we have $20,000 per family on a $214,000 salary or almost 10% of the salary going for Medicare in addition to 50 years of contributions!

Whereas some 30 year old with no job and a family gets to ride for $50 per month!

What is wrong with this picture? Oh and yes, there is a deductible as well, and drugs are barely covered. And also these costs are NOT tax deductible! So this is what the ACA has brought, taxing the older folks to pay for the younger ones without jobs. Generational warfare?

Thursday, October 15, 2015

Excellent TPP Summary

The TPP trade agreement may have far reaching implications. The CFR has an excellent summary that is well worth reading. Of course the muddle is in the details which we have little access to. But reading the CFR overview shows how broad this is.

Wednesday, October 14, 2015

"Seek, and ye shall find": Matthew 7:7

One of the interesting effects of modern medicine is that we can find things that we never thought were there. A hundred years ago one went to the physician when one had a complaint. The physician then examined the patient and considered the complaints and then made a diagnosis, if possible. The a treatment is available was prescribed.

Today we do lots of tests and find things we would never have susp[ected were there, many just the vagaies of the human. The more we look the more things we are likely to find. Kidney stones, gall stones, osteoarthritis, etc.

Now along comes a new set of tests for those who can chell out $50,000 each time, the full body MRI and full genome scan. As Xconomy reports: 

Top executives and others who come to Health Nucleus for their annual physical will receive a battery of medical tests, including many that are not FDA-approved because they are so new (and unproven), said Brar, who is the current president of the American Academy of Private Physicians. Health Nucleus was able to sidestep FDA restrictions on the clinical use of experimental tests by operating—at least initially—as a clinical research project under Institutional Research Board (IRB) protocols,

A comprehensive workup at Health Nucleus would include:

—Whole genome sequencing of all 6 billion DNA base pairs (According to Health Nucleus, most DNA tests today examine less than 2 percent of the entire human genome.)
—Genome sequencing of the microbiome—the microorganisms that live in the human gut and on the skin.
—Metabolome sequencing of the small-molecule metabolites found in the human body.
—Whole-body medical imaging with advanced MRI (medical resonance imaging) from GE that enables Health Nucleus to quantify the exact volumes of unhealthy visceral fat, the various components of the brain and other tissues that may reveal the progress of disease. 

And of course the price:

Executives and others who arrive for a Health Nucleus checkup would pay $25,000 or $50,000 each, depending on the number of people in the group  

That is just for all this data. The problem with this approach is in my opinion several fold:

1. Clearly those with the $50K get the tests, the rest of humanity do not.

2. Tests will always find something, the incidentaloma. Then what?

3. Research does not research just those people who can pay to be Lab rats, it should covera a broader base of the population.

4. When do we treat something? That is always the question. Take Prostate Cancer. If your family history is such that aggressive types was present at a close proximity, say First degree, then a good bayesian would treat. If however no one ever died in your family of the disease then perhaps one could wait.

5. The data is overwhelming, and one should have a plan and process to deal with it. Not clear here.

6. Cancer is real sneaky. Yes germ line genetic problems may be a warning, say BRCA. Yet having your genome may not be the answer for somatic cells which have become methylated. Or we have mRNAs popping up where they should not.

One suspects this type of thing will appeal to many who can afford the tests, but larger samples would be useful.

Friday, October 9, 2015

Saint Vladimir

When I returned to Russia the first time after the collapse, I believe it was 1993, it was to Saint Petersburg, not Leningrad. What I noticed even then was that the Churches were filled, weddings, funerals, old women, young people. In less than 3 years religion returned.

Then for my ten years in an out of Moscow I saw the churches rebuilt to a state that exceeded even the best under the Czars. The Metropolitan of Moscow, the alleged, and historically the actual, successor to the Bishops of the Church, regained their positions and aligned themselves with the Government, Putin especially.

In the Montefiore piece in today's NY Times I believe he gets some but not all of the depth. Hie piece should be read, especially by those in Washington. They seem clueless. I suspect they have no idea of the 30 Years War, but I put that aside.

You see the Metropolitan in Moscow is the successor to the Bishop of Constantinople, a clear un-broken line back to Peter. The Bishop of Rome was abandoned during the Avignon Papacy, when the French Kings controlled what was the "Papacy", the Bishop of Rome, who moved to Avignon. That broke the unbroken line. Moscow sees itself unbroken, Rome was demolished for over 100 years. No wonder Moscow is not interested in a conversation.

But the Metropolitan speaks for the people and he speaks for Putin. The Orthodox Church has replaced Communism in a way Lenin and Stalin would never have believed. The Montefiore piece is only part of the tale. Cyril and Methodius sent Christianity to the Slavs and ironically it had become part of the Russian soul. They have a strong and well founded belief in their destiny, and Putin is not acting foolishly, he is acting to accomplish that destiny.

Remember the window in Prague when the Papal delegate was thrown out onto the dung heap. Thirty years of religious war. Who will be landing on the dung heap this time. Doubt it will be Saint Vladimir.

Wednesday, October 7, 2015

Kendall Square

I have seen Kendall Square for well over 55 years and have seen it from the days of a well worn 19th Century factory location to what it is today, a hub for biotech.
In a recent article at A Slice of MIT they discuss the evolution of the area. They state:

As part of the new initiative, the MIT Museum will move to a new building next to the T station, opening out onto a park with Ping-Pong tables, fire pits in winter, public art, and other amenities…all ventures will set aside 5 percent of their square footage for ‘innovation space.’” ...“‘You could imagine years from now going and tracing something back to Kendall Square that really changed the world,’ says MIT Treasurer Israel Ruiz “If through our efforts we will have made it possible to solve something that we otherwise wouldn’t have been able to solve, that will be the best prize.”

The problem that the seem to have missed, and missed in a really big way is that of traffic flow. It appears that Google has absconded with all the parking places in the Marriott garage, and the parking rates if one exist have gone from $11.50 a day to over $50! Beats mid-town New York. Public transportation on the T is useless if you are trying to get to one of the buildings inside the area, halfway between the Green and Red Lines. Traffic flow still has to deal with the narrow streets great for 18th century horse traffic.

It would have been nice if MIT and the City of Cambridge would have done some Urban Planning. Just putting in more buildings does not work. It comes to a stand still.

Thursday, October 1, 2015

Trees and Diversity

In a recent Nature article the authors estimate the number of trees on the globe. Their conclusion is:

The global extent and distribution of forest trees is central to our understanding of the terrestrial biosphere. We provide the first spatially continuous map of forest tree density at a global scale. This map reveals that the global number of trees is approximately 3.04 trillion, an order of magnitude higher than the previous estimate. Of these trees, approximately 1.39 trillion exist in tropical and subtropical forests, with 0.74 trillion in boreal regions and 0.61 trillion in temperate regions. Biome-level trends in tree density demonstrate the importance of climate and topography in controlling local tree densities at finer scales, as well as the overwhelming effect of humans across most of the world. Based on our projected tree densities, we estimate that over 15 billion trees are cut down each year, and the global number of trees has fallen by approximately 46% since the start of human civilization.

 Now I decided to map my small patch of land in New Jersey, about 13,000 sq feet. Some 2,000 sq feet is my Hemerocallis "Lab" where we do genetic research. There is a house, a driveway and some 124 trees. Yes, some 124 trees, of some 32 different species. I have the densest collection of Ginkgos and Metasequopia in North America. Did not know that until I did the count. Both from China and both extinct in nature. And both bearing seed and quite healthy.

The above is the details. Now if we compare this to the Nature article we see:
Note that from the above Nature date our density of 928 trees/Hectare is well near the highest level on the chart.

So what does this say? Well we humans are lovers of plants, in my case specimen trees and Hemerocallis. We have managed to repopulate near extinct species.

There may be hope after all.