Wednesday, May 31, 2017

What is a Species?

That question has been around for a while. Mayr had proposed a definition that essentially said a species was a collection of animals or plants which had the capacity of breeding among each other. As Kevin de Queiroz has stated:

Ernst Mayr played a central role in the establishment of the general concept of species as metapopulation lineages, and he is the author of one of the most popular of the numerous alternative definitions of the species category. Reconciliation of incompatible species definitions and the development of a unified species concept require rejecting the interpretation of various contingent properties of metapopulation lineages, including intrinsic reproductive isolation in Mayr's definition, as necessary properties of species. On the other hand, the general concept of species as metapopulation lineages advocated by Mayr forms the foundation of this reconciliation, which follows from a corollary of that concept also advocated by Mayr: the proposition that the species is a fundamental category of biological organization. Although the general metapopulation lineage species concept and Mayr's popular species definition are commonly confused under the name “the biological species concept,” they are more or less clearly distinguished in Mayr's early writings on the subject. Virtually all modern concepts and definitions of the species category, not only those that require intrinsic reproductive isolation, are to be considered biological according to the criterion proposed by Mayr.

In the current Nature there is an ongoing debate as to the many conflicting definitions. The authors state:

The assumption that species are fixed entities underpins every international agreement on biodiversity conservation, all national environmental legislation and the efforts of many individuals and organizations to safeguard plants and animals. Yet for a discipline aiming to impose order on the natural world, taxonomy (the classification of complex organisms) is remarkably anarchic. There is reasonable agreement among taxonomists that a species should represent a distinct evolutionary lineage. But there is none about how a lineage should be defined. 'Species' are often created or dismissed arbitrarily, according to the individual taxonomist's adherence to one of at least 30 definitions. Crucially, there is no global oversight of taxonomic decisions — researchers can 'split or lump' species with no consideration of the consequences.

 The problem is that especially in plants we have a significant amount of inbreeding potential between what we call species. The plants have the same number of chromosomes of the same length with genes in the same positions, almost. Then why call them different species? All too frequently it is in the eye of the beholder.


One of the interesting things about Medical School is that every part of the body is open for examination and treatment, except the teeth. "No teeth!" Teeth are the exclusive purview of that clan of practitioners called Dentists. They have their own "school" and they stick together like taffy on teeth.

Now along come a piece by Alan Alda and his experience with this clan. I can sympathize with him greatly. Alda states:

I’ve come to see my exchange with the dentist that day as something that happens frequently in life — a brief encounter that threatens a relationship’s delicate tissue; the tender frenum of friendship. I wasn’t looking for friendship that day, but at least I wanted the feeling that I was actually being seen by him. Even though his gaze was intense, I realized that as far as he was concerned I wasn’t really there — not as a person. If I was there at all, I was something on his checklist. He was speaking into the vague mist of interpersonal nothingness. That few minutes in his chair has become a symbol for me of really, really poor communication and of what causes it: not really seeing the other person. Since that day, I’ve spent a lot of time on two socially useful pursuits: figuring out how to be a little more engaged — and uncrooking my smile.

In my experience, one which has occupied the last year or so,  began on a much more friendly manner. A nice dentist suddenly sends a letter telling us he is no longer practicing. OK, so find another dentist. Then get told you need 14 crowns, 4 of which are implants!. For those counting that amounts to three semesters at Harvard, room, board and tuition. Fortunately grandson number one is off to WVU to study Civil Engineering so that was not as expensive. But upon asking the dentist, now one of several, I have a dental "team", what happened, I was told that it was the way they did dentistry 30-40 years ago. I then asked what if the same is true with what he does today? The answer was; "You won't live that long." So Alan had a smile problem, mine was, as I suspect would be his at this time, that any mistakes would go with me to the everlasting!

So what of dentists. We only spend a few tens of billion each year. Why s low you may ask for a total health care bill of $3 trillion! Insurance. Most people have none and those that do can only get reimbursed for a tiny amount each year. 

Teeth are important. A bad abscess can kill a person, a poorly inserted implant can lead to osteonecrosis and off goes the immune system. But dentists occupy a special place in our society. They treat us with at best lidocaine/procaine and in turn we sit there for hours with our mouth ajar while they are conversing as to what happened over the weekend and we can feel the drill, the extraction, or whatever, and I suspect the psychic damage can be significant.

Perhaps it is a result of my first dental visit. I believe it was 1949, a former Navy dentists who my father swore by, after all he was Navy all the way, and I sat there looking out his office onto Forest Avenue. Then he started the drill. I think a foot driven thing from some German camp. I instinctively let out a cry, then he slapped me across my cheek, and told me to sit still while he performed his torture. Somewhere there is an embedded limbic valence to this event! I think it is one of those things that get handed down genetically, some epigenetic modification, some methylation of a promoter somewhere in our DNA.

Thus if Alan has a smile problem, I have methylated DNA that turns on some abject terror reflex. I would rather have a 40 core prostate biopsy than a visit to the dentist. Yet as the good nuns told us, this is just another offering to make up for our sins. I wonder what dentists do to perform their penance? I dread to think! Thanks for the warning Alan, hope the smile thing works out!

Sunday, May 28, 2017

Ya Think?

After a week of meeting with many world "leaders" the Telegraph reports:

Europe "must take its fate into its own hands" faced with a western alliance divided by Brexit and Donald Trump's presidency, German Chancellor Angela Merkel said on Sunday. "The times in which we could completely depend on others are on the way out. I've experienced that in the last few days," Merkel told a crowd at an election rally in Munich, southern Germany. "We Europeans truly have to take our fate into our own hands," she added. While Germany and Europe would strive to remain on good terms with America and Britain, "we have to fight for our own destiny", Merkel went on.

Frankly after seventy two years is it not time to grow up. Poland learned and look where it is going, well past Germany if all keeps on pace. Yes indeed Germany should finally take full responsibility for itself. Relying on the US is not only morally wrong it is just plain dumb. If someone is paying for your defense and then you complain because you are now being asked to ante up what you said you would do is wrong, what logic is that based upon.

Germany and to some degree France have managed to build their economies. They did so with no burden of defense. But the question is; is the threat Russia or what we see as an entity already destroying its peoples.

As for the "destiny" of Germany, we have seen that several times, just ask the French.

Friday, May 26, 2017

Global Warming?

Over the past 25 years we have been monitoring the bloom dates of four Hemerocallis species. Namely H. flava, minor, dumortieri, middendorfii. We measure the date of bloom from the start date of the year. Thus a data of bloom of 125 is 125 days from January 1 of the year. Now the smaller the bloom date the earlier the bloom.

So what does it have to do with Global Warming. Well over a 25 year period the blooming data is a function of the integral of total input heat. Daylight hours, location, soil conditions etc have all been held constant. The more heat the earlier the bloom.

Now here are the four flowers:

We see in the data a minimal if any trend downwards, namely more heating. In fact if the CO2 lever were greater we would expect even faster blooming.

Thus this set of canaries in the mine have not been tweeting too much if at all. Just some facts from the front.

Thursday, May 25, 2017

Another Day on Public Transportation!

I try, I really do! Take the train, don't use gas, keep the old CO2 down and all that stuff. Well today was another experience. Train to Hoboken, train to WTC. Now try and get home!

The run trains every three hours. This train made an old Aeroflot Tupolev look like a Rolls Royce!. Roof leaks, really water spraying into the car, windows sealed with duct tape, seats unstable etc. And here is the tale for those of you so anxious to get to New York!

1. From Hoboken to the towns on Mid Town Direct stations, the largest and most wealthiest in NJ, they run once ever 3 hours and are 6 cars long.

2. From Penn Station the same trains run once ever hour and are 12 cars long.

3. Amtrak, that grossly incompetent Government agency, remember the ACA and the VA folks, is closing Penn Station to the MD trains from July to September!

4. That means that somehow these 3 trains totaling 36 cars must get stuffed into one train of 6 cars! That means a 6:1 increase! What will this be, Bombay at holiday season? People grappling to the roof of decrepit cars!

5. Govs Cuomo and Chubby are clueless, really. It is one month away and there is NO Plan! Yep, not a single idea as to what to do! There should be some extensive communications to the citizens as to what will happen. Instead Amtrak and its morons are just closing Penn Station! Yep, just closing it. And frankly who says it will ever reopen! These are Government types, we should know them by now!

6. And where is the Fed Govt, the Senate's head's wife who allegedly is in charge of Transportation is probably off about God knows what, it is not anything about the millions trying to create an economy to pay this exclusive couples salaries and keep them in the style for which they have become accustomed!

Summary. We have an incompetent Government run railroad, with local Governors who appear to be clueless and a Federal agency who is out to lunch. Can the people take over and sub-contract to the Chinese. They seem to have no problems. Please, please China, we can pay you to fix this mess! We can even give you California as a bonus.

Wednesday, May 24, 2017

Reality in Healthcare

Over the past ten years I have examined in some detail the various healthcare proposals and laws. The CBO announces a putative loss of coverage for some 20 million plus people. Why? Simple. The ACA covered people making up to 4 times the minimum wage and if perhaps you were a banjo player of "professional" graffiti artist making nothing at all, you were covered and paid a pittance.

See the following:

Artists: From the Wayback Machine only, scrubbed from HHS site! Music is my life. I’m a lead guitarist and a singer with my sister Kim in the Breeders and other bands. But, in order to pursue my passion, I had to make sacrifices, and health insurance was one of them. Prior to the Affordable Care Act, as many artists know, health insurance on the individual market was hard to come by at an affordable price. For me, having a pre-existing thyroid condition, coupled with an uncertain paycheck from touring, recording and song writing meant I couldn’t afford health insurance. And that was probably true for other artists as well. Thanks to the Affordable Care Act, I’ve been able to afford health insurance as a single, self-employed female for the first time in my life – and it feels really good. It’s something that I can budget for. I feel empowered to be a participant in my health care.But this security is now in jeopardy for millions of Americans, like myself, and especially musicians, artists and others who rely on the Affordable Care Act. So as part of the #CoverageMatters campaign, we are designating today, January 12, as Artists Day of Action. So if you are a musician, writer, actor, painter, poet, sculptor, or artist of any stripe, share your story about why you support the law, what it’s done for you and any personal Affordable Care Act story you or your families and friends may have on social media using #CoverageMatters.
 SideGig: I’m a creativepreneur. My goal is to encourage people to add creativity in their lives to reduce stress, express themselves and spend quality time with their family and friends. I call it spreading the gospel of glitter. And I’ve done it by sharing tutorials, business tips, videos and classes, as well as writing books and speaking across the country.My husband is an artist and musician, and together, we have crafted a life following our passion of making, selling and teaching art. But we couldn’t run our business full time without the security of health insurance for our family.Before the Affordable Care Act, I had researched health insurance plans on the private market and could not find one we could afford. Thanks to the ACA and the Health Insurance Marketplace, I was able to leave my full-time job with health benefits in 2015 to start my own business. My side gig became my main gig, and my business has thrived. The Marketplace plan was perfect for our budget and lifestyle. The first year, I was even able to cover my then 23-year-old daughter because of the law’s provision allowing adult children up to the age of 26 to stay on their parents’ plan. My children are now employed at full-time jobs that offer coverage.
Farmer:I’m a fourth generation farmer, and farming is all I want to do. I raise corn, soybeans and Angus beef. It’s been rough economic times for many farmers, and I’m no exception. I had health insurance when I was younger, but the premium kept going up 10 percent each year. It seemed like a waste of money, so I dropped it.It was also pretty difficult to get coverage at all because I had diabetes. Before the Affordable Care Act, insurers could refuse coverage to people like me with pre-existing conditions.I was pretty much on my own before the Affordable Care Act. Most people don’t see what’s going on out here. As farmers, we’re all individuals. We don’t have group insurance. I was hit with Hepatitis C in 2006 and had to get colon surgery in 2007. My medical costs for the two years amounted to about $100,000. I had to refinance my 760-acre farm (I rent and farm another 440 acres as well) to pay my medical bills because I didn’t have health insurance.There was no question about what I would do when the Health Insurance Marketplace opened in 2013. No one asked me about my pre-existing conditions, and I found an affordable plan for 2014 that would fit my needs for about $400 a month after tax credits. My premium for 2015 was about $364 a month and about $390 a month for 2016.
 So all of these folks are riding on the rest of us who work for a living. Musicians, SideGigs, Farmers, are having the rest of us carry them so they can follow their dreams! Yet the CBO says if we do not continue to pay for their healthcare as well as ours then we will not have music, gig stuff, or whatever this farmers is making. So what! Let them get a job just like those who are currently paying for them!

A note to the current Administration. You should keep these stories alive and at hand. It explains why we are in this mess!

Saturday, May 20, 2017

Microsoft Does It Again

In my opinion Microsoft is truly evil. Now that is my personal opinion. I have studied the meaning of evil and especially the work of Augustine and therein I believe I may have a valid opinion.

You see they update W10 again, 1703 "upgrade". Yes, a full complete, five hour upgrade. Dead in the water. Then they moved things around. You see, after 3/4ths of a century I know where things are on my desk. Pens in the right hand drawer, stapler to the top right, phone on top left. And so on. But what do these people do? Change everything as well as the location of everything. I guess they never had a mother who told them to put things back where they belong! The move things, not big moves, but evil little moves.

Then the upgrade kills off expensive software. Drivers do not work, files messed up, etc. One gets to spend a full day trying hopelessly to rearrange your desk! Yet every few months these people change your desk. For the better? Hardly.

Saturday, May 13, 2017

Secure Networks

The most recent flap on intrusion into large scale public networks has evoked responses by people who appear in my opinion and in my experience to have little in any understanding of what was and what is. For example the NY Times has apparently some Librarian commenting on the recent flap. The author states:

It is time to consider whether the current regulatory setup, which allows all software vendors to externalize the costs of all defects and problems to their customers with zero liability, needs re-examination. It is also past time for the very profitable software industry, the institutions that depend on their products and the government agencies entrusted with keeping their citizens secure and their infrastructure functioning, step up and act decisively.

But take a look back forty years, to the mid seventies. We worried about Soviet intrusion into networks and at the same time we were intruding into theirs. One of my best employees had been with the Brits and managed to [penetrate East German telephone lines. It was simple, just climb through the sewers, tap the copper pairs, and hope you do not get caught.

But in a similar fashion we had three key elements. First we had secure lines. They were not shared. They were encrypted. Finally we had secure Operating Systems, Kernelized OSs. What was a KOS? Simple it was an OS with a secure outer kernel that only allowed access to the OS functions such as DB access and I/O access in a fully secure manner. However, the MS/OS is an open system allowing third party software. It is a pure kluge. At least Apple has a somewhat better system. But MS systems ate a patch quilt of ports and access points that have evolved into an uncontrollable mess. Anyone can get into them. Then add the Internet, an "open" network by design, and you have a recipe for disaster.

Thus what is the solution? Go back 40 years. Why is the NHS using the Internet! It is grossly insecure. Why do they use XP, it also is insecure. And finally, what do the people always open stuff they should not? What would one expect, just a disaster.

Tuesday, May 9, 2017

Mabs and CAR-T

Immunotherapy has become an explosive field. We have been focusing on Mabs, which have been around for quite a while, plus CAR-T cells which have been available for about five years. There is an interesting report by Research and Markets which sizes up the CAR=T cell market. They state:

As per report findings, the promise of CAR modified T cell therapy derives from its combined immunologic benefits and include the specificity of a targeted antibody, the ability to expand the T cell population and the potential for long term persistence to facilitate the ongoing tumor surveillance. The success in early phase trials, assess the feasibility of evaluating the treatment modality across the multiple centers and in larger patients. Currently, there are 99 CAR T Cell based therapies in clinical pipeline and most of them belong to Phase-I and Phase-I/II clinical trials. 

We have examined this approach over the past few years and it does present potential. They also note the following players:

12.1 Autolus
12.2 Bellicum
12.3 Bluebird
12.4 Celgene
12.5 Cellectis
12.6 Celyad
12.7 Eureka Therapeutics
12.8 Fortress Biotech
12.9 Immune Therapeutics
12.10 Juno Therapeutics
12.11 Kite Pharma
12.12 Novartis
12.13 Sorrento therapeutics
12.14 TILT Biotherapeutics
12.15 Ziopharm

It is well worth watching this landscape evolve.

Monday, May 1, 2017

Bridge vs Tunnel

Just a thought. What is they built a bridge to Penn Station in New York rather than a tunnel. Here is the result. First for a tunnel, I have used the average estimates from various sources:

Amount $20,000,000,000 
Duration  40 
Interest 4.00%
Passengers per day  600,000 
Passenger days  156,000,000 
Fee per Trip $6.48

Annual Bond Payment $1,010,469,786 

Then for a bridge. I assume that one just duplicates the Tappan Zee Bridge.

Amount $4,000,000,000 
Duration  40 
Interest 4.00%
Passengers per day  600,000 
Passenger days  156,000,000 
Fee per Trip $1.30

Annual Bond Payment $202,093,957 

Thus for a $1.30 a trip we can get a bridge in about 3 years! So what is the problem?