Saturday, December 27, 2014

The End of an Era

My father passed away December 11, 2014.  Below is his obituary.

Walter Kuzyk, 98, of Philadelphia

Walter Kuzyk was born on June 6, 1916 to Walter and Maria Kuzyk in the town of Przemyśl on the
border between Poland and Ukraine during the peak of World War I.  Walter, his sister Lydia and his parents moved around the Galicia region until they took residence in Lviv, which is now in Ukraine.

Soon after, Ukraine fell under control of the Soviet Union.  Living in the city, they avoided the artificial famine imposed by Stalin that took as many as 7.5 million lives, but, were later caught on the battle lines of World War II.  Walter's father, a lawyer and a judge, fled from Ukraine in 1941 to escape the NKVD ’s purge of the Ukrainian Intelligentsia prior to the German invasion.  Walter was arrested as punishment for his father's departure.  In response to the imminent fall of Lviv to the Nazis, the NKVD hastily executed its political prisoners.   Walter escaped the midnight firing squad when freed by an officer who recognized him as a musician from the local dance hall.  His fiancée, Irene Bernakiewicz, was also detained for several days by the NKVD, where she was coerced into becoming an informant against her parents, who were both teachers (and her father a principal), to insure that they were loyal Soviet citizens, indoctrinating their students with approved dogma.

These events forced Walter and Irene to flee to Germany through the advancing Nazi front, using their high-school documents -- which featured a Polish eagle that resembled the German coat of arms, to fool the German border guards.  Through a network of friends, they located Walter's father, who had gained employment in Germany as a supply clerk, using his fluent German to convince the local authorities that he was a native.  Walter and Irene were married soon after they arrived.

Walter's father hid the young couple in his small apartment for the duration of the war.   Since necessities were rationed, and Walter Sr. could barely support himself, they gathered weeds under the cover of night to supplement their paltry food supply.  After the war, Soviet rule over Ukraine was restored, making it unsafe for Walter and Irene to return.  They were sponsored by a Ukrainian friend with US citizenship to immigrate to the US in 1949.  Walter's father’s application to the US was rejected, so he immigrated to Australia.

Walter's Master’s Degree in engineering and Irene's degree in Pharmacy from Ukraine were not recognized in the United states, so they worked outside of their professions, taking multiple jobs as custodians, dry cleaners, and assembly line workers until Walter eventually secured a job as a draftsman with Westinghouse.   In 1958, their son Mark was born.

While at Westinghouse, Walter attended the civilian division of Pennsylvania  Military College in Chester, PA, where he earned a BS degree in Mechanical Engineering in 1965.  At age 50, he landed his first engineering job at the Philadelphia Naval Base, and remained with the civil service until his retirement in 1987.  Throughout his life, he was active in the Holy Ghost Ukrainian Catholic Church in Chester, PA, where he sang in the choir and served as cantor.

After his wife Irene passed away in 1990, he moved to Philadelphia so that he could immerse himself in the vibrant Ukrainian community.  Until he suffered a stroke in 2013, he volunteered at the Ukrainian Center, where he served senior meals, worked at the library, and interacted with his lifelong friends.  He enjoyed his independence, regularly attending operas at the Academy of Music in Philadelphia and driving to Cape May to enjoy the beach.  While he was frugal, he generously sponsored poor students in  Ukraine, supported organizations such as Children of Chernobyl, and lavishly indulged his grandchildren.  Walter was known for his extravagant devotion to his family, his appreciation to the US for giving him the opportunity to live in freedom and prosperity, and for the pride he took in the rich culture of his Ukrainian heritage.  He passed away on December 11, 2014, after having lunch in the company of friends.

The funeral liturgy in the full Ukrainian tradition was celebrated at St. Michael the Archangel Ukrainian Catholic Church in Jenkintown, PA, on the morning of December 17.  He was laid to rest at Saints Peter and Paul Cemetery in Delaware County.   He is survived by his son Mark, daughter-in-law Patricia, grandchildren Mark Kuzyk and Alexandra Brune, Lexa’s husband Stan Brune, and great grandson Jack Sawyer Brune.

Tuesday, November 4, 2014

An enlightened sexist

A letter from John Gray appeared in the July 1863 issue of Scientific American,
“Messrs. Editors: All machinery requires attention, and occasional ‘fixing’; and the women are not good at such work. Every now and then it is: ‘John, I wish you would look at that sewing machine’; or ‘John, that wringer has something wrong about it’; and so on. Well, the only way to meet that is to buy the very best machinery; you will then have little trouble. Some churls may say: ‘I won't buy so-and-so; what else have the women got to do? Let them work!’ All I have to say to such is that I hate to see the women of the family borne down with the fatigue of severe labor; and if it is a little troublesome to fix machinery for them, I for one am content to endure that trouble. —John Gray”
John Gray clearly considered himself enlightened, and perhaps he was for his times.  Makes me cringe at myself from the perspective of the future...

Monday, November 3, 2014

A note on global warming

Larry Kirkland wrote an opinion piece that appeared in the Moscow Pullman Daily News on October 22.  The gist of his  piece is that the media is only reporting the politically correct view of anthropogenic climate change when in reality, climate change is a hoax.  I wrote the following response to his editorial, only to find that Jeff Hicke had already provided a suitable response.  Since my piece addresses specific points brought up in the original editorial, I thought it would be useful to post it here.

I agree with Larry Kirkland's statement In His View  that truth is essential to making informed decisions. However, he provides no evidence to support his claim that the mainstream media is providing false information.  I suggest that he call upon the original sources rather than relying on the spin doctors with whom he agrees.

Kirkland ridicules the change in terminology from "global warming" to "climate change," implying some sort of conspiracy by scientists and the media.  For the record, Prof. Wally Broecker is generally credited with coining the phrase "global warming," which came from his 1975 Science paper, "Climate change; are we on the brink of a pronounced global warming?" Though the title leads with "Climate Change," "global warming" resonated with the media and the public. To be precise, we should use the term global heating: the trapping of solar energy by a thickening blanket of CO2, to which humans are contributing in large measure.  Heating can (1) lead to processes such as melting, which are not associated with a temperature increase; (2) perturb delicate steady state cycles to make them chaotic; and (3) result in temperature increase.  All three consequences of heating are being observed according to predictions.

Kirkland states that "...the globe quit warming some 18 years ago."  This is false. Figure 1 plots the global land-ocean temperature index from data I downloaded from NASA's website.  The index was lower in 2013  than it was in 1998, but this is within statistical uncertainties as can be seen from the scatter in the data.  Selecting the two data points that support your conclusion and ignoring the rest is a dishonest practice called cherry picking.  The globe is indeed warming and the truth is out there if you care to dig more deeply.

Kirkland criticizes studies that show 97 percent of scientists believe in global warming, claiming that this was proven false in 2013.  The 2010 paper by Anderegg et al, which appeared in the Proceedings of the National Academies of Science, assembled a list of climate researchers whose opinion on anthropogenic climate change (ACC) is known based on authorship of scientific assessment reports and membership on multi-signatory statements.  Of those scientists who were deemed to be active climate researchers based on publications and citations, they found  "97-98% of the climate researchers most actively publishing in the field surveyed here support the tenets of ACC outlined by the Intergovernmental Panel on Climate Change, and (ii) the relative climate expertise and scientific prominence of the researchers unconvinced of ACC are substantially below that of the convinced researcher."  Several other studies since then show similar results.  A separate study by John Cook, which reported similar percentages, was criticized by Forbes contributor James Taylor.  Even if Cook's methods were flawed, this does not invalidate the 97% figure determined from scientific studies such as those by Anderegg, as Kirkland would lead us to believe.

Kirkland states that "None of the complex computer models of the Earth's climate have been able to accurately predict historical and current climate patterns." It is true that the models are not perfectly accurate, but they do predict the correct trends. Even the lower end of the predicted range is cause for concern.

If Kirkland wants honest science reporting, he should read Scientific American, an excellent magazine that reports on significant breakthroughs and gives in-depth reviews of important cutting-edge research area.  Articles are written by writers -- most having a science degree; and, by researchers -- a large fraction having Noble prizes.  A thoughtful Letters section provides a forum for further debate.  What you describe as the PC view happens to be the consensus view of scientists.

It is a simple matter for an internet savvy individual to cherry pick data, misrepresent climate scientists, and yes, even find some true mistakes in data and methodology in scientific papers.  After the dust settles, the preponderance of evidence convincingly supports the claim that the climate is changing due to human activity, and the consequences need our attention. Rather than debating whether climate change is real, which has been established with a high degree of certainty, we should be using the best available evidence to come up with a risk/cost/benefit analysis, and shift the debate to what actions should be taken and in what proportions.  Requiring 100% certainty is an excuse for inaction that we cannot afford.  Let's move forward and debate the real issues.

Wednesday, October 22, 2014

Teaching Creationism and Intelligent Design as Science in Public Schools

About a month ago I got a Linked-In notification of a post on the American Physical Society group about a White House petition to ban the teaching of Creationism and Intelligent Design as Science.  Being an educator who takes science literacy seriously, I happily signed the petition.

The petition was motivated by the relentless push of fundamentalists to teach Creationism and Intelligent Design as part of the Science curriculum in public schools.  I was surprised by the criticisms posted in response to the petition.  Below are the critical comments and my response.

You are trying to ban free speech. This is not an issue of free speech. The petition would only ban the teaching of Creationism and Intelligent Design AS science in public schools.

Not everything true is science. Science is a method that has been shown to be incredibly successful in understanding and controlling the material world.  Because Creationism and Intelligent Design do not provide falsifiable hypotheses, they are religion not science.  It is disingenuous to teach religion as science.

If science is all one can teach then education is reduced to propaganda.  We should only teach science in a science class.  There are plenty of non-science classes in the public schools.  Nobody is calling for only teaching science, though I think we need way more science education.

Who controls what is science?  Nobody controls science.  It is not a hierarchical system like a church where rules are handed down from authority.  Scientists pose hypotheses and do experiments to test hypotheses.  Once a huge body of evidence explains many things in a simple way, it is elevated to the status of a theory.  Scientists gather theories and distil them into books to help others learn what is known.

I know a number of big science personalities that act as bullies against even other scientists for any idea that is not pure status quo. The status quo is routinely turned on its head as new evidence accumulates.  A scientist may be protecting his or her turf, but the community as a whole moves (sometimes glacially) in the direction that evidence takes it.  Many of the greatest ideas were proposed by young whipper snappers, which have become the basis of many of our most successful theories.

Banning the theory of creationism and ID sounds inconsistent with the scientific method. Scientifically we don't ban theories, we simply conclude that the theory is not supported by experimental results.Scientists are not banning Creationism and Intelligent Design.  The petition specifically bans only the teaching of Creationism and ID as science.

Wow, it is a bit disturbing to know that there are those who think that banning ideas is in harmony with our Constitution. Many have heard that old saying, "The church is a refuge for scoundrels". That truism is even truer for "science". Indeed, before condemning the teaching of "Creationism" in schools, one should feel some obligation to define "science". It most controversial discussions, the subject being discussed is never succinctly defined. Science has a precise and hopefully universally-known definition which is well stated on Wikipedia as follow: Science (from Latin scientia, meaning "knowledge"[1]) is a systematic enterprise that builds and organizes knowledge in the form of testable explanations and predictions about the universe.[2][3][4] In an older and closely related meaning, "science" also refers to a body of knowledge itself, of the type that can be rationally explained and reliably applied. A practitioner of science is known as a scientist.

It is said history repeat itself. This petition remember me the French revolution and the campaign waged by the radicals to dechristianize France under the same banner, the age of reason and how Maximilien Robespierre delivered his speech in the festival of reason (The Cult of Reason), and also remember me the Stalinists when their leader Stalin said: "There are three things that we do to disabuse the minds of our seminary students. We had to teach them the age of the earth, the geologic origin, and Darwin's teachings". In both cases the radicals used the same tool to eliminate their opposing views, they used the power of government.  Science has determined the age of the earth, describes its geological origin, and understands the evolutionary process.  Each of these areas meets the definition of science.  The fact that some ruthless individuals in the past advocated for science is irrelevant.  Also, the goal of the petition is not to use government to snuff out religion, only to not teach Creationism and ID as science.

I won't be signing. Why get involved in debates about the unprovable? Evolution (of new species) and creationism/ID are all unprovable. I see a magazine cover on the news stands this week with Bill Nye "fighting" for evolution - I guess - he likes to debate the ID folks, but he can't prove anything either. Science never proves anything.  However, there is overwhelming evidence for evolution that has met rigorous scientific testing, so scientists accept it.  It is a false dichotomy to say two propositions are equivalent because they or both not 100% provable.  In these cases, the preponderance of evidence is used to make the choice. 

 I'm afraid if this banning happen we are going to end up with the burning of the books of creationism and ID in Washington, D.C. and the professors who insist to teach creationism and ID are going to be arrested (because it is illegal), just like what happened in Germany in May 1933. I mean the Nazi book burnings.  The petition does not prohibit the teaching of Creationism and ID, only teaching these topics as science in public schools.  It is frankly insulting to equate Nazis with those who defend science education.

Today's great theory is tomorrow's folly! The question whether our reality came about through creation or evolution is characteristically a 19th century question. Today, with our understanding of relativity and our technological advances, no scientist would ask such a question. However, the fact that there is a large body of scientists and creationists still asking and fighting over such a question, is a subject of keen scientific investigation in itself. For that reason, we cannot ban hypotheses. It's a very unscientific thing to do. The fact that lots of people are fighting for Creationism is not a sign that there are legitimate scientific issues that remain unresolved.  Creationism is not science because it offers no testable hypotheses.  The fight is between science and those who do not like where the evidence is leading.

Stating the earth is flat is not fraud in my opinion; it is inaccurate and lacking critical scientific evidence and completeness. Creationism and ID are not amenable to test under the scientific method and therefore not fraud to state in public--you cannot disprove or prove scientifically the existence of God. Why do you jump to conclusions and say it is falsehood. How do you know the context that creationism or ID is presented in every classroom where it is done. Because Creationism and ID are not amenable to scientific tests, it should not be taught as science.  This is not an issue of fraud.  At least the flat earth is a local approximation to a sphere but Creationism and ID do not overlap with anything that is testable.

Facts are debated before the are established. Many theories and dogma that were believed to be fact have been discarded in the past when new information displaced them. Why should Creationism/ID be any different? The truth here is that you are being even more dogmatic than the Creationists/ID whom you are trying to ban. They are not advocating the banning of science or evolution. They just want equal time for their dogma, theory or whatever....truth shall prevail. The scientific method itself is dogma that needs to be scientifically validated from time to time as we learn more about our reality. I learned the scientific method and I learned creation. Today I am in a position to make arguments for or against either of them....they both have "issues". Do you want future generations to be ignorant simply because you fall on one side of the argument? Asserting that "Creationism/ID is not science therefore should not be taught in a science class" Is equally foolish because the scientific method knows nothing sacred. Everything is subject to investigation. I would doubt that Francis Bacon or Karl Popper would agree that there are any subjects which are "out of bounds" for scientific inquiry.  Science is not a dogma, but a way of gathering information that leads to a body of knowledge that is objectively true, in the sense that its elements are testable and reproducible.  Creationism and ID are dogma that cannot be tested.  Competing scientific hypotheses deserve equal time, but Creationism and ID are not science so should not be presented as a competing scientific view.  Popper and Bacon would disagree with you.  Popper proposed that only falsifiable propositions are testable, and religious dogma is not.  Similarly, Bacon espoused the scientific method. Creationism and ID are not suitable candidates for study based on the nature of the claim.

Belief in either ID or Spontaneous Generation origin theory (neither are yet proven and re-producible law) takes a leap of faith. What is unscientific about considering more than one origin theory? It appears that many SG advocates are emotionally invested in their origin theory, and this makes than uncomfortable with comparison beyond what they can demonstrate.  My personal observation of trends is that science is on the verge of proving ID of new life forms, and this makes SG 'experts' more than a little uncomfortable -- to the point of demanding censorship of ID origins theory. If ID presented testable and falsifiable hypotheses, it would be the object of scientific study; and, if the hypotheses were shown to be true, ID would become accepted on the evidence.  SG theory, as you call it, has many testable hypotheses.  For example, how are complex molecules made?  ID people say GOD created them.  What is the testable hypothesis?  None are offered.  Scientists propose that SG requires that early earth conditions should spontaneously yield complex molecules from simple ones.  Miller and Urey  did  the experiment by simulating early earth conditions in a test tube.  They exposed  water (H2O), methane (CH4), ammonia (NH3), and hydrogen (H2) (known early earth atmosphere and oceans) to an electric discharge (lightening).  A goo forms on the bottom of the test tube.  An analysis shows that it contains amino acids - the building blocks of life.  There are thousands of similar experiments that test various aspects of SG.  This is science.  ID is not.

There are at least a billion people who pay taxes and believe in Creationism....and you want their children to grow up ignorant of the implications of what they are supposed to believe? About there being two creation stories; have you heard of Einstein's twin brothers analogy? While it has its issues, those issues are not germane to it's analogy of the two creation stories. In my view both the evolution and creation narratives suffer from the concepts brought about by the twin brother analogy. Creationism IS a creation story and evolution, big bang cosmology, etc. IS science.  Teach science as science and Creationism as religion.  People can teach their children whatever they want, but in a science class, we are paying schools to teach science so that we can produce scientists who cure diseases, make our lives comfortable, and give us leisure to pursue our interests.  The money spent on science returns dividends that surpass the investment.  That is why we invest in science.

Parting Comments

People take advantage of what science produces but are uncomfortable when the knowledge gained conflicts with their religious beliefs.  The comments posted here testify to the respect that Science has won; everyone wants their beliefs to be associated with science as proof of their veracity.  Since Science carries so much weight, it is natural for Creationists and IDers to

push there agendas by forcing these topics into science classes.

Science, unlike people, is honest.  It is the best process to create an accurate representation of the material world that allows us to control nature and understand our origins.  The scientific method works best when its practitioners approach it without preconceived notions about how the world should be.  Forcing Creationism and ID into a Science curriculum corrupts the process and at its root is a dishonest act of self interest.

Those of you who think that banning the teaching of creationism is stifling free speech should read the decision of Judge Jones in the famous Dover case. He is a conservative christian appointed by Bush and gave the most impeccably logical arguments of why ID/creationism is not science and should be banned from being taught as science.

It's ironic that so many people use the argument that we can't disprove religion/creationism/ID so leave us alone and let it be taught in schools. This is exactly what makes religion/creationism/ID not science so it should not be taught as such.

The bottom line is that we are wasting precious classroom time teaching non-science that should be dedicated to teaching science; and in the process making students willfully ignorant citizens who will not believe that HIV is real, that vaccines cause autism, and that climate change must be a conspiracy because it snowed in my backyard.

Tuesday, October 14, 2014

Trying to get the price of internet service from Time Warner -- A transcript

After hooking you with introductory deals, internet service providers raise the rates. Seeing great rates advertised, I was in the market for upgrading my bandwidth with Time Warner and couldn't get a straight answer about how much it would cost to get faster service. Instead, the rep kept on trying to sell me bundled packages and would not tell me how much the bundle would cost after the 12 month introductory period.

Below is a transcript of the online chat. It took 30 minutes before I got an answer. Fortunately, I was able to read emails and do some work while I waited for the rep to respond.

info: Thank you for contacting Time Warner Cable. A representative will be with you shortly.

info: You are now chatting with Thalia.

info: ** Please do not share credit card information in this window. If credit card information is required, the agent will push a separate and secure form to you.  **

Thalia: Thank you for contacting Time Warner Cable, home of the best Triple Play offer. My name is Thalia, would you like to learn more about our current Triple Play packages?

Mark: Not interested in triple play.

Thalia: I'll be happy to assist you with your concern.

Mark: I already have internet service with you. Would you please check what internet speed I now have and what other options are available? I see that there is an online deal for $64.99 for the ultimate 50 package.

Thalia: So I can properly address your concern, let me check your account first.

Mark: OK

Thalia: May I have the account number?

Mark: I don't have it on me. Can you use my phone number?

Thalia: Yes that's fine.

Thalia: May I have it please?


Thalia: Thank you.

Thalia: Bear with me please.

Mark: OK

Thalia: Please verify the last 4 of your SSN.

Mark: *****

Thalia: Thank you. I can see here that you have the Turbo internet.

Thalia: I can add home phone for only 10.00 plus I can upgrade you internet for only additional 30.00 monthly.

Mark: Not interested in phone.

Mark: I am online at the page where I can select the Ultimate 50 package. If I select this, will my service be upgraded to the 50 without the need to install a new modem?

Thalia: After that you need to swap the equipment to the nearest TWC store.

Mark: Also, I think I am paying somewhere around $70 so do you mean I would need to pay $100 for a package that is offered for $64 online?

Thalia: Yes you are paying a standard rate, adding phone will help you get the promo price again.

Mark: So what exactly is the rate if I do not get the phone. The price I see online for $64.99 is internet only.

Thalia: The 64.99 is only for new ciustomers.

Mark: So what is the price for me?

Thalia: If you won't add phone, monthly will be $90+

Mark: And what is it with a phone?

Mark: And what do you mean by $90+. I want to know the total charge.

Thalia: With our home phone service, you can do unlimited calling within US Canada Puerto Rico and Mexico plus free 13 calling features including Call waiting, 3 way calling, Enhanced *****, Anonymous call rejection, and Charged block. This is a good alternative for being over charge for your mobile phone charges while calling your family.

Thalia: If we add phone the monthly will only be 10 home phone + 69.99 ultimate internet + 5.99 modem lease.

Mark: IS that forever or only the first year?

Thalia: If we don't add phone, then the monthly is more than 90+.

Thalia: This one will be good for 12 months as well. You may still modify your account without extra cost.

Mark: What will it be after 12 months at the present rate?

Thalia: The pone can go up to 40.00.

Thalia: But before that, you will receive an email informing you about the promothat is about to be expired.

Mark: OK, the phone can go up to 40, what about the internet?

Thalia: For the internet, its standard price is like what I mentioned earlier.

Mark: So after 12 months it will still be 69.99 for the service and 5.99 for the modem.

Thalia: Within the promo period the monthly is 69.99 internet + 5.99 modem + 10 home phone.

Mark: But what about after 12 months?

Thalia: When promo expird, the internet can go up to $90+

Mark: OK, could you please tell me the rates for me today for the following internet only services: Standard Turbo Extreme Ultimate

Thalia: Here are the promo price for the following: standard internet 39.99, turbo 49.99, extreme 59.99, and ultimate 69.99.

Thalia: All of that is less than $5 online because it is only for new customer.

Mark: But I am not a new customer. What would it be for me?

Thalia: You already have an account with us, so we can not apply the less than $5.

Mark: That's fine, so does that mean that I will pay standard internet 44.99, turbo 54.99, extreme 64.99, and ultimate 74.99?

Thalia: The prices you typed is for news customers.

Mark: SO I am asking what is it for me right now?

Thalia: If we add home phone, you may get the promo prices again which are standard internet 39.99, turbo 49.99, extreme 59.99, and ultimate 69.99.

Mark: But if I do not want the home phone, what are the prices to me NOW?

Thalia: Well if you don't want the home phone, these are the prices for the internet speed you might get: standard internet 57.99, turbo 67.99, extreme 77.99, and ultimate 87.99. Equipments are not yet included.

Mark: OK, thank you. That is the info I wanted.

Thalia: To help you save money,

Thalia: we can add home phone.

Mark: I understand. Thanks you.

Sunday, October 12, 2014

I'm Depressed

There is so much to be depressed about.

ISIS (or ISIL), a group of religious fanatics, is marching through Syria and Iraq, beheading, crucifying, and killing all whose beliefs they find offensive.  Sadly, they are using hardware that the U.S. gave to the Iraqi army, whose soldiers fled when ISIS approached their positions. In the meantime, the U.S. is showing its impotence with air strikes that don't seem to be doing much.  Turkey is standing by idly as ISIL is taking over the border town of Kobane.  By the time we take serious action, it will be too late.

Israel's action on the Gaza Strip might have achieved its military objectives, but 2100 Palestinians were killed.  In recent interviews in the border regions, hatred between the Israelis and Palestinians is heating up, which will undoubtedly set the stage for future conflict.  During an interview of Palestinian school children, rockets flew overhead from Hamas positions.  They cheered, exclaiming that they hoped the missiles would hit the United States. 

Russia claims it is not supporting the rebels in Eastern Ukraine.  Remember those insignia-less soldiers driving unmarked military vehicles in Crimea who Putin claimed were not Russian?  They were.  Satellites clearly show tanks crossing the Russian border to Eastern Ukraine.  Igor Girkin, the self-proclaimed defense minister of the Donetsk People’s Republic, boasted about shooting down a plane on Russian social media before he knew it was a commercial airliner. Later, against all objective evidence, Putin claimed that the Ukrainian military had targeted the jet.  The rebels left the bodies to rot in the fields and prevented Dutch authorities from recovery operations.  The rebels, however, found the time to desecrate the bodies -- removing jewelry, rings and other valuables.

Putin continues to lie about Russia's involvement as the west allows this unjust war to rage.  The fighters are fired up by a vision of making a worldwide Slavic utopia.  Putin, who is clearly lying, is getting away with this farce, laughing at the impotence of the west, whose leaders care more about losing automotive contracts than they care about a new and dangerous Russia.  Putin is able to get away with his actions at home by controlling the press and firing playing on Russian nationalism.

If humans don't kill each other, Ebola has come on the scenes to finish the job.  This deadly disease
has found its way into Monrovia, with a metropolitan area of almost a million people with high population density, making it more likely that the virus will spread.  Based on the known numbers of infected individuals, the virus' incubation period, and transmission rates, the number of people estimated to contract Ebola in the next month exceeds the number of available beds.  Western aid in adding to facilities will not be enough.

Closer to home, a person who helped treat Thomas Eric Duncan (the first case diagnosed in the U.S.) may be the first person to contract the disease while in the United States. The health care worker is from Texas Health Presbyterian Hospital and tested positive on Saturday after reporting a low-grade fever Friday. The CDC is working to confirm the diagnosis.  Will an Ebola outbreak hit the U.S.?

Now that I have finished grading an exam and writing an NSF proposal, I can spend some time doing research, which will happily distract me from the ills of the world.

Good night...

Friday, May 30, 2014

Can a zero-carb ketogenic diet fight cancer?

Let me start by answering the question honestly.  I don't know, so I am not advocating a zero-carb diet as a therapy for cancer.  However, I think it is an interesting hypothesis that deserves to be studied.

As background, consumed carbohydrates are readily converted into glucose in the bloodstream, which provides nourishment to all cells in the body.  In high fat and high protein diets, where carbohydrates are absent, ketones are produced, which are an alternative fuel.  When the percentage of carbohydrates are reduced below some critical level, which varies between individuals, a state of nutritional ketosis results (not to be confused with the dangerous condition in diabetics).

As an example, I am particularly sensitive to carbohydrates so to maintain ketosis, I try to keep my carbohydrate intake as low as possible, which is around 5% to 10% of the total calories I consume.  Protein also can interfere with ketosis, so in the case of my diet, I average about 70% fat, 22% protein and 8% carbohydrates.  How did I determine these ratios?  I used urine strips and a blood ketosis device to monitor my ketone levels at differing proportions of these three macro nutrients.  Incidentally, the Atkins diet is incorrectly called a high protein diet but is in fact a high fat diet.  Eating large amounts of protein can be dangerous, so when decreasing carbohydrates, fat consumption must increase.

The cultural preoccupation with fat as being bad is undoubtedly the reason why the Atkins diet stressed protein.  Since the purpose of this post is not to discus this complex issue, I will not give an analysis here but will merely point out that high fat intake is dangerous when combined with high carbohydrate consumption, not when carbohydrates are eliminated.

It takes the body about two to three weeks to acclimate to a ketogenic diet.  After this period, the body readily converts consumed fat into ketones and efficiently uses ketones as an energy source.  The body then also more readily converts fat in cells to ketones, an explanation of why ketogenic diets lead to weight loss.  Ketogenic diets are starting to be used by high-endurance athletes for energy and reducing bonking, where the brain shuts down due to a short supply of glucose.  In contrast, fat cells in an athlete in nutritional ketosis more readily provide ketones that powers the brain and other organs.

Since cancer cells ravenously consume glucose to grow and spread, reducing this fuel may weaken them.  If cancer cells have a preference for glucose over ketones, and since the body seems to function efficiently on ketones in acclimated individuals, a ketogenic diet may add an extra punch to traditional chemotherapy or radiation therapy.

A Phase I study is in progress to test whether or not a Ketogenic Diet with concurrent chemoradiation for non-small cell lung cancer improves longevity.

On a related topic, it is well known that many animals live substantially longer on a very low calorie diet.  Controlled studies of such diets in humans are not possible;  how many people would volunteer to be at the edge of starvation for a lifetime, and how could cheating be monitored?  These are issues that make any long-term observational studied of populations flawed and impractical.

A hypothesis for this observation is that glucose - the mitochondrial fuel source, is responsible for shortening life spans.  If this were so, replacing glucose with ketones as an alternative fuel might do the trick.

Cynthia Kenyon of UC San Fransisco has been studying the effects of diets in tiny worms.  She found that worms on a diet devoid of sugar can outlive their sweet-tooth brethren by a factor of two, a dramatic effect that has a sound genetic basis; sugar is part of a biochemical pathway that interferes with cell repair.  These results may not carry over to humans, but it is an interesting hypothesis that also deserves a test.

After discovering the affect of sugar on worm longevity, Kenyon herself went on a low glycemic index diet, totally avoiding sugar accept for those in dark chocolates.  As a scientist, she does not advocate such diets.

Given that a zero-carb diet maximizes ketosis, which might starve cancer cells and turn on the cell-repair mechanism, I would have a serious discussion with my physician about ketongenic diets if I or someone close to me were struggling with cancer.

Thursday, April 3, 2014

In an age with a record number of sicentists, could we be missing new phyiscs?

In the late 1800s and early 1900s, classical theories of physics began to crumble in light of new evidence accumulated by experiments on the quantum scale.  The new explanations proposed at the time irked some of the biggest names in physics, mathematics, and philosophy.

For example, Poincare's philosophy of science was based on what philosophers call instrumentalism, which dismisses unobservable entities.  (see for example the paper by Milena Ivanova)  This viewpoint is dismissive of the reality of atoms because they are not directly observed.  Even when the evidence mounted, Milena Ivanova argues that, "...Poincaré’s paper motivates a non-fundamentalist view about the world, and that this is compatible with his structuralism. ... Poincaré advanced structural realism, which commits one to the structural claims of scientific theories and not the claims regarding unobservable entities."  In other words, the theory describes what is observed in terms of a mathematical structure, but the observation does not imply, for example, that atoms - an assumption underpinning the theory - exist.

The early 1900s must have been an exciting time of discovery.  Scientists had to shed their preconceived notion about certainty and absolute space.  I wonder if I would have been a staunch supporter of the status quo or if I would have accepted the new way of thinking.  We'll never know, though I'm sure many of us would fancy ourselves falling on the right side of history.

Quantum mechanics became accepted as the theory of atoms and molecules because of its success in predicting atomic spectra and differential scattering cross-sections. As such, the underlying structure of atoms and molecules as suggested by the theory have become accepted as reality.  Our classical view and intuition about the world falls apart at the quantum scale.  Electrons are not tiny point-like particles whose position and momenta can be simultaneously determined to arbitrary precision.

The rates of thermodynamic processes are typically accelerated when the temperature is increased, but we find a dramatic decrease in the rates of self healing when we turn up the heat.  Many such strange things characterize the underlying process.

In the modern era, physicists picture a single electron in an atom as a fuzzy cloud rather than the old planetary picture of one tiny particle orbiting a nucleus.  An electron can pass simultaneously through two slits in a wall and two particles can be entangled so that measuring the spin of one particle instantaneously determines the spin of another one on the other side of the universe.  Observations like these are so commonplace that we accept them without question.

We have warmed to the reality of something very bizarre because all measurements support this view.  Is it really that way?  I would respond, yes, because reality is probed by observation, even if by indirect means.  Because of the theory's great success, it is assumed to work for highly complex systems even when it is impossible to test the theory because of our computational limitations and inaccurate experiments.

In my field of nonlinear optics, we measure the nonlinear susceptibilities of molecules and compare them with theory.  However, the measurements have large experimental uncertainties and the calculations use approximation techniques that render the calculations imprecise.  It would be wonderful if experiments and calculations could reliably reach 10% uncertainties.  In many cases, it's more like 25-50% uncertainty. Contrast this with the test of quantum electrodynamics in which theory and experiments agree to 12 decimal places.  That is an amazing theory!

One of our projects seeks to understand the self-healing process and our experiments suggest that strange things are at work.  When a material is burned with light, it does not recover just like ashes don't recombine into a log from which they came.  We have been observing self-healing of molecules after being burned with highly intense light.  Though this may seem weird to most physicists, it is commonplace in our lab, where we have been observing the phenomena for over a decade.  The rates of thermodynamic processes are typically accelerated when the temperature is increased, but we find a dramatic decrease in the rates of self healing when we turn up the heat.  Many such strange things characterize the underlying process.

As described in a previous post, we postulated that molecules in the company of others heal more quickly.  We call these groupings domains.  At elevated temperatures, thermal jiggling breaks up the domains and therefore self healing is suppressed.  Do domains really exist?  We haven't seen a domain but every measurement is consistent with the predictions of the theory.   In other words, the mathematical structure corresponds to the reality of what we are measuring.  At what point can we say that domains actually exist in our samples?

It takes lots of evidence for a theory to be accepted as the true description of a phenomena, and the picture that it suggests starts to become accepted slowly as the theory predicts other phenomena that were not intentionally added to the theory when it was originally formulated.  For example, the famous Dirac Equation accurately predicts all of the relativistic corrections to the hydrogen atom, and naturally includes spin, which in the Schrodinger theory needs to be separately added -- an inelegant solution.

Dirac's theory of the electron worked flawlessly, but also had a major defect; it had negative energy solutions that were not observed.  Dirac perseverated over this flaw and tried many approaches to sweep the problem under the proverbial rug.  The negative energy solutions were later shown to be those of the positron, the anti-particle to the electron.  The Dirac equation in effect predicted the existence of antimatter.  Dirac quipped that his equation was smarter than him.

While to the best of our knowledge, the domain theory of self healing has not been making any new predictions, we have been testing it in new ways.  One of my students (Ben) wrote a dissertation that focused on measurements of self healing under the influence of an electric field.  An electric field induces an electric dipole moment in a molecule.  The molecules in a domain will then interact with each other through the electric fields generated by the induced dipole moments.  It is straightforward to calculate the energy of interaction, and thus determine if a domain grows or gets torn apart by the electric field.

Ben's calculations of the effect of the electric field on the distribution of domains in a sample, and thus it's healing properties, agrees well with his experiments.  As the evidence accumulates, the domain model is not only holding up well, but predicts with reasonable precision what we observe.

The problem is that we have not actually "seen" a domain.  It may be possible to do scattering experiments in which particles such as neutrons probe the microscopic structure of a domain.  We have also been trying to come up with an explanation of the nature of a domain and how it is held together.  My preferred picture is that a domain is made of molecules that are attached to a polymer chain (the domain model suggests wispy string-like domains and not clumps) rather than a string of molecules connected to each other.  Our model allows us to determine the binding energy of a molecule to a domain, and experiments show it to be in the ballpark of hydrogen binding energies between molecule and polymer.

There is even a more intriguing possibility.  This system may be exhibiting a phenomena that arises from the complexity of the system, and cannot be reduced to a description in terms of simpler units.  Perhaps the picture of bonds and molecules starts falling apart when many large molecules interact with each other and with long polymer chains.  The bond, which chemists hold sacred, is not as sacred as the Schrodinger equation, but rather a convenient form of book keeping that helps chemists understand what molecules are formed in reactions between smaller units.

Chances are that the explanation of the phenomena is more mundane than we propose.  At worst case, we may be deluding ourselves into seeing something that is not there.  We won't know until we do lots more work and other researchers test our models with new experiments.

too much research these days is focused on narrow topics, so new and interesting work might be missed simply because it falls outside the mainstream.

Our group enjoys the luxury of having a huge lead in this area of research. We may be sitting on a very interesting discovery.   Though my talented grad students have done lots of excellent work to eliminate hypotheses, we are still puzzled by what we are observing.  We continue to whittle away the false hypotheses in our quest to uncover the truth.

This lead is a two-edged sword.  Our paper on the affect of the electric field on self-healing, which we submitted to Physical Review E and which appears on the Physics Archives, has been sent to half a dozen reviewers, all of whom have turned down the request to review.  The editors subsequently  notified us that they were going through a second wave of review requests.  Because we are so far ahead, other researchers may not understand our work.  Another unfortunate consequence of our sequential series of papers is that we reference a large number of our own papers.  This is unavoidable since we have done all of the foundational work on the topic.  But, it raises eyebrows in the community, which makes us cringe.  However, I am happy to report that our paper eventually got two reviewers who made some good suggestions that we implemented, and the paper is in print.

I believe that too much research these days is focused on narrow topics, so new and interesting work might be missed simply because it falls outside the mainstream.  Perhaps the huge success of science has lead to such a high volume of activity that researchers can only understand work in their own narrow area of specialization.  We are too busy studying the scales to see the huge serpent wriggling in our midst.  This is not to say that one research paradigm should be pursued at the exclusion of all others.

A balance needs to be struck between detailed narrow work, which can miss the big stuff, and broader investigations, which may temporarily lead us astray but eventually lead to something big.  Though the process is sloppy, science has a way of eventually sorting through the trash and finding the real gems.  Hopefully, my lifetime commitment to the process will eventually uncover something of value.  Even if I fail, I take comfort in the fact that we are all part of a highly interconnected human network, where each part contributes to the success of the whole.

We must take pleasure in the process of discovery, give it our best shot, and see where it takes us.  I am fortunate to be part of the most incredible journey, keeping me excited throughout my life.  I still suffer fitful nights, being kept awake by ideas running around my head and starting the morning with impatience for all the administrative obligations that keep me away from my true passion.  The professorial life still gives a fair amount of time and more importantly encouragement to pursue the big ideas, giving me the resolve to pursue my ideas even if in a quixotic manner.  For this I am eternally grateful.

Saturday, January 4, 2014

Thanking the editor for rejecting our paper

Here is an email that I sent to an editor who rejected our paper.  The names have been changed to hide the identity of the journal and editor.  I probably should not have removed the names because the "lord almighty protects the innocent as a matter of daily routine" - from, The Sirens of Titan, by Kurt Vonnegut Jr.

Dear Editor,

I am writing this letter to you directly, and not through the editorial office, to commend you on your work as editor of Journal X.   I know that this is a tough job and papers such as the one my colleague Prof. Awesome submitted to you take lots of time and effort to adjudicate; and, are emotionally taxing, taking us away from what we love - doing Physics.

I just wanted to let you know that although you rejected our paper, I believe that you did so for all the right reasons, balancing the requirements of the journal with the input you got from the referees.  We understand that our work overlaps a little bit with lots of areas, making it too mathematically complex for quantum chemists, has applications in nonlinear optics which graph people do not appreciate, and deals with abstract objects that main-stream nonlinear opticians know nothing about.  Though we believe that the work is significant, the field needs to develop for there to be a critical mass of researchers that can appreciate the topic.  As such, I agree with your assessment that though the paper may be correct, it will probably go unnoticed for many years.

Again, we appreciate your efforts and the thoughtful manner in which you approached our paper.  I hope that our paths will someday cross and wish you all the best for the new year.


Mark G. Kuzyk
Regents Professor of Physics,
Washington State University
Pullman, WA 99164-2814

Phone: 509-335-4672
Fax: 509-335-7816

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