Interview: Is climate change caused by solar inertial motion?

The questions were asked by Mr Vítězslav Kremlík M.A., a historian and a blogger at klimaskeptik.cz; see original URL

An interview with Ing. Ivanka Charvátová, CSc. from the Geophysical Institute of the Czech Academy of Sciences (Prague). The story of one politically incorrect scientific discovery.

(Translation of the original Czech interview published at Osel.cz in May 2011 - link - also by V. Kremlík)



Motion of the barycenter of solar system relative to the Sun.

Your field of study in the Geophysical Institute is solar inertial motion (SIM). Could you explain what it is?

It is a movement of the Sun around the barycentre (centre of gravity) of our solar system. This motion is due to the varying position of the planets, especially the giant planets.

Already Sir Isaac Newton in his PRINCIPIA (1687) intuitively came to the following conclusion: “… since that centre of gravity (centre of mass of the solar system) is continually at rest, the Sun, according to the various positions of the planets, must continually move every day, but will never recede far from that centre.” This effect is not insignificant. The Sun moves across an area the size of 4.3 solar radiuses, i.e. 0.02 AU or 3.106 km. As a coincidence, the average solar speed is around 50 km/hr. Just like the speed of a car driving downtown. The first study about SIM was written by P.D. Jose in year 1965.

You are the author of quite a breakthrough in this field of study. What is it?

First I studied the SIM periodicity and in 1987 I came to survey the geometry of this motion. I discovered the solar motion can be classified into two elementary types. Motion along a trefoil-like trajectory governed by the Jupiter-Saturn order. And another motion type which is chaotic. This gave us a precise homogeneous basis, upon which it became possible to study the solar-terrestrial and climatic variability. You may find it comforting that no matter how the Sun wiggles, every 179 years it comes back to a regular trefoil path. It is important to note, that the periods of chaotic motion coincide with the long-term minima in solar activity such as the Wolf Minimum (1270-1350), Spörer Minimum (~1430-1520), Maunder Minimum (~1620-1710) or Dalton Minimum (~1790-1840). During the trefoil periods the ST-phenomena are stable – the sunspot cycles are 10 years long, volcanic activity is muted and in the middle of the trefoil period there is a temperature maximum down here on Earth.




Later I discovered also a 2402 year long cycle of solar motion. After the lapse of this period the Sun always enters a segment, when for almost 370 years it moves continuously along the trefoil trajectory. This is when the natural conditions are stable, there is a long-term thermal maximum. The latest symmetry of the motion trefoils was around 25 AD. The NASA scientists called this 2402 yr cycle as “Charvatova Cycle”. The prospective solar motion can be calculated in advance (celestial mechanics), which gave us brand new solar-predictive capabilities. So far our predictions exploit the observation that the same solar motion trajectory tends to generate similar phenomena. (I was the only one in the whole world who got the 23rd sunspot cycle prediction right). The physical mechanism is not known yet.



Figure 1: The trajectory of the Sun centre divided into two basic motion types: trefoil trajectory according to JS-ordering (top) and disordered (chaotic) (bottom). The Sun returns to a trefoil trajectory, which always lasts for 50 years, once every 179 years. The chaotic segments correspond to long-term minima of solar activity (see above). The dark yellow circles in the top images represent the Sun.

What made you study solar motion?

In the 1980s the director of our institute was academic Václav Bucha. At some conference abroad he met the renowned American geologist and climatologist Rhodes W. Fairbridge, who was currently studying solar motion along with J.H. Shirley from JPL (Jet Propulsion Laboratory), NASA, Pasadena. Mr. Bucha could smell important topics miles away, so we decided to research this too.

Did the world notice your discovery?

Even before my major discovery came, Prof R.W.Fairbridge contacted me after I published an article about SIM periodicity in Paris. It was published under my former name Jakubcová. He and J.H.Shirley published an article in Solar Physics at the very same time. R.W.Fairbridge wrote me a very friendly letter of praise. There was a communist dictatorship in Czechoslovakia in that time, so any post coming from the Capitalist West was inspected by censorship. Surely you can imagine what a fuss there was about this letter. Not only it had NASA on the envelope, but on top of that Prof Fairbridge mentioned in the letter, that he knew Prague because he had been here in 1968 during the Prague Spring at some Geology Conference. And he mentioned to have seen the “eastern visitors”, the tanks of the occupants invading Czechoslovakia. He and Jim Shirley were so excited at my trefoils that when they edited the Encyclopaedia of Planetary Sciences in the early 1990s they invited me to write the main article on “Solar Motion” there. I was the only author from the whole Eastern Block in that very Encyclopaedia. And I was the most cited one.

Did you two meet in person?

No, we did not. But we maintained very lively correspondence. He used to send me articles that were not available in my country. He also invited me to write an article to the Proceedings published on the occasion of his 80th birthday anniversary (published in the Journal of Coastal Research.)

Another well known researcher who studied solar motion is Theodor Landscheidt. Do you know each other?

We do not and I believe he is not alive any more. We agree that in the first half of the 21st century the solar activity might be lower and even the temperatures might go down. But he does not cite me and I cite only one of his studies.

Apparently there are lots of scientists who explain climate change by other factors, not merely by CO2. However in the Czech Republic, where you live, most people know only one climate sceptic. Your president Václav Klaus.

Oh my. I would rather not comment on that. I only browsed through his book “Blue Planet in Green Chains” in the bookshop.

There are many climate sceptics in the world, they have their organisations, especially at the American or Canadian universities. Many professors of theirs have contacted me. For instance Prof. O. Manuel, the former chief researcher of the Apollo project. They even published a book “Slying the Sky Dragon“, where they document the scandals of the climate change research and thus also the uncertainties in the temperature measurements of the last 40 years or so.

The UN climate panel (IPCC), which is so harshly criticised by your president Klaus, has had lots of scandals lately. Have you heard about Climategate?

Of course. The director of CRU (Climatic Research Unit) P.D. Jones had to step down.

What does the IPCC’s Fourth Assessment Report (AR4 2007) say about solar motion?

Nothing at all. They are allergic to SIM. Their whole research fails to consider the solar-terrestrial phenomena (solar, geomagnetic, volcanic activity etc.) and they take into account only temperatures since 1860. However in Europe we have a number of continuous instrumental temperature data sets dating back to mid 18th century. The Jesuits started the measurements. With my colleague we processed these data and we showed their relation to solar motion and published an article on it in the Climatic Change journal, Stanford University. In mid 18th century the temperature was as high as in 1940 (both in the middle of a trefoil). But was there any industry, air pollution? No. They even fail to take into account the climate reconstructions (temperatures, proxy data) derived from tree-ring width 18O or 10Be isotopes in ice cores etc., though they are already available for periods deep in the past and are of good quality at least for the Holocene period.

But how do they explain why every 180 years there is a long-term temperature maximum? How do they explain the significant temperature maximum around 1000 AD, when even Greenland was settled? How do they explain the long-term minima?


They don’t. They pretend it did not happen.

Explaining climate change by other factors, not only by greenhouse gases, it is almost a heresy in our times. Were you aware of this when you discovered the trefoils of yours?

In 1987 when I realised there are trefoils in the solar motion (note: there are trefoil symbols in the gothic cathedrals too), I shivered. I realised immediately, that it is connected with almost everything, that nobody was going to do the work unless I do and that I would have to face unbelievable enmities. I raised my hands to the sky and I almost cried: “Why me?!” On top of that, it was exactly 300 years after Sir Isaac Newton, in his PRINCIPIA, formulated his intuitive conclusion about solar motion.

You are from a Christian family. Did you face any persecution under the communist regime?

My maiden name is Kryšpínová. The brother of my grandfather, a school headmaster, was a famous constructor of steam locomotives and he even became a director of the ČKD company. Unfortunately, we lived in the same house as the family of powerful communist bureaucrats. The mother of Vasil Mohorita was an influential Communist Party secretary in Prague 7. When I was finishing my elementary school, she rang a bell in our place and she yelled at me that a relative of the bourgeoisie ČKD director would never be allowed to study at any secondary school! Times changed, today my uncle Vojta is in the textbooks of the Transport Faculty of the Prague Technical University (ČVUT) as a constructor of world fame. He even has a street named after him, he has his stamps etc.

How did you solve it?

My uncle Vojta advised my parents to send me to the other grandparents to Jilemnice, at the foot of the Krkonoše Mountains. My grandfather was an engraver who printed cloths, almost worker class, so we though this might be acceptable to the communists. It worked, I even had the support of the grammar school headmaster in advance. It was a fine school. It had great teachers, including some scientists who were expelled there from universities for political reasons. This school was established as early as in 1909 when my country was part of the Austrian Empire and it was one of the few secondary schools where lectures were in the Czech language. Many Czech artists studied there such as the song writer Jiří Šlitr, actor Stanislav Zindulka, photograph Zdenko Fejfar or the director Karel Palouš. It is unbelievable, that now some madman wants to close this great school. Only Hitler was so insolent to do that. There are protests, demonstrations, so far in vain.

Yet the communist regime let you study at a university

I went to ČVUT (Czech Technical College), the Faculty of Civil Engineering, since my father was a civil engineer. The communists did not censor technical fields so much. I did not enjoy the first grades much, meliorations, road construction, surveyor work, but in the higher grades we could specialise – higher maths, (early) computers, cartography and others. I chose astronomy. In the building of the old Technical College at Karlovo Square, the magnificent Prof. Emil Buchar chaired the “Institute for Astronomy and Elementary Geophysics”. He always took only a couple of students. I was the first woman among them. This autumn it is the 110th anniversary of his birth.

You work at the Geophysical Institute of the Czech Academy of Sciences. How did you get here?

The end of my studies was coming soon, when suddenly one day, late at night, the telephone rang. Prof Buchar called that the next day I was to go to the Geophysical Institute at 9 AM for an interview. He informed me he had already registered me. So I went there and I passed. I have been working here ever since.

Aren’t you sorry that after 20 years SIM is still not in the elementary school textbooks? That climate changes are still explained only by CO2, as if climate was influenced by no other factors whatsoever?

Publishing of my (our) articles has always been a bad dream. Some editors rejected our article without review, saying their readers would surely not be interested. Another editor told me, that they would not allow having anything about SIM published in their magazine! I even received a “peer review” consisting of a single sentence: “All articles about solar motion should be banned!” In spite of all these enmities, we succeeded to have articles about SIM and ST-relationship published in renowned world journals with high impact factor (e.g. New Astronomy (Harvard University, IF 2.2), Surveys in Geophysics (IF 3.1) or Climatic Change (Stanford University, IF 4.)

And my results are in the prestigious textbook of physics for American universities – “Fundamentals of Physics“.

What welcome did solar motion research get among the scientists in your country?

The enlightened ones, and they are many, support it and help me a lot. The others use this topic for target practice. I was sorry to hear dr. Grygar, Czech astronomer and member of the Czech branch of CSI, compares SIM to some astrology. I wonder when he will grow tired of doing that. And our climatologists? I represent our institute in the Czech National Climate Programme. These people “research” only greenhouse effect vs temperatures. I call them “heaters”. Sometimes I feel like a lone Hussite warrior – myself against all. They deny the existence of solar influence on climate let alone the influence of the whole solar system. Most of them refuse to talk to me, most of them even do not say hello, when we meet. Even now when many world journals publish articles about the influence of the Sun on climate. Probably this requires more time. Many discoveries had to wait, some very long. I do not waste my time fighting windmills. God will sort it out when the right time comes.

And what about the Czech media? What is their attitude to solar motion? Has there been any documentaries on TV about this?

Some two years ago people from the ČT2 television channel came to me and we filmed a half an hour interview for some TV magazine. I was sceptical. Will you really broadcast it? Sure, it’s already in the TV Guide. And then, some 2 hours before the broadcast, some powerful person called them and banned the broadcast.

My only media “presentation” was when I was invited to an entertainment TV contest on the PRIMA TV channel (The “Guess Who I Am” programme). It was fun and I used the opportunity to sneak a short description of the trefoils and solar motion into my speech.

But your work is known and cited abroad

It is. I am very cited in both Americas, Canada, I am cited by the Germans, Italians, Australians, Scandinavians, recently even by the Chinese. I am cited even in other fields of study, for instance in the journals Nuclear Physics, Neutron Repulsion Journal ... In 2009 as part of the European Geophysical Union congress there was a Great Panel on Sun and Climate. I had an invited talk there. And I had another invited talk at the meeting of the American Geophysical Union in Brazil 2010.

I hear you are cited also by the scientists who study exoplanets? How is it related?

Yes, I am cited by the Germans, the astronomers from the Heidelberg University. I suggested that we might expect barycentric motion in the stars, which manifest variable irradiance. Which means such stars probably have planets. I wrote this for CTS (Centre of Theoretical Studies) in year 1995, when no exoplanet was known yet. Now we know over 400 of them.



Figure 2 No, these are not jewel designs. These are four examples of barycentric path of stars with exoplanets (from Perryman and Schulze-Hartung, Astronomy& Astrophysics 525, A65, 2011).

Is there any message you would like to send to the readers?

When you fight for a good cause, you must never give up. I am from a family of keen followers of the Scouting traditions. My father was a founding member of the 5th Group of Water Scouts in my country. As a Boy Scout he had the honour to welcome our first president, the founder of the first independent Czechoslovak Republic, when T.G. Masaryk was returning from emigration. Thanks to his resilience my father succeeded with many things in spite of the communists. And I have a personal example too. To keep sane during the communist era I privately translated the great Russian poet Anna Akhmatova. My translations could be published only after the end of the communist regime, on the 100th anniversary of her birth (Modrý večer, ODEON, 1990, translated by Ivanka Jakubcová). Ms Anna had a difficult life. In the Stalinist era she was persecuted, she could not publish her poetry for decades, her son was imprisoned in Gulag for almost 20 years. But look now - her poetry is read by the whole world.

Interviewed by
Mgr. Vítězslav Kremlík, the founder of the Czech Climate Skeptic website www.klimaskeptik.cz

(The Czech text was authorised by ICH)

Profile:

born 3. 12. 1941 in Jilemnice, Czechoslovakia

education: ČVUT, Faculty of Civil Engineering, subject: geodetic astronomy and geophysics               

doctorate: CSc. 1991

current position: Geophysical Institute of the Czech Academy of Sciences since 1963 (Institute website - link)

List of publications
(note: some of the publications are downloadable from Klimaskeptik.cz - link)

Bucha, V., Jakubcová, I. and Pick, M. 1985 Resonance frequencies in the Sun’s motion, Studia Geophys. et Geod., 29, 107-111.

Jakubcová, I. and Pick, M., 1986a The planetary system and solar-terrestrial phenomena, Studia Geophys. et Geod., 30, 224-235.

Jakubcová, I. and Pick, M., 1986b Is there any relation between the Sun´s motion and global seismic activity? Studia Geophys. et Geod., 30, 148-152.

Jakubcová, I. and Pick, M.: 1987 Correlation between solar motion, earthquakes and other geophysical phenomena, Annales Geophysicae, B, 135-142.

Charvátová-Jakubcová, I., Křivský, L. and Střeštík, J., 1988 The periodicity of aurorae in the years 1001-1900, Studia Geophys. et Geod., 32, 70-77.

Charvátová, I., 1988 The solar motion and the variability of solar activity, Adv. Space Res., 8, 7, 147-150.

Charvátová, I. 1989 On the relation between solar motion and the long term variability of solar activity, Studia Geophys. et Geod. 33, 230-241.

Charvátová, I., 1990a The relations between solar motion and solar variability, Bull. Astr. Inst. Czech., 41, 56-59.

Charvátová, I., 1990b On the relation between solar motion and solar activity in the years 1730-1780 and 1910-60, Bull. Astr. Inst. Czech., 41, 200-204.

Charvátová, I., 1995a Solar-terrestrial and climatic variability during the last several millennia in relation to solar inertial motion, J. Coastal Res., 17, 343-354.

Charvátová, I., 1995b Solar-terrestrial variability in relation to solar inertial motion, Center for Theoretical Study, CTS-95-04, March 1995.

Charvátová, I., 1995c Solar-terrestrial variability in relation to solar inertial motion, Center for Theoretical Study, CTS-95-08, 2nd Edition, November 1995.

Charvátová, I., 1997a Solar-terrestrial and climatic phenomena in relation to solar inertial motion, Surveys in Geophys., 18, 131-146.

Charvátová, I., 1997b Solar motion (main article), in: Encyclopedia of Planetary Sciences, (Eds. J.H. Shirley and R.W. Fairbridge), Chapman & Hall, New York, 748-751.

Charvátová, I., 2006 Solar motion (main article), in: Encyclopedia of Planetary Sciences, (Eds. J.H. Shirley and R.W. Fairbridge), Springer, Berlin, 748-751.

Charvátová, I., 2000 Can origin of the 2400-year cycle of solar activity be caused by solar inertial motion?, Annales Geophysicae, 18, 399-405.

Charvátová, I., 2000 The cycle of 2402 years in solar motion and its response in proxy records, Geolines, 11, 12-14.

Charvátová, I., 2007 The prominent 1.6-year periodicity in solar motion due to the inner planets, Annales Geophysicae, 25, 1-6.

Charvátová, I., 2009 Long-trm predictive assessments of solar and geomagnetic activities made on the basis of the close similarity between the solar inertial motions in the intervals 1840-1905 and 1980-2045, New Astronomy 14, 25-30, doi: 10.1016/j.newast.2008.04.005.

Charvátová, I. and Střeštík, J., 1991 Solar variability as a manifestation of the Sun’s motion, J. Atmos.Terr. Phys., 53, 1019-1025.

Charvátová, I. and Střeštík, J., 1995 Long-term changes of the surface air temperature in relation to solar inertial motion, Climatic Change, 29, 333-352.

Charvátová, I. and Střeštík, J., 2004 Periodicities between 6 and 16 years in surface air temperature in possible relation to solar inertial motion, J. Atmos. Solar-Terr. Phys., 66, 219-227

Charvátová, I. and Střeštík, J., 2007 Relations between the solar inertial motion, solar activity and geomagnetic index aa since the year 1844, Adv. Space Res., 40, 7, 1026-1031, doi: 10.1016/j.asr.2007.05.086.

Paluš, M., Kurths, J., Schwarz, U., Novotná, D. and Charvátová, I., 2000 Is the solar activity cycle synchronized with the solar inertial motion?, Int. J. Bifurcation and Chaos, 10, 2519-2526.

Paluš, M., Kurths, J., Schwarz, U., Seehafer, N., Novotná, D. and Charvátová, I., 2007 The solar activity cycle is weakly synchronized with the solar inertial motion, Physics Letters A, 365, 421-428, doi: 10.1016/j.physleta.2007.01.039.

Charvátová, I., Klokočník, J., Kolmaš, J. and Kostelecký, J., 2011 Chinese tombs oriented by a compass: evidence from paleomagnetic changes versus the age of tombs, Studia Geophys. et Geod. 55, 159-174.

Sidney Coleman's QFT lectures: TeX, PDF

E-mail from Bryan Chen

Dear Lubos,

It's been a few years since I wrote you. I thought you might be interested that the LaTeXing of Coleman's notes has had quite a bit of recent progress.  Indeed, the project was more or less stalled in 2008, until last year, when Ting Yuan Sen (a student at National University of Singapore and Ecole Polytechnique) began writing me that he was continuing the typesetting. Indeed, within a few months, he finished all the rest of the lectures!

Earlier this week, I wrote Brian Hill (who originally wrote the handwritten version), and at my request, he gladly contributed a short preface to the project, giving a bit of context to the notes, and I've compiled it with all the lectures into one 338 page PDF file.




The files are in the same place they've always been.  There are various readmes in that directory as well, saying basically the same things as this email:

www.physics.upenn.edu/~chb/phys253a/coleman

Here're the links to some specific files:

The PDF of the full notes (338 pages, Google Docs Viewer):

www.physics.upenn.edu/~chb/
phys253a/coleman/coleman.pdf

A convenient ZIP file containing the source files:

www.physics.upenn.edu/
~chb/phys253a/coleman/
coleman_latex_
source_20110314.zip

The TeX project should surely be improved with (at least) two more things, which I don't have the energy for:

1. The formatting between lectures is rather inconsistent, especially with regard to "section" headings and the like.
2. The lectures would benefit greatly from an index.

I'd appreciate it if you might spread the word on your blog!

Best,
Bryan

---

P.S. (by LM): Just to be complete, videos from the lectures are available at Harvard:

Physics 253: Quantum Field Theory: Lectures by Sidney R. Coleman

They cover both semesters, 253a and 253b, and were recorded in 1975-1976.

Vít Klemeš (1932-2010)

Guest post by Demetris Koutsoyiannis

It is a year since Vít Klemeš is no longer with us. He took “residence on cloud no. 17” as he used to say.



Vít Klemeš (left), laurelled by local admirers in the Greek island of Cephalonia in June 2005, with the humble writer of this guest post

Vít Klemeš was one of the world’s greatest hydrologists, as recognized, inter alia, by his awarding with the International Hydrology Prize (1994) (jointly awarded by the International Association of Hydrological Sciences (IAHS), the United Nations Educational Scientific and Cultural Organization (UNESCO) and the World Meteorological Organization (WMO)) and his election as President of the IAHS (1987–1991). He was born in Moravia and educated in what used to be Czechoslovakia (Brno, Bratislava, Prague). Following the Soviet-led invasion of Czechoslovakia, Vít and his family moved to Canada in September 1968, where he worked and lived until his death in 8 March 2010.

Vít’s involvement in science went far beyond hydrology. He had an informed opinion about broad scientific and philosophical issues. In addition to being a scientist and engineer, Vít was a conscious and active citizen of the world, having strong positions on all contemporary political, societal, economic and even religious affairs and problems. His recent book, entitled “An Imperfect Fit: Advanced Democracy and Human Nature”, is one of the testimonies of his activity of this type. Vít Klemeš was an unusual and unorthodox personality resembling more an ancient philosopher than a specialized modern scientist.

Some of his works were recently published collectively in a book with the manifest title “Common Sense and Other Heresies”. I have written the “Prolegomena” of the new edition of this book, jointly published by the Canadian Water Resources Association and International Association of Hydrological Sciences. There I have tried to provide a synopsis of his work and personality. Here I will let him speak providing a few quotations.



The cover of the new edition of his book, which has just gone to print

From his paper “Dilettantism in hydrology: transition or destiny?”; though he refers to hydrology, I think his thought applies to contemporary science in general:

The identification of misconceptions [common in contemporary hydrology] did not make them vanish, nor did it prevent emergence of others, nor did the revelation of their consequences have a strong retarding effect on their proliferation. Fighting them has been as difficult and frustrating as combating the legendary Hydra: as soon as one of its heads is struck off, two shoot up in its place.

From his last talk, entitled “Political pressures in water resources management: Do they influence predictions?”, which he gave in the International Interdisciplinary Conference on Predictions for Hydrology, Ecology, and Water Resources Management (Prague, 2008):

[P]olitical pressures often set the agenda for what is to be (or not to be) predicted, and sometimes even try to impose the prediction result thus transforming prediction into prescription.




...

Well, how anybody in his right mind could propose wasting precious resources on such petty things when political pressures command their use for the noble cause of saving the planet from Climate Change? But, could it not be that the present climate-change-impact models and all sorts of Al-Gore-ithms aimed at helping this noble cause will repeat the history of the noble causes of the past, like the previously mentioned environmental quality models or the ill-fated ‘socialist model’ meant to save the planet by imposing a ‘climate change’ on the social fabric itself?

From his book “Imperfect Fit”:

The more the reality diverges from the way prescribed by the ideology, the more ruthlessly it is forced in the prescribed channels and the more brutal are the means by which the noble ends are pursued.

From his presentation entitled “An unorthodox physically-based stochastic treatment of tree rings” at the XXIV General Assembly of the International Union of Geodesy and Geophysics (Perugia, 2007), which is perhaps the best testimony of his heretic humour—and certainly deserves a close look:

The most fun and perhaps the greatest value of doing something is in doing it. The results may well go up in smoke, be wrong, become obsolete and forgotten, but some new ideas may have emerged in pursuing them, and some of them may somewhere, sometime, bear fruit.

The last one is his anecdotal response to the Canadian Geophysical Union’s (CGU) request to sign the Climate Change letter, which on the occasion of 2009 Copenhagen Conference was addressed to the Government and Parliament of Canada. The letter begins as “At the Copenhagen Conference of the Parties to the UN Framework Convention on Climate Change, the eyes of the world will be on Canada. We, the leaders of the following Canadian scientific societies, urge the Government to negotiate an outcome that will rapidly and adequately address climate change.” Vít emailed me his reply and, since it bears his signature, I felt that I have his consent from “cloud 17” to make it public:

November 20th, 2009

My answer is NO

Reasons:

The Draft reads like a document prepared by an alarmist pressure group, not by a scientific institution.

First of all, the introductory statement is rather arrogant in its exaggeration of Canada's importance in the world. Such self promotion can only hurt Canada's image.

The term 'climate change' is a misleading popular slogan. Climate has never been stable but has been, and will continue to be, changing, regardless of human interventions. The issue is the rising temperature as is after all obvious from the second paragraph where all the effects listed refer to temperature rise. The first sentence of the second paragraph should thus be reformulated accordingly. Moreover, "Some current and anticipated impacts..." would be a more honest statement.

The statement "...that greenhouse gases resulting from human activities have contributed to the warming of the atmosphere..." is trivial – even Suzuki's and Al Gore's farts "contribute" to it. No "rigorous international research" is needed to establish this. The issue is that human contribution has not yet been rigorously quantified and, until it is, nobody can tell how "serious risk" it represents. It is the quantification of the various effects where rigorous research is needed and where Canada could perhaps make some contribution.

The statement "Human activities must be optimized to significantly reduce emissions..." is logically inconsistent. One cannot prejudge that "optimization" of human activities (whatever that is) will necessarily require a "significant" reduction of emissions. Given the finite resources, "optimization" must balance the economy with the management not only of CO2 emissions but of other environmental pollutants such as, for instance, toxic substances released into soil, water and atmosphere. To concentrate solely on CO2 reduction hardly qualifies for "optimization" and "responsibility".

The exhortation "We must act now" is cheap unless accompanied with responsible proposals and priorities for action. And this is what Copenhagen should be about! Your exhortation implies that the participants would not know this unless reminded by your outcry.

Sincerely yours,
Vit Klemes

Four reasons why I like string theory (guest blog)

Guest blog by Phil Gibbs

It is exactly one year since I started this blog, so to celebrate I will give my four top reasons for liking string theory.

This is partly a response to a recent survey on Cosmic Variance which included a question about what likelihood people gave to string theory being correct. With about 170 people responding, about half of them gave string theory 10% or less, many said 1% or even 0%. Now, science isn’t settled by democratic votes especially by a random sample of commenters on one particular blog. Nevertheless it is a revealing outcome and there are plenty of other physicists who think the same. The reasons people gave were roughly along the lines of “It has not had any experimental success after a long time” or “it is unfalsifiable”. I dont agree that these are real issues but instead of talking about that I want to review why I think it is still a theory worthy of being excited about.




(1) My top reason for thinking that string theory is a correct approach to unifying physics is that it provides a consistent perturbative description of particle physics with the inclusion of gravitons, and there is no known alternative. Gravity is a very weak force and spacetime is nearly flat on small scales. There must be some perturbative description of the quantized interaction of particles with gravity as a series of approximations. A direct quantisation of GR cannot do this, but string theory can.

Furthermore it achieves this in a way that did not have to work, but it does because of surprising cancellations. There are five consistent string theories in 10 dimensions which are all related by non-perturbative dualities. The reductions to 4 spacetime dimensions is a consistent process which is now reasonably well understood, except we dont know the correct compactification manifold. The only alternative way to get a consistent perturbative theory is possibly from supergravity, but by now we understand that supergravity too is just another limiting case of string theory. Some physicists have suggested that there may be a chance of finding other non-perturbative solutions to the quantum gravity problem, but no complete solution of that type has been found yet. Until it has, this reason alone is a very strong indication that string theory is on the right path.

(2) Supersymmetry! There are many ways that string theory can reduce to low energy particle physics and not all of them would result in observable supersymmetry. On the other hand, supersymmetry is a natural byproduct of string theory and if it does exist in nature at scales currently being probed by the LHC then it can explain several mysteries. These include the hierarchy problem, dark matter, a light Higgs and the convergence of the running coupling constants at the GUT scale where SUSY says they all have a value of around 1/24. In the last few weeks we have seen the exclusion limits for SUSY greatly extended by CMS and ATLAS. They say that if you throw a frog into hot water it will quickly jump out, but if you put it in cold water and gradually heat the water up it will stay there until it is boiled to death. You should not try this experiment at home but it seems like nature is trying it on physicists who like supersymmetry. In the 1980s we thought that supersymmetric partners would have light masses to avoid fine tuning. If this was right they would have been seen at LEP or the Tevatron. Now the LHC has pushed the minimum masses to uncomfortably high values implying quite a lot of fine tuning. The water is heating up but we will stay put because we now know that the multiverse allows for such fine tuning provided it is in the best interests of our existence. Perhaps the higher masses were needed to allow dark matter to form galaxies or some such.

(3) My third best reason for supporting string theory is that it provides a solution to the black hole information paradox via the holographic principle. This is a much more theoretical argument but it is still quite convincing, I find. Although there may never be any evidence for Hawking radiation from black holes, we know theoretically that it has to be there. Some reasoning using semiclassical quantum gravity tells us the laws of entropy for a black hole, and this should remain correct for any complete theory of quantum gravity such as string theory. Further arguments also tell us that the rules of thermodynamics must obey a holographic principle to avoid the paradox of thermodynamic information being lost inside a black hole. Again, any theory of quantum gravity worth its salt has to comply. It is therefore a triumph for string theory that the AdS/CFT correspondence shows that string theory does (or can) realize the holographic principle. It is another indication that string theory is on the right track.

(4) My final reason for liking string theory is that it comes with a multiverse. For some people this is the favourite reason for not liking string theory and my reasoning for thinking otherwise is partly philosophical, so only people with similar philosophical leanings will agree with me. Ten years ago I did not favour anthropic reasoning. That was because the anthropic principle requires a range of theories that the universe can choose from so that one customised for intelligent life can be selected. I am comfortable with the platonic view that all mathematically consistent universes exist and we just inhabit some part of that realm, but in order to explain the symmetries that govern the laws of physics I think you need to invoke a further principle. For me that principle is universality in the sense of universal behavior seen in complex dynamical systems such as those seen in critical phenomena. I think there is a universal behavior of some type in the realm of complex mathematical systems which overwealms all other possible laws of physics so that only one unique possibility complete with all its beautiful symmetries can be what we experience. You can see that this does not fit well with the anthropic principle. However, there are good indications that the laws of physics are somehow selected to promote intelligent life in a way that would not be consistent with a single unique set of physical laws, contradiction! Luckily the multiverse comes to the rescue in the form of the string landscape. It turns out that string theory does indeed follow from some unique over-arching M-theory, but it can be realized in many forms in lower dimensions by a choice of vacuum determined by the compactification manifold. A wide range of these vacua are stable and there could be as many as 10^500 of them, plenty enough to account for anthropic reasoning. In my view it is the perfect outcome.

So those are my four best reasons for liking string theory. This does not mean that I don’t value other approaches to quantum gravity. We still need to find its complete non-perturbative formulation andIi am sure that such a thing must exist even if string theory has nothing to do with the laws of physics. Other theories such as Loop Quantum Gravity, Non-Cummutative Geometry or Group Field Theory lead to rich mathematical concepts. I see this as a sign that they are telling us something about our world, but I think you have to look for what it says about possibilities for non-perturbative string theory. For example, Loop Quantum Gravity tells us that knot polynomials and spin networks should be important. I like the fact that recently Witten has explored implications of high dimensional generalisation of the knot polynomials (Khovanov homology) to branes from M-theory. This is the kind of outcome I expect from alternative approaches.

So what of the problems people say are issues for string theory? I see the multiverse landscape as an asset, not a problem. It means that string theory cannot tell us much about low energy physics so we will have to look for Planck scale effects instead. Such predicted effects may not be known until the non-perturbative side of string theory is understood, and after that it may be a long time before technology allows us to test them. That I am afraid is the nature of the game. We have no automatic right to expect nature to be kind to us and provide an easy test of any theory of quantum gravity. We are suddenly in a position where almost anything we can observe seems to be covered by the standard model + general relativity so it should be no surprise that testing string theory is very difficult. Any other theory of quantum gravity is likely to have the same problem.

Adventures in self-publishing an e-book novel

Guest post by Ann Houston

I'm a newbie to writing fiction. Having just completed my novel, Blind Tasting, six months ago, I immediately began pursuing traditional publication channels. I researched potential literary agents (ones who represented books in my genre) and I tailored query letters to those agents, steeling myself psychologically to receive dozens, maybe hundreds, of rejections in the hope of getting one or two offers of representation. I created a database of agencies and publishers and sent my email and snail mail query letters along with synopses and sample chapters -- according to each agent's preference. I was prepared to wait, hearing that it often took weeks, months, for agents to reply, given the volume of unsolicited work they receive.

A week after sending off the first batch of queries I came across Smashwords, a recent online self-publishing service. I had been warned by those in the literary know to shun 'vanity presses' as exploitive dead-ends, but Smashwords didn't come across as a vanity press. Smashwords was inviting authors to retain most of the royalties for their self-published e-books and they were offering access to big e-book distributors (Sony, Apple, Barnes & Noble, Amazon (pending)). Acceptable works for self-publication included both long and short pieces, fiction and non-fiction covering most genres. Mark Coker, who founded Smashwords, sees huge potential for self-publishing digital material at this point in time, given the available reading platforms now in existence. Writers don't need the bankroll and the typesetting machinery to get their works to potential readers any longer, and thus they also don't need agents and traditional publishing houses. These professions are playing a smaller role as gatekeepers in deciding what the public gets to read. (Smashwords has published over 900,000,000 words to date, which is more than 12,000 titles of average 75,000 words in length. It's actually a much larger set of titles, because many works are short pieces.)

I then had an epiphany about my own novel: in the best-case scenario, (not to be counted on) my title would not appear in print via a traditional publisher for at least 24 months. Assuming an agent liked it, they would have to shop it to editors at publishing houses, which would add more months, and assuming someone bought it, the time to publication and distribution to retail bookstores would be more months. My novel is set in an ultra-contemporary time and place, and I worried that part of its intended appeal had an expiration date. In two years it might not create the same impression I was hoping for now.




Then and there I decided to go with Smashwords. It was a very smart and gratifying decision. It was also not without some hair-tearing and time commitment. For authors considering self-publishing, let me point out the major highlights of this experience in the hopes it will help your own effort be productive and successful. By the way, a month ago Amazon announced that, for the first time, it sold more e-books online than print books for a given reporting period -- 140 e-book units to 100 print-book units.

1) The most important point is that self-publishing technology is changing rapidly; in the five months I've been exposed to it things have changed in non-trivial ways, and they will likely keep changing. Changes are occurring in a) who the providers of self-publishing are, b) the distribution channels available to different self-publishing services, c) the input formats allowed for conversion to e-book outputs, d) the reading devices available for e-books, e) the style guides to follow when formatting your e-book for a given service, f) the royalties, pricing and copy-protection options available to authors, and g) the quality of available format-conversion programs and viewers.

2) The industry appears to be converging on one standard, ePub (Apple, Sony, and Barnes & Noble use this format), but Amazon (a huge player) uses mobi, and there are others. The most important point to remember about formatting an e-book is to forget about pages and think of a continuous flow of text whose appearance to some extent (font size, font styles) is under the control of the reader. Keeping your input formatting as simple as possible will result in fewer headaches and fewer surprises in how the output looks. This constraint poses more challenges for authors with technical books containing tables and charts; it's not so difficult for fiction writers. Style guides and user forums for e-book formatting are uneven in quality and coverage, but hopefully will improve in the future. If you are a computer-oriented geek, you may be used to online forums that provide clear and useful questions and answers; fiction writers as a group aren't as technically savvy and, unfortunately, there are a lot of confusing questions and answers posted on forums and websites, regarding specific formatting details and bug reports for various devices. You may have to sift through a lot to find useful information. Smashwords does provide a free on-line Style Guide which is quite helpful in understanding how to avoid ugly output and succeed in achieving attractive output for their conversion process. Smashwords accepts only Word docs as input format, and produces a variety of outputs, including ePub and mobi, PDF, html and others via their master converter -- which is named the Meatgrinder. (Boy, that name gave me pause :-) ) I found formatting for Amazon's Digital Text Platform more confusing -- Amazon has put a lot of effort into helping the big publishing houses get their authors' titles converted to e-books, and doesn't provide as much information to self-published authors. They do respond nicely to your email questions, however. I wanted exposure on Amazon and didn't want to wait for Smashwords 'pending approval' there. (Smashwords does not restrict you from pursuing any other publishing venues, by the way.) MobiPocket and Calibre are free programs that will help authors convert their input document into suitable mobi output for Amazon. I prefer Calibre, probably because it runs on the Mac as well as PC (MobiPocket is only for PC).

3) The effort required to market a self-published work cannot be over-emphasized. I completely neglected marketing efforts of my novel prior to publishing it -- a big mistake according to the e-book marketing gurus. If you want to make a splash when the book goes public, you must already have laid publicity groundwork. Social media can provide efficient ways to market the work: write a blog, have a presence on Twitter and Facebook and link your author profile to these and other similar social media sites. What e-books need most, however, are reviews -- word-of-mouth is what sells books, and nowadays, online reader reviews (e.g., reviews on Amazon) are what creates buzz for an e-book, or printed book, for that matter. Authors of e-books need to find their piece of the 'long tail'; in traditional publishing I read that 7 percent of the titles account for 93 percent of the sales, and 85 percent of all titles never sell more than 1000 copies. There are only a very few super hits. Most authors need to find their niche -- it's probably easier now than ever to do this, via social media and all the resources the Internet makes available, but it does take time and energy. Authors of e-books must be prepared to put in some hours to help potentially interested readers find their works. But, it's pretty exciting to see your book's cover appear at a major distribution site like Amazon, Apple or Barnes & Noble, and see a review, and that you have actually sold copies of your work! I was deep into this process, and about to upload a revised version of the novel, when I finally received replies to my first batch of queries to literary agents. They were all rejections, all nicely worded and they all encouraged me to continue to seek representation out there in literary-agent land. But, they came to me months after I'd sent them, and served as a vivid reminder of how slow old publishing moves compared to digital self-publishing.

-A.C. Houston
~ author of Blind Tasting ~

http://www.blindtastingthenovel.com
http://wordtravelstheblog.com

---

(Thanks, Ann! The URLs and images added by L.M. - Ann is too modest to include them herself.)

Samir Mathur: comments on fuzzballs

The author, Prof Samir Mathur, is a physicist at Ohio State University

The information paradox arises if we assume that the effects of quantum gravity extend only over Planck distances. String theory, as a complete theory of quantum gravity, must offer us a way out of this paradox. The way it does this is that string theory states "puff up" in proportion to the number of quanta they carry, changing the notion that there is no information stored near the horizon.

There have been some comments on this blog regarding the classical / quantum nature of microstates. Here are my brief comments on the issue; for more details one can look at the reviews hep-th/0502050 or hep-th/0510180. More details on the nature of states etc can be found for example in hep-th/0607222, hep-th/0609154.

The simplest model is the 2-charge extremal hole. We can dualize the charges to NS1-P; that is, a string carrying momentum. The total winding and momentum are taken large, so that we can match the entropy to the Bekenstein-Wald classical value.




The entropy arises from the way the momentum can be partitioned among harmonics. Let us first look at some special (i.e. non-generic) states. The simplest possibility is to put all the momentum into a large number of units N of the lowest harmonic. Recall that each Fourier mode of vibration is a harmonic oscillator. Thus the lowest frequency oscillator is in the state /N>. Since N is large we expect some classicality. To get classical motion we can replace /N> by a suitable superposition of states ... /N-10>, /N-9>, ... /N+10> ... This makes a coherent state, which gives a classical "pendulum motion" to the oscillator. The string then carries a helical wave, with a small quantum spread (order 1/N) around the helical profile. The generated metric will also be close to classical, with a small ~1/N order spread from quantum fluctuations.

We already see a key feature: the transverse oscillations of the string give it a transverse size that grows with N. Dualizing to D1-D5, the geometry has a "throat", but instead of ending at a point-like singularity, it ends in a locally AdS3 "cap".

Now let us split our energy among, say, five different harmonics. This gives more complicated string profiles, but also note that since the occupation number N of each mode is smaller, the quantum fluctuations are slightly larger. But since N was big to start with, we can still think of a family of classical string profiles.

The generic state of the string is given by a thermal distribution of vibrations. The occupation number for harmonic k is

• n(k) ~ 1 / [ exp(k / sqrt N)-1]
  

There are ~sqrt(N) different Fourier modes excited. The average harmonic order of the modes is ~sqrt(N). The "occupation number" of each Fourier mode oscillator is now ~1, so it is not helpful to try to make a coherent state. So we will not describe the state by a string profile, but just say that the transverse vibrations generate a largish "fuzzball". (The term fuzzball is supposed to signify that the generic state is very "quantum fuzzy".)

How big is this fuzzball? We are given a total energy of excitation. One finds that the transverse size of the state depends on the mean harmonic number that is excited, while the fluctuations depend on the occupation number of the typical mode. So to estimate the size of the generic state we take the wavenumber k=sqrt(N) and put all our energy in it - this gives an occupation number sqrt(N) >> 1 so we can use the classical profile description. One then finds a size that is just the order of the horizon radius of the 2-charge hole, so fuzzballs are horizon-sized objects. Now imagine splitting the energy into more modes, still with sqrt(N) as the mean. The size remains the same, while the fluctuations grow larger. Finally, we reach the generic state where the size is as computed, but fluctuations are O(1).

I would expect that this general idea remains true for 3 and 4 charge systems ... special states can be classical and help us to understand the behavior of generic states; the generic states themselves are very quantum "fuzzballs". Iosif Bena has talked of a "strong form" of the general conjecture where the situation is as above for 2-charge, but the states become much more classical for 3-charge. I do not understand these arguments well, so I will take my conservative view that for all cases the generic states are very quantum string-theoretic objects.

The work of Bena-Warner has shown that large families of 3-charge objects can be made by having different arrangements of "dipole charges". These can be reduced to 4-D by a method of Bena-Kraus, and Balasubramanian-Gimon-Levi have obtained large families of four-dimensional solutions with different locations of poles containing different possible dipole charges. The simplest cases have just two poles, but as we go to a limit where the numbers of these poles becomes large I would expect that quantum effects set in - stringy degrees of freedom get excited between the charges at the poles, and all we can say is that we have a very "quantum fuzzball". For the non-BPS hole one would use brane-antibranes degrees of freedom, which will generically give a very quantum state, too.

(Gautam Mandal commented that a similar thing happens in LLM: when all the fermions are in their lowest state we can write a classical geometry, but for a general state of the fermions we will get large fluctuations.)

Thus the important point of the fuzzball proposal is that the size of the bound state is always large (horizon size) and not Planck size. Classical solutions are obtained for specially chosen microstates, but these help us understand the size of the generic state. The throats of extremal holes end in "fuzzy caps" rather than in a horizon, and this solves the information puzzle.

Tommy Anderberg: On a journal system failure

By Tommy Anderberg, the unique visitor #800,000

First of all, my thanks to Luboš Motl for his kind offer to host this text on the Reference Frame. Next, my apologies for the parts which you, the reader, may find either too trivial or too dense. Just skim the former, skip the latter (maybe returning to them later), and you'll be fine. As I am addressing a mixed audience, I'll consider it a success if everybody finds something different to complain about. - T.A.

Back to the future, Kantrowitz style

Unless you've been living under a rock lately, you know that NASA is going back to the moon in a big way. There is every reason to be excited about the reopening of the "high frontier", a term last heard in the 70s. While the past three decades have certainly seen great advances in the application of space technology to everyday life and science, most of that activity - and all of it involving humans - has been confined to low earth orbit. Mankind took a "giant step" back in the 60s, only to then retreat abruptly and stay put ever since. Why?




...

Unfortunately, due to a large size of the file (69kB) and formatting issues, you must click to see the rest of the essay. Thanks.

Technicality: I have temporarily suspended the background music because we now have about 50 visits per minute after a link was mentioned at instapundit.com and I don't want to overload the server where the music file is located.

On a theory of biology: two responses

If you're interested what other people interested in the essence of biology think about

• Mohammed AlQuraishi's essay,

you may want to look at the texts of

• André Brown,
• Razib from ScienceBlogs and many commenters.
• Bonus: Evolgen (yes, I know the difference between 2 and 3 but I don't want to break the links)
  

Needless to say, I didn't understand some technicalities of Mohammed's essay. Equally importantly, however, I think that he is right that a theoretical core of biology as a pure science - unmotivated by its applications in medicine and agriculture - should be developed and should strengthen, much like applied biology surely will.

Now, biology and its mechanisms are extremely important for our lives but they are not fundamental in the physical sense. This simply means that there must be several fundamental concepts in biology including evolution, genetics, and macromolecular dynamics that co-exist.



Razib correctly says that one can't find counterparts of electroweak and strong interactions in a four-chambered heart. There are just too many possible structures in biology that seem comparably important. While biologists won't ever need QCD for their work, by definition, I think that the biologists who are closer to the theory are expected to imagine genetics, evolutionary dynamics, as well as the processes at the molecular scale. Of course many of them do. ;-)

So far I was talking about biology as a pure science. But even in this context, it is of course extremely important not to get decoupled from reality. The degree to which biologists are theorists should form a quasi-continuum. In the zeroth approximation, there should be "real" theorists as well as "phenomenologists" and "experimenters" and the adjacent groups should always interact with each other. This spectrum always protects the theorists from losing their contact with reality, and it gives the experimenters inspiration and increases the chance that their work will lead to qualitatively new insights: it's protecting them from monotonic work without new ideas.

Razib says that the biologists would escape from the classroom once the first integral would be written on the blackboard. That's okay, the proposal is of course not to torture everyone. The proposal is to allow those who are not scared by the integral to approach the subject slightly differently.

André thinks that some of Mohammed's proposals are already reality and sketches the basic notions that, in his opinion, lie in the core of biology. He argues that a single theory of biology is not possible and the constant interplay between theory and experiments is partially fictitious in biology as well as many other fields. No doubt, I agree with that.

The theoretical foundation for all of chemistry and biology has been on the table since the late 1920s: it is called the multi-body Schrödinger equation. However, it is hard to deduce the consequences of this equation for more complex systems. Let me emphasize the word "hard": unlike Robert Laughlin, I really don't think that it is impossible. We have already discussed the tension between reductionism and leading condensed matter physicists on this blog.

If Prof. Laughlin thinks that the laws of superfluids - and the parameters - can never be calculated from the underlying Schrödinger equation, he can refine his argument and post it to hep-th as a falsification of the Standard Model because the Standard Model definitely claims otherwise. Prof. Laughlin thinks that the word "emergent" means that the processes can't be derived from deeper laws. I happen to think that "emergent" means, on the contrary, that these processes emerge i.e. can be derived by an application of the fundamental laws in a complex situation but they could also emerge from other fundamental laws.

More seriously, I think that some young theorists in the condensed matter physics - both hard as well as soft - should be encouraged to try to fill the gap between the underlying equations and the effective equations and notions that are used by the mainstream condensed matter physicists. It is wrong if all the physicists are being discouraged by an anti-reductionist ideology from looking at a body of knowledge that will definitely be established sometime in the future: it is just a matter of time.

Mohammed AlQuraishi: On a theory of biology

The previous article about theoretical biology was an interview with Franziska Michor. Below, you find a completely unedited article by Mohammed. The links to at least three reactions to the article below are listed here.

Thanks to Lubos for the opportunity to write on this blog. Naturally, many potential topics presented themselves, but I ultimately chose to write about the subject that is dearest to my heart, and that is the emerging hard science of biology. I said emerging because while biology as a scientific discipline has certainly existed for many decades, and in some sense centuries, it has only recently started acquiring status as a genuinely hard science. The next few paragraphs will concern themselves with the challenges and opportunities that face us today as biologists, as we embark on formulating a quantitative theoretical foundation for biology.

I will enumerate three main points, all of which represent both a challenge and an opportunity. The first will deal with a scientific challenge of a theoretical orientation, namely the lack of a theory for biology. The second with the sociological organization of biologists and biology departments at the leading research institutions. And the third will be part science, part sociology, having to do with the focus of current experimental methods and programs on biomedical research as opposed to basic biological research. The challenges are listed according to my own judgment of their importance.



First is the need to develop a unified theory and formalism for biology. No true theory of biology exists today. Instead, the field is characterized by a collection of disparate models, each concerned with a particular subset of the general biological space. Furthermore, each subfield employs its own set of formalisms, ones that are in some cases fundamentally incompatible with the formalisms used in other subfields. One such example that has received considerable attention in the past several years is the field of genetic regulatory networks, or GRNs. This class of problems deals with the regulatory relationships that exist between genes. The products of certain genes, known as transcription factors, are able to bind to the DNA molecules encoding other genes and regulate their production. Transcription factors that ‘turn off’ genes are known as inhibitors, and ones that ‘turn on’ genes are known as activators. Such relationships are typically encoded as graphs in the computer science sense, with nodes representing genes, and edges representing different types of relationships, for example inhibition or activation. Initial work in this field, such as that pioneered by Harley McAdams and Adam Arkin at Stanford and UC Berkeley, respectively, employed electrical circuits, modeled by ordinary differential equations, as the underlying formalism. More recent work, such as that by Eric Davidson at Caltech and Hamid Bolouri at the Institute for Systems Biology in Washington, makes extensive use of the sequence properties of the genes—specifically the presence and arrangement of DNA motifs, short sequences of nucleotides such as “AGGTA”, that can be used to predict whether a given transcription factor would bind or not, and the resulting logic of a given binding combination, for example if X and Y bind then activate, if X or Z binds then repress, etc. Yet, GRN models typically lack any grounding in the kinetics of the underlying enzymes, or the structural basis that determines how transcription factors bind to the DNA molecule. Thus, they are fundamentally ad hoc, and so cannot be used to predict the behavior of previously uncharacterized genes and transcription factors. Many other examples exist—biochemical networks make extensive use of kinetic data, also typically formulated as ODEs, but encode no spatial information. Protein folding models do make extensive use of spatial information, and are typically simulated using quantum mechanics-based molecular dynamic simulations or classical rigid-body dynamics. Yet the timescales at which such simulations are made make it entirely impractical, for the foreseeable future, to combine structural data with the other types of models mentioned. Other structural models, such as those used for the morphology of cells or even organisms, completely forgo continuous models and instead employ discrete formalisms, such as cellular automata. Integration in this instance becomes difficult due not only to the vastly different physical scales at which the phenomena is occurring, but also to differences in the very formalism that is representing said phenomena. The opportunity is clear: Develop a theoretical framework that can coherently combine all the aforementioned disparate models, along with an underlying mathematical formalism that can quantitatively and elegantly capture it. To address this problem one cannot rely on better ‘motif-finding’ algorithms for DNA sequences, or more accurate clustering methods for microarrays. The challenge is not building software to process biological data—it is to construct a theory of what biology is.

The second challenge that I will address is a sociological one. It can be summarized as follows: Experimentalists think theoreticians don’t do 'real work' because they’re sitting behind computers all day, and theoreticians think experimentalists are charming individuals whose work will ultimately be automated by robotics. Neither picture is true. What makes experimental work difficult is not performing the experiment, but the careful and thoughtful experimental design that is required to obtain the sought results. Nor is the difficulty of theoretical work merely writing software or solving equations, but the insight necessary to abstract from separate experiments a coherent quantitative picture of what is truly taking place. To address this problem, various institutions have attempted to bring biologists, computer scientists, physicists, and others to the same table and address the problem from their individual perspectives. At Stanford, where I am currently pursuing my graduate research, there is BioX. The University of California campuses at Berkeley, San Francisco, and Santa Cruz have QB3. And up in Washington there's the Institute for Systems Biology. On the east coast, Harvard recently opened a Systems Biology department, and MIT is now offering a Computational Systems Biology major. Alas, I think this approach alone will not solve the problem. Collaboration between different departments is a step in the right direction, but ultimately a new generation of scientists will need to be trained as quantitative biologists. Scientists who care about biology as a science, and who are expertly trained in mathematics and computer science, much like their physicists counterparts. Stated differently, we need one brain with two things in it, as opposed to two brains with one thing in each.

Moving away from sociological factors and half way back to science, the third challenge I would like to outline is an experimental one. Current experimental work, and biology as a whole, suffer from a serious problem—the perception that their existence is only justified as a tool for medicine. Biology is a science, with its own set of fundamental and basic objectives. To require biological research to forgo the foundations and focus on applications is bad for both. I will provide one example to illustrate this point. Significant resources are allocated to the model organisms closest to humans, namely mice and to some extent the fruit fly Drosophila melanogaster. Less is given to simpler eukaryotes like Yeast. And yet less to prokaryotes like Escherichia coli. But in view of the first challenge above, it is imperative that biologists work on as simple an organism as possible. Initial work in quantum mechanics solved the hydrogen atom, not ununoctium. Stated differently, it is as if someone tasked with learning a programming language for the first time decides to examine the source code of Microsoft Windows for tips--unlikely. Instead, beginning computer scientists are usually tasked to write a simple ‘Hello World’ program. I hate to break it to everyone, but we biologists are still at the ‘Hello World’ stage. One organism in particular, Mycoplasma genitalium, has the potential to serve as the hydrogen atom of biology. It is the simplest known organism, yet its status as a model organism for experimental research is very poor. If we are in the business of constructing a quantitative biology, simple organisms deserve to receive a lot more attention, even if they lack immediate biomedical applications.

I will conclude with a parting thought, and an accompanying question. Biologists are rumored to suffer from 'physics envy', an affliction known to arise from the purportedly inferior mathematical skills of the working biologist with respect to her physicist colleague. It appears however that for at least parts of biology, it is not quite clear that a physical model is the right one. Certainly for constructs such as a 'cell', one can think of objects existing in physical space, enzymes, nucleic acids, large protein complexes, etc, and interacting according to the laws of physics. But other biological constructs don't fit the bill as neatly. Consider the 'genome'. What physical object does it map to? One may argue that the chromosome of any one organism is in fact such a physical object. But evolutionary biologists speak of turnover rates for specific nucleotide positions, and 'ultraconserved' regions existing between distant extant organisms as far apart as humans and yeast! Clearly the word 'conserved region' means little in the context of one specific chromosome, as an individual physical object. Perhaps one can escape this dilemma by arguing for the need to examine things on a longer timescale, not simply to consider one single chromosome as a physical object, but the physical life of many such chromosomes over many years and millennia. Or perhaps not. My question is:

Are we trying to construct a physical theory, albeit one on a restricted temporal and spatial scales, like chemistry? Or are we coming up with an entirely new abstraction, much like computer science, where the underlying physics are ultimately inaccessible?

And that, as in the words of one Lubos Motl, is the memo. [LM: Bill O'Reilly will certainly forgive us.]

Mohammed AlQuraishi, visitor #600,000

Mohammed AlQuraishi: a portrait of the 600,000th visitor

You could ask: who are the people who visit this blog? Surely it can't just be just the set of my e-friends, nice women plus the e-non-friends and the crackpots and other nasty folks whom all of us know and who e-reproduce on the dumping ground of the blogosphere. Let me avoid a description what they must be e-doing before you e-reproduce. ;-)



Instead, let us start differently. Anousheh Ansari, a 39-year-old Iranian American multimillionaire who has earned a lot of bucks in the telecommunication industry and who is the chairwoman and co-founder of Prodea Systems Inc., will pay a symbolic fee of a few million dollars to become the world's first female space tourist. I suppose that it is harder to earn the fee than to master everything you need to know to become a space tourist. You see that although there are no female CEOs of Dow Jones companies, Ansari doesn't need any affirmative action, despite being a member of at least three minorities: the birthplace in the Axis of Evil might be the strongest handicap among them. :-)

I don't know whether she reads this blog; the 600,000th unique visitor of the blog is Mohammed AlQuraishi. If you look at his screenshot, you will see that Internet Explorer 7 looks kind of nice, it has tabs, and the rankingblogs.com icon still doesn't work! ;-)



According to the freely available data, he is an interesting person, too. When he was 6 years old, he started to make computer programs. As soon as he entered the high school, he founded a company in the Bay Area that created software for wireless and small electronic devices. Having received degrees in IT engineering, biology, and logic, his goal is nothing less than to transform the core of biology into a rigorous member of the family of exact sciences.

Recall that Quraish was the Arab tribe that was the strongest opponent of the prophet Mohammed (PBUH) throughout his life: it was his own tribe. (A similarity with Jesus and Jews is rather obvious.) If you're Mohammed AlQuraishi, that's quite a combination. ;-) Because Mohammed is the 600,000th unique visitor - the uniqueness means that at most 1 visit from an IP address is counted every day - he can also contribute any uncensored posting he wants or postpone this right to someone else.

Barton Zwiebach: a letter to the editor

By Prof. Barton Zwiebach, MIT

Dear Editor:

As a string theorist and an enthusiastic daily reader of the Journal I was baffled by the gloomy assessment in "Has String Theory Tied Up Better Ideas in the Field of Physics?", of Friday June 23, 2006. In this column, science reporter Sharon Begley presents the viewpoint of those who regret the twenty-year old dominance of String Theory in the marketplace of ideas in High-Energy Physics.

The "Not Even Wrong" epithet is hurled, suggesting that string theory is a sloppy and speculative work that cannot even be judged. To the contrary, string theory is an extraordinarily precise and rigorous framework where facts can be proven beyond doubt and computations give unequivocal answers. As every theory in science, it is speculative until confirmed by experiment -- hardly a reason to single it out. The cited naysayers correctly state that string theory has a myriad solutions, each describing possible universes. From this they conclude that making predictions, or disproving the theory, is impossible. Not really. All that is needed to confirm string theory is finding one solution that describes our universe. All that is needed to rule out string theory is showing that no solution describes our universe. An answer must exist.




Rather than speculate on the ideas that might have developed in the absence of string theory, we can celebrate the remarkable insights that have emerged from it. It has explained, for example, why black holes have entropy and temperature. It has also demonstrated a surprising fact: theories of strong nuclear forces are equivalent to theories of gravity. Over the last two months, several new papers use string theory to describe the motion of quarks in the plasma created by the Relativistic Heavy Ion Collider at Brookhaven! Not bad for a theory whose critics say is pie in the sky.

As in other collective endeavors, there is a bandwagon effect and many people rushed to string theory at the early start. There have been market corrections and a healthy equilibrium exists where string theory and other good ideas are explored and compete for attention. In this competitive environment, string theory continues to hold its own and to excite physicists with its possibilities.

Barton Zwiebach
Professor of Physics
Massachusetts Institute of Technology
Cambridge, MA 02139

Prof. Zwiebach is the author of the famous textbook "A first course in string theory" based on his award-winning MIT undergraduate course, and a world's leader in string field theory.

Rae Ann: Alien recycling

By Rae Ann, one of the four winners who have seen the #400,000 figure.

My first grader brought home some interesting EPA publications for school children. While I totally support teaching children to recycle and be mindful of wise use of resources I think it's a little off to tell them that 'garbage leads to climate change'.

• epa.gov/epaoswer/osw/k00-001.pdf

And what's with the little flying saucers and aliens (graphics in the publications)? What do they have to do with climate change and garbage?? One publication does open with the statement, "Space creatures might think the idea of reusing containers is an alien concept but here on Earth it's easy to keep an old jar out of the trash and give it new life." (That is a direct quote and the missing comma is their punctuation error.) Well, how does the government know that aliens don't recycle? Is it because they have left a bunch of their stuff here? Hmm? Sounds like a very prejudiced and discriminatory attitude to me. What is that teaching our kids about aliens??




I'm sure some homeschoolers would use this as another reason not to send their kids to public (government) schools, but I use things like this to open up a dialogue about different points of view and how it's good to analyze what you read and are told. It's a good lesson for the kids to learn that while something has some points of value it might also have questionable content.

Also TVA uses methane gas from landfills to produce energy...

• tva.gov/greenpowerswitch/landfill.htm

Uncle Al: on the equivalence principle

By Uncle Al who has submitted a #400,000 screenshot.

Does the Equivalence Principle have a parity violation? Weak interactions (e.g., the Weak Interaction) routinely violate parity conservation. Gravitation is the weakest interaction.

Either way, half of contemporary gravitation theory is dead wrong.

Gravitation theory can be written parity-even or parity-odd; spacetime curvature or spacetime torsion. Classical gravitation has Green~Rs function Newton and metric Einstein or affine Weitzenböck and teleparallel Cartan. String theory has otherwise and heterotic subsets. Though their maths are wildly different, testable empirical predictions within a class are exactly identical...

...with one macroscopic disjoint exception: Do identical chemical composition local left and right hands vacuum free fall identically? Parity-even spacetime is blind to geometric parity (chirality simultaneously in all directions). Parity-odd spacetime would manifest as a background pseudoscalar field. The left foot of spacetime would be energetically differently fit by a sock or left shoe compared to a right shoe.

String theory could be marvelously pruned. Does a single crystal solid sphere of space group P3(1)21 quartz (right-handed screw axes) vacuum freefall identically to an otherwise macroscopically identical single crystal solid sphere of space group P3(2)21 quartz (left-handed screw axes)? Both will fall along minimum action paths. In parity-odd spacetime those local paths will be diastereotopic and measurably non-parallel -- a background left foot fit with left and right shoes.

A chiral background pseudoscalar field diverges Big Bang evolution of matter and antimatter. It sources biological homochirality (exclusively left-handed chiral protein amino acids and right-handed chiral sugars). At a 10^(-10) difference/average or smaller level it is consistent with 420+ years of physical observations.

The world has lots of Eötvös balances with 10^(-13) difference/average sensitivity. The proper challenge of geometric gravitation is test mass geometry. More than 2100 tonnes of single crystal quartz are grown annually. Somebody should look.

Salman Awan: The truth is...

The truth is, The Prophet of Islam can neither be symbolized/drawn nor can be characterized in any way and anytime.

First of all I would like to pay my gratitude to Mr. Luboš Motl for giving me an opportunity to express my point of view on Danish Cartoon illustrations. Secondly, English is not my first language, however, I will try to communicate the intended message at the top of my abilities. Thirdly, most of you won't agree with what belief we Muslims and majority of the world share, but I am happy that I am into the act of Jihad through Pen.

Well, I am studying Business here in London and I am a Muslim by religion.

Firstly, I would to clear some misconceptions about Islam. Islam means "to make peace" and it struggles to maintain peace. We are no way terrorists, but all over the world we are looked upon as terrorists only because of few individuals who misunderstood the true meaning of Islam and were used by some economies for political reasons and benefits. After the 7th July, 2005 incident I have been stopped and searched 23 times at various London Underground Stations under a section, which says that I might be a terrorist. Well, that's another issue but the issue I will discuss here is concerning the height of disrespect our Prophet (PBUH) is treated with.

There is a lot happening at present in Muslim countries and wherever Muslims live. Yeah, its all emanated from Danish Cartoon Illustrations (DCI), moreover, these DCI are compelling Muslims to be defensive. Condoning or punishing such acts is a personal opinion shaped by religion, culture, values and heritage.

Prophet Muhammad (PBUH) was the last of all messengers and Islam was completed during his life. For us, Muslims, he is the best of all human beings and we try to follow his footsteps in every walk of life to get the best of the both worlds. Concisely, he is a model of excellence, and our love for him is unlimited.

The Prophet's Distinctive Characteristics as a Reformer

1. The most Successful of Prophets
2. Universality of the Message
3. Unity of Human Race
4. Development of entire Human Race
5. Greatness in all Directions
6. Not a Product of Environment
7. Universal Peace

The Prophet's Sublime Morals

1. The Prophet, an Exemplar
2. No Work was too Low for him
3. Simplicity
4. Food
5. Dress
6. No Attraction for Comforts
7. Cleanliness
8. Love for Friends
9. Generous to Enemies
10. Equal Justice for all
11. Humility
12. Sympathy for the Poor and the Distressed
13. Hospitality
14. Gentleness
15. Faithfulness
16. Forgiveness
17. Modesty
18. Affection
19. Respect for Others
20. Courage
21. Steadfastness

He possessed all the qualities we can think of and the qualities beyond our imagination. All these attributes make us fall in love with him. The DCI aimed to depict him as violent and terrorist minded, moreover, it's an attack on his attributes and not only that every Muslim is deeply offended and insulted our religion Islam is also disgraced and disrespected. I will not forgive such callous, disdainful, condescending disregard of things dear to me, things that I love.

No one has ever dared to draw his sketch except DCI, it's because of the respect we all hold for other religions. As CNN refused to post the DCI:

"CNN has chosen to not show the cartoons out of respect for Islam."

(This comment by CNN is an act of respect)

He was so perfect that we cannot bear anyone manifesting him as a terrorist or any other character as depicted by DCI. We treat each other with respect, I have respect for your values and religion it doesn't means that you can abuse my Prophet or Allah. Cartoons are no way means of depicting such personalities. The truth is, The Prophet of Islam can neither be symbolized/drawn nor can be characterized in any way and anytime.

It's a grave mistake by the Danish Prime Minister to oversimplify it into an issue of freedom of speech and religious sensitivities; it would miss the point completely. The Danish editors cannot claim that they were only exercising freedom of expression because hiding behind that guise would misrepresent what they did, and what they did was deliberately incite. That defeats the very purpose of a freedom of expression.

What should we do? We will be intolerant of such actions. We will not pretend that you have the right to insult our religion. But, we will be intolerant without being violent. We will use this forum of speech, and expression and non-violent action, to make ourselves heard. This is not on. This will never be on. We will fight, but our fight is not violent, at least not yet. Freedom of expression is not a vice. It is a virtue. Let us not forget that. Let us not forget that it is open to us too. That we can tell them it is wrong, and we can continue telling them, until they listen to us. But just because they don't listen to us right now, does not mean we burn and we torch, and we kill. Our fight is better than that, our fight is smarter than that. It is a longer, more difficult fight. But it is the right fight. And that is what matters. That is what Muslims are supposed to be about.

Also, I will make it crystal clear that who the fight is against. It is not against a civilization. It is not against non-Muslims as a whole. It is not against American governments as a matter of default. Our fight is against, those who believe our religion is not worth being respected. We need to earn our respect. We earn it, by being patient, by showing all the good that our religion stands for. We earn it by respecting them, and by respecting theirs. That is what we do.

So far there have been some deadly protests and I stand against them.

Salman Awan
awansalman at msn.com