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, "...PoincarĂ©’s paper motivates a non-fundamentalist view about the world, and that this is compatible with his structuralism. ... PoincarĂ© 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.

Regards,
Mark

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

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

Web Page: www.NLOsource.com

Wednesday, December 18, 2013

Geezers Undefeated in 2013



Written with Pat Kuzyk

While the Seattle Seahawks boast the best NFL record this season with only 2 losses, and Philadelphia fans recount with pride the Flyers’ all-time NHL-record  35-game winning streak, the humble Palouse has hosted an athletic achievement that trumps those celebrated performances.   On Tuesday night, December 17, 2013, the TerraGraphics Geezers, a local ice hockey team, won their last game of 2013, having dominated every challenger it faced since January.  The unbeaten streak has straddled two seasons and includes winning the Puckapalousa tournament, which was held in March just before the Moscow rink closed for the summer.

You may scoff that the Geezers’ opponents were unworthy. How can one mention the NHL and the B-Division of the Palouse Elite League in the same sentence?  Isn’t the team’s accomplishment vitiated by the amateur nature of its adversaries? NO - because this triumphant hockey team consists of a group of old men who - with the help of their young goalkeepers,  Erika Rader and Ben Anderson – have consistently prevailed over players half their age.

Goalie: Erika Rader; Middle Row:  Jim Parsons, David Rauk, Alan Brown,
and Bob Denner; Back Row: John Odowd, Paul Swetik,
Jerry Grzsbelski, Mark Kuzyk and Paul Gessler
The average skater on the Geezer team is 57 years old. By day they're carpenters, realtors, scientists, foresters, medical professionals, or retired; but by night (that is, one night a week) - and at heart, these men are devoted hockey players.  Some limp into the arena, while others rub their backs and sigh as they ceremonially don their skates and pads.  Creaking knees interrupt the locker room banter, but all eyes are bright in anticipation of the battle ahead.

The TerraGraphics Geezers may look comical in their retro yellow and brown jerseys, but on the ice, they're a force to be reckoned with.  What they lack in speed they redress with cunning, dexterity, and seamless collaboration. The key is team play. Win or lose, they are a joyful bunch, doing what they love and developing a lifelong camaraderie.

Despite the dazzling success of their hometown team, sports fans of the Palouse remain oblivious to its existence – foregoing numerous opportunities for joyful bragging. It’s time to rescue the Geezers from obscurity and give them the kudos they deserve.

GO GEEZERS!

Saturday, September 21, 2013

The nasty revewier strikes again - the third time is not a charm!

We sent a paper to a third journal and appear to have had the same reviewer again!  The review appears below.  Is it the same person?

The manuscript contains a  confusing and irrelevant approach to estimate maximal values that second and third order dipolar polarizabilities  can attain. The authors  also claim that this approach can be exploited to find   nonlinear  materials with optimal values for these coefficients without specifying  structural, chemical or other related  material characteristics: the Holy Grail in the quest of  nonlinear optical materials.

The approach is an extension of previous ones  with vaguely similar ingredients  and claims that  appeared in a series of publications  essentially by the same group and are extensively and exclusively referred  in the ms .  For a change this time the approach is disguised  with  “cartoons”   representing  “quantum graphs” (QG) and “star motifs”  that can be stressed and bent to any purpose with adjustable assumptions and parameters  to meet the authors  wishful  claims. These QG bear little, if any,  relation to chemical  structural  characteristics of the material as the usual quantum chemical  approaches  do and are far more complicated  to  estimate and guide the search for  nonlinear materials .

In a way  their approach is a disguised, unphysical  and complicated  version  of a  qualitative “assessment” of the nonlinear polarizabilities/susceptibilities based on  an expansion of the  induced  el-dipole/polarization in terms of the parameter  (E/Eat) where E is the el-field of the light  and Eat is an average  atomic(roughly the  ionization field) or cohesive el-field   of the atom (molecule)/solid.  This qualitative approach served  to qualitatively justify the use and range of the perturbation approach in powers of E and to also get a rough estimate of the susceptibilities   in the form of ?(n+1) = 1/(Eat)n; although the estimates  were  order of magnitude off  some  trends  were plausibly  accounted.  A short account of this approach is given in any respectable book on nonlinear optics (see  for instance introductory chapter in  Y.R. Shen,  The Principles of Nonlinear Optics, John Wiley). The present authors  in a cavalier manner  make no reference  to this approach  and  proceed  with  their complicated and useless to any purpose approach .

I shall accordingly not comment any longer on the inconsistencies of their  approach and  the  irrelevance of their quantum graphs  for  conceiving  nonlinear  materials  with optimal values for the second and third order coefficients. In fact the whole discussion in the ms proceeds with ill defined  terminology and unsubstantiated  vague statements. I do not recommend acceptance  of the present ms for publication in JOURNAL XXX.

Thursday, September 19, 2013

The survey results are in!

My previous posts have described a reviewer who continues to trash our papers not on the basis of the science, but motivated by a personal vendetta.  These attacks are not limited to just my papers, but also to those of past students; I may get annoyed when this happens to me, but I go ballistic when my former students are treated unfairly.

I have several former students who are now young researchers starting promising careers, some of whom are angling towards faculty positions.  A few negative paper reviews and a declined proposal can be the difference between tenure and unemployment.  If their work is inferior, fine, they don't deserve tenure.  However, if a reviewer harms a career by maliciously rejecting papers and proposals solely due to association, this goes well beyond unethical behavior; it's criminal.  In such cases, the reviewer should be punished to the maximum allowable degree.  Since the editor stands at the divide between the author and reviewer, (s)he should be proactive in taking action to punish misdeeds and prevent further infractions.  As head editor, I would convene an investigation of the editor and reviewer.  If my editorial board determined that malicious intent on the part of the reviewer was highly likely, I would move to reveal his or her identity to the authors.  As the acting editor, I would support this move.

To get your opinion on this matter, I prepared an unscientific survey.  While the results are still trickling in, the responses continue to be similar, as I report below.

Given that it is unusual for a journal to keep secrete the identity of the editor, it is surprising that less than 15% of you thought that the identity of the editor should be revealed.  I expected 100%!  Below are your responses to the question about the head editor's actions against the acting editor.



Since the actions of the reviewer are unethical and I believe criminal, he or she should loose the right to anonymity.  The review process demands that the reviewer act in good faith and make every possible effort to be unbiased.  If a reviewer's actions cross the line into actively campaigning against a group of individuals, his/her identity does not deserve to be kept confidential; not just to punish him/her, but to prevent future attacks from behind the blanket of anonymity.  Without knowing the identity of the reviewer, how can this individual's unethical and vitriolic behavior be prevented from spreading to other journals where we publish and funding agencies?

Why did only 20% of you think that the reviewer's name should be released?  What kind of reasons do the other 80% of you have? Are you concerned that the names of conscientious reviewers might be too easily released by pressure from whining authors?  Do you think that the privilege of anonymity trumps all, including the sabotage of a career?  Do you feel that you might be guilty of similar behavior, but perhaps to a lesser degree?  I would be interested in hearing your arguments pro and con on this topic.

FYI, the survey results with regards to the acting editor are shown below.


Let me know what you think.

Saturday, August 31, 2013

August 31, 2013 update on the nasty review saga

The short update to the saga of the nasty reviewer is that another member of the editorial board reviewed our paper and it got rejected.  The fact that the paper was rejected is of minor significance compared with how the process was handled as well as the implications to my former students as well as to all my readers.  You could be next!

In my case, a rejected paper is a small delay in a long career, and its marginal impact small.  However, I have an obligation to make sure that the system remains fair, especially when my former students are being targeted, placing them at a disadvantage.

My letter below speaks for itself.  After reading it, please take the two-question survey by selecting the link below.  I spent a couple minutes designing the survey, so apologies for its unscientific design.  I am interested in getting feedback, either by a quick click of the survey page or by leaving a comment here on my Blog.  Thanks for reading and giving me all your input as a sanity check.  It is gratifying to see that a couple thousand of you have read these posts.

If you are so inclined, please pass a link to this page along to coworkers and colleagues.

Happy Labor Day weekend.  Today my students are coming over for a cookout.  We are wishing three of them the best of luck as they move on in their careers with their newly minted PhD's.  Good luck to them!

Take a web survey by clicking here.

Previous post as background, click here.










Dear Editor-in-chief,

I thank you for your time and effort on the issue of our manuscript.  Now that email communications between various authors, editors and staff have settled down, this is the time to calmly focus on the important issues that go beyond the fate of any one manuscript.  As I made clear in my first email, I wanted to decouple our paper from my broader complaint, but the large volume of chatter distracted us from this goal.

First is the issue of reviewer integrity.  It is inexcusable for a reviewer to recommend rejection of a paper on the basis of personal attacks.  This behavior is even more egregious when it is found that the same reviewer may have recommended that the paper of my former student be rejected, also without basis.  This brings up the issue of the integrity of the editorial process.

In the case of my student's paper in THE OTHER JOURNAL (I was not a coauthor), the editors immediately recognized that the review was inflammatory and technically baseless.  As a result, the editor discounted the review as unreliable and sent it to another reviewer.  In contrast, your editor concluded that our paper was wrong based on the vitriolic reviewer's assessment, totally discounting the positive review.  Even upon casual reading, a non-expert will conclude that the positive review was based on the technical contents of the paper and the other one was personal.

I am grateful that you have offered to act as the editor of our future papers that are submitted to your journal to insure that the process is fair; but, don't all authors have the right to a fair process?  The editor is responsible for upholding the integrity of the review process by mediating the discussions between the two parties, and I do not believe that this is possible unless that editor can publicly stand behind his or her decision.  Keeping confidential the identity of an editor who is deciding the fate of a manuscript, which appears to be your policy, is a bad idea.  Based on the tone of the editor's decision, many of us are under the impression that the reviewer is the editor or someone closely associated with the editor.  A more transparent system would avoid such suspicions.

Finally, the review process that followed our complaint was not objective in its execution, though I am sure that the editor who supplied the review did make an honest effort reading and understanding the work.  Discounting the nasty review, we have one positive review that recommends publication and a review from a board member, who made positive technical comments but felt that the paper was not suitable for Your Journal.  In reality, then, there are two positive reviews but a split decision of the suitability criteria.  The paper should have been sent to an independent reviewer, giving the editor two reviews to use in rendering a judgment.

Several questions remain unanswered.  First, the editors of THE OTHER JOURNAL informed me that they had contacted you to determine if the same reviewer was involved in both papers.  If so, this is irrefutable evidence that this individual has hijacked the review process for a personal vendetta and should be censored.  In the present model used by many physics journals, the reviewer's identity remains anonymous.  I believe that an individual who has repeatedly shown such extreme unethical behavior loses his or her right to anonymity so that future problems in other journals can be avoided.

I have a moral obligation to assure fairness to my past students, and I would hope to all young people who are starting new careers.  A lunatic reviewer who is out to sabotage the publications, grant proposals, and tenure packages of past students associated with a particular research group could ruin the career of a young person in a tenure track position.  While placing this reviewer on a do-not-use list is a good first step, it does not go far enough.  Reviewers should know that they must stick to the science when reviewing a paper and that there are consequences if they don't.

Secondly, we deserve closure on the actions of the first editor.  What steps have you taken to determine what failed in the editorial process and what safeguards are needed to prevent recurrence?  At minimum, I believe that the identity of the editor should be reveled and that his or her relationship with the reviewer disclosed.  In addition, we deserve an explanation from the editor of why he/she made the decision he/she made.  Assurances that all is well without disclosure perpetuates the problem.

This kind of behavior if ignored can seriously damage our field.  Unethical behavior by even a small number of individuals tarnishes our collective reputations, and being apathetic is inexcusable.  I have waited until the fate of our paper was determined to respond to your email to make it clear that I am not motivated by trying to get a paper published, but rather to contribute to the integrity of the process that I hope will benefit us all.  I was a topical editor at JOSA B for 5 years, and withstood the wrath of many angry authors and reviewers.  But in the end, I stood by my decisions not through a veil of secrecy, but through open discourse.  I would be comfortable if my editorial files were made public.  I hope that the editorial board at Your Journal can say the same in our case.

Please feel free to call upon me at any time.  I look forward to hearing from you in the near future.

Best,
Mark


SECOND BOARD MEMBER REPORT

The review below of the second board member is fair.  The individual clearly read the paper and knows about some to the topics.  Because the points are made clearly and logically, we would have been able to make a compelling case for publication.  Unfortunately, this review was not open for debate and was intended to close the door on this chapter of our paper.

I found this to be an interesting paper but I do not think it is suitable for Our Journal. Here is my full report.

The purpose of this paper is to compute the response to an applied electric field of electrons confined to connected one dimensional quantum wires under a wide variety of two dimensional geometries. The authors introduce the calculation in the context of nonlinear optics however it seems to me it would have been better to introduce the paper in the context of quantum chaos and periodic orbit quantisation.

The model is purely Hamiltonian. Real nonlinear optical  systems have dissipation and the approach of the paper ignores this entirely. Ignoring dissipation and dephasing assumes that the wires are in the ballistic regime in which only single particle states are excited in the conduction band.  This single particle regime ignores the possibility of Coulomb interactions resulting from multiple excitations and also phonon-electron scattering.   I assume this assumption is justified if the applied electric fields are kept weak? The authors should have made some comment on the physical applicability of the model.

Despite this idealisation the authors do obtain some highly non trivial results for optimal  second and third order susceptibilities using a novel methodology, he “star graph motif”.  I assume these optimal results must also bound what might be possible were dissipation included.

he analysis is very comprehensive, perhaps too comprehensive. One begins to loose sight of the key physical insights for example, that optimal response is usually associated with an effective three level structure. This is of course well known in nonlinear optics.  In the context of this paper I would have liked to have seen a connection made to the underlying periodic orbit quantisation: for example what are the conditions for which a three level model in quantum wires is appropriate?

There is also no attempt to link the results to possible experiments for example, the response of GaAs/AlGaAs confined wire structures to microwave driving.

In view of the rather restricted physical assumptions underpinning the model and the lack of any link to an experimental context, this paper is not suited to the Our Journal in my view. It is unlikely to be accessible to the broad readership of the physics community that Our Journal seeks to address. The authors should seek a more appropriate technical journal. Alternatively they could extract a  smaller more compact paper that addressed some key physical principles, such as links to periodic orbit quantisation or possible experiments in ballistic electronic systems with microwave driving.