Friday, April 17, 2015

I propose a challenge to Maximal Flow theories by a new theory:Indifferent Time


I'm giving people an early peek at a new theory that I have developed in response to essentially another kind of theory, (or a system of theories) which involves optimal energy dissipation and or system flow optimization. So called "Flow optimization" as well as optimal heat dissipation are related in principal, a principal that I specifically am addressing with my own work. I hope this derivation will serve as a chapter in a larger work.
The theory that I am specifically disproving here is a flow optimization theory, called "constructal theory." But this formal disproof would also apply to other maximization theories, such as maximal entropy production.


 [This discussion is relating to a very large kind of theory, a very broad theory about systems. It is not of course specific in any way to specific experiments or individuals or in any way related to specific engineering feats, but to a theory relating to how systems work which encompass behaviors/phenomenon at a very high level, say the "40,000 foot view" but possibly higher. It would not have anything to do with the quality of someones experiment they did on a Tuesday, this discussion relates to what that work itself might mean in terms of thermodynamics, the heat dissipation of the building etc., to use perhaps an awkward analogy which is partly true, as dissipation should be independent of "how" people are working as should the "optimized" work flow of their activities. After all, constructal theory HAS been applied itself to such wide ranging examples as to why a World Cup Football team wore white instead of a darker color..(*constructal.org)]


If my derivation is correct, then this notion of constructal law" and OTHER dissipative or optimizing theories, would not be relevant at this level, which is again very theoretical and broadly encompassing. The "constructal law" has been widely promoted by Dr Bejan as a thermodynamic law, with some 10,000 scientific references, and is accepted as a text book on thermodynamics (see link to Constructal.org). So my derivation challenging the constructal law, would certainly be significant.



One of the very difficult things about constructal theory is to understand what it is, in fact claiming. That is to say, to find a definitive scientific argument. This is unfortunate. In general, most scientific papers should not be so difficult to read, and it is not simply because it is technical. I would reference (by way of general comparison), Prigogine’s Nobel lecture, England’s paper (which I blogged on earlier), or any number of chemical papers that I read routinely where one can list the main arguments, the relevant data and the clear discussion about how the hypothesis might account for them. The thesis is easily understood, as are the claims. Sadly, this is not the case for constructal theory. It seems that some other standard of science applies to these papers, but what is striking are the few references to other obvious subjects, like biology and chemistry, and possibly if there were more of these, Dr. Bejan would not make claims like "Science generally believes that evolution cannot be observed in our lifetime..." a claim that seems truly uninformed about papers in biology that study mutation in bacteria. But there is also the general claim of a theory linking the inanimate with the animate that never mentions genetics or biochemistry? One of the terms I have attempted to understand in constructal theory is Dr Bejan’s use of “evolution”. It is not clear at all what this term means physically in the larger “constructal theory”.  I have at least three text books of advanced chemistry on my desk, and none of these ever talks about “evolution” as a chemical descriptor of chemical behavior. So what exactly is this meaning? I highly doubt you will find, this theory in any physics text book. And for good reason. The particle theories have been formulated to descrirbe these very behaviors discussed in "constructal law", in chemical and physical terms. I hope that my disproof of theories like Constructal law will help rather than hurt progress forward. I cannot imagine that a misinformed theory at best, taught in schools, should in any way help progress forward in science. It appears that its proponents are not too keen to share their knowledge or answer questions. What nonsense is this? And what does it say about the status of theoretical science?

At the Constructal.org Blog itself, I posted [1][2] what I thought was a fair question on this point, attempting to get more description or clarification about constructal paper. Unfortunately, the Constructal.org blog editors it seems, are not really interested in replying to scientific inquiries or even clarifying what they mean. You can read the exact post I made here, which is not on the Constructal site because it is still “awaiting moderation”.  The Constuctal.org blog is said to be “an intimate” blog of Dr Adrien Bejan, who postulated constructal theory in 1996.

Let me state very generally, that I simply don’t agree with constructal theory’s misconstruction or reconstruction of physics, whatever the case may be. It is a reversal in my opinion, of progress in science.This kind of physics, in which inanimate nature is deliberately imbued with function and purpose in order to operate, was moved away from thousands of years ago. The paper itself is laden with anthropomorphic presumptions. There is a very big difference between using expressions or metaphors, and invoking these as direct mechanisms ,or even "laws". I note also that Dr Bejan claims in some recent papers that the Constructal Law is (comparable) to the Second Law of Thermodynamics. [I have pointed this out specifically in a previous reply (see this one) as I believe many of these arguments essentially “beg the question,” that is, they must be first accepted in order to make the premise itself, tenable. That is another point I explore previously, and if that is really the case, then that is truly unfortunate. What are the objectives of this essay? They are very clear: to explore the SCIENCE of these notions expressed by constructal theory, they are obviously defining in their numerous scientific papers and teaching books, a "territory" of science. So the exploration of a scientific hypothesis, is in a sense, an exploration of science itself, that is the objective on equal grounds with virtually any other scientific pursuit. The other objective is to delineate and differentiate my own theories from what is extant.]

 I have, in reply to this paper specifically, a hypothesis which is a stand alone theory, but coincidentally, disproves the constructal theory premise, which I call an “indifferent time” theory. "Indifferent time" states that at any given time point the flow through the system, is indifferent, it is neither optimized nor unoptimized in terms of maximal flow or minimal flow. (1)
I have derived this from Newton’s laws of motion, and it can be shown at microstates or macrostates. The burden as I see it, is on the constructal theory to provide evidence that there is some physical data, or data suggesting that there is an imbalance of forces at some time point. If not, then we can only assume that the normal forces (due to flow) are in perfect equilibrium with the system, be it a river delta or any other inanimate physical system at any time t. The basic premise of a system changing to “optimize” flow would essentially be false as it is always in perfect equilibrium with its surrounding forces. Since the presumption of change (evolved or optimized) can’t be substantiated, the data itself would be challengeable. I object to the use of partial differential equations in this paper (and as I've indicated elsewhere, without physically defined units, it's not at all clear what they might actually reference). In my opinion, one would not provide a formal equation or analysis, until the problem area is clearly established.  What you will find however, in this review, is that I am not actually showing the conflict here between constructal theory itself, but this is more broad in scope and likely encompasses other optimization and/or dissipation theories, really more broadly, to the concept of ones physical state “leading” towards another because it is more preferred. In that sense there are many theories which propose optimization in different forms either via entropy gain or heat dissipation.

According to constructal theory, the earth is an “engine”.
As Bejan states : “Because the flowing Earth is a constructal heat engine, its flow configuration has evolved towards paths that generate less irreversibility.”
The problem with this claim-i.e. the assumption that a physical system will “evolve” is that to evolve, it is implied that such a system would need to be in a less preferred state (at some initial time) and then alter itself (at a later time) to become a more preferred state. That is the understanding that the word “evolve” conveys. The statement..”evolved towards” some path” implies that it is heading in a direction and is obviously, not yet there. And actually, Bejan does indicate that this is what these systems do, and in fact some are not “alive” but will be once they take on the property of maximal flow.

As he indicates in Fig. 4, “(Bejan & Paynter 1976; Bejan 1982, 2006). The constructal law governs how the system emerges and persists: by generating a flow architecture that distributes imperfections through the flow space and endows it with configuration. The ‘engine’ part evolves in time towards generating more power (or less dissipation), and as a consequence, the ‘brake’ part evolves towards more dissipation.” There is an implication in that statement, that there is a physical difference that can be made, tested or proven to exist, between for example, a system which dissipates “less”, and a system that dissipates more. The further implication is that at some point in time t, the physical system is not optimized, or not configured” to dissipate. In reality, there is no physical distinction here, which is what we would expect of a natural system. (2)
As I have just stated in Indiffernt Time: any system, is already dissipating its "ideal" amount of energy in accordance with the localized physical laws that apply. The physical laws are not "behaving" differently in one region or another, thus we have no reason to believe that these laws would "care" to increase or decrease optimization. Nor would we be able to state that at one time point the system was NOT optimized and at another point it WAS optimized. (3)
It is not clear how one would go about showing what this difference is. (4)
What is clear, and what I believe constructal theory is not realizing, is that even when a system doesn't APPEAR to be optimized for heat dissipation, it actually is. Again, it is indifferent, and Nature cares not if you view a system perfectly "functioning" hurricane, or a light trade wind, each of these systems is in perfect harmonic balance with the localized forces that apply. And we further can see the universality of this statement and the implications of my hypothesis, Indifferent Time, to other theories which portend to operate upon the assumption of "preferred" or optimized dissipation of energy. (5)
The surprising result is that there is no optimal dissipation of energy in a given system it is always optimized because the forces are in balance at any time t. Further, the notion that a system is not optimally dissipative at one time point, and more optimally dissipative or flowing at another time point is anthropomorphically applying rules that aren't there. You can do that with equations, you can make various relationships and possibly make the claim, but what I'm saying is that you won't be able to prove this with the physical model. (6)

Constructal theory apparently claims that there is some distinction (be it flow optimization or heat dissipation) that can be made between a system at different times, which we might call configuration I, II, III etc. This is the problem specifically with the implication, the strong implication of animation and of anthropomorphing something like a river delta or erosion patterns on a mountain. Unless some argument is provided to the contrary, or some evidence is provided, we must assume the system is the same, (in terms of "optimal" heat or mass flow) before there are any river patterns, in other words it is already “optimized” at every time point. System state “I” is identical to II and identical to III and so on. That is a fact about these physical systems that is incorrectly asserted in this paper. It is purely anthropomorphic to observe that the flow of the river is much higher and thus it is more efficient. Nature makes no such assessment of efficiency. (7)

TEST: One can also easily show that constructal theory cannot be a "physical law" that such a river pattern is an optimized physical dictate, like gravity or the second law of thermodynamics, both laws which are inviolable under ANY condition. We NOTE that the river actually can be made more efficient? How? By the use of machines, ships or other devices that pump water down stream, are far more efficient. Yes they take energy, but that is beside the point. We have deomonstrated that we can violate constructal law. We cannot do such an experiment with the 2nd law of thermodynamics, or with gravity, etc. [3]
Fig. 1 Showing a microstate of the river bank and relevant forces.

 

To evaluate the causality of a simple flowing system we can perform an operation in which we look at the various forces involved and by a simple process of addition, determine if anything is out of balance. The force of the water against the bank (black) is depicted by the vector in blue (proportional to its velocity), the force acting equally and opposite the force of water, i.e. the river bank, is in black. We also have a downward force of the water, its weight which is the pressure of a column of water.  Note that we are not adding up forces to create a vector, which would be a convention. We are actually doing something very different, this is adding up “causality”, again to simply see if there is some inbalance of cause or forces present in the system. (8)

A stagnant body of water has tremendous weight, if there was no normal force opposing this pressure, the water would break out.



(Force of water against bank, Fbank) + (forces of water weight, Fweight) =(Normal force of river bank opposing water Nbank)+ (normal force of river bottom against river weight Nbottom). Rearranging we have (Force of moving water) + Force of water weight+ Normal force of bank opposing moving water force + Normal force of river bottom opposing weight) OR, more simply…. Fbank  + Fweight  + -Nbank + -Nbottom= 0.  (9)
When Fbank =0, in the case of a non-moving body of water, then we see an identical expression where the normal forces of the river bottom are in balance with the weight of the body of water. (10) (*see note 21)It should be noted that we are neglecting the pressure against the bank, for simplicity, but could express this as Fbank= (Sum) F pressure+ F bank )
Now we can also examine this system in accordance to time or a possible change over time. According to Indifferent Time, meaning no preference, we can again look at the same equation of these forces we just did, but at different times: call these arbitrarily, time initial, I,… and II (a time later). What Indifferent Time means is that we do not see a difference between these states I and II in terms of their equilibrium as we just calculated for a micro condition somewhere on the river bank. Since there is no difference in force balance over time, meaning no preference, we state that the system is “indifferent” essentially to changing.  (11) How would this be disproven? In other words how do we test this condition? If we can show that in the equation above, there is in fact some slight change in a force, either the river force or the river weight, that is changing with respect to some other impetus, call it a “wild card” force, then this would in fact disprove my condition of indifferent time. (12)
The more simplified concept is to imagine that we see no direction here in how the equilibrium is fluctuating. In other words, since the forces are always in balance, according to Newton’s law of motion, “any force will see an opposing force directly against it” (i.e. with gravity or collisions of balls), and the additional stipulation I have introduced, “at any time” we can see that we could plot the relationship above and show that it has no trend. This has an implication to dissipative preferential equations and so-called selectively enhanced dissipative equations .(13)

 Fbank + Fweight  + -Nbank+ -Nbottom= Diff at I, and Fbank + Fweight + -Nbank + -Nbottom= Diff at II. Diff I- Diff II/ Diff (time I-time II) would be a formula for showing a rate of the change in the system (moving away from equilibrium, or towards it, greater or lesser). (14)
 Of course the “slight difference” we are defining here would be in theory, a difference between the Fweight and Nbottom, in other words one is out of harmony with the other. When would such a condition exist? It cannot. (And this is actually Newton’s third law of action-reaction Fw=-Fn ) (15)
(See note 28. We are showing with the difference formula (14) that the normalizing force, is the "optimization" intrinsically done by the microstate, or microstates and thus we cannot see optimization between arbitrary states I, II, ...III etc. Any "wild card" vector would have associated with it, a normalizing force. This rule applies as the river undergoes any slight deformation, as delta F= delta N] 

So we have also just proven that there is no causality to be found in a strict formal sense in a natural flowing stream or other natural system. Causality is purely artificial, and can only be demonstrated by artificially assuming that a force is entering the microstate (such as wind, water or other forces), but in reality this only appears to be causal, as these forces are not correctly accounted for and find imbalance only because the model of accounting forces them to be imbalanced. (16)

It is the convention in physics texts to assume that a free floating force will be examined and often times, its source is not relevant to the problem. But that assumption is not valid in these types of problems involving causality.
 

*in reality, these forces are not “entering” the system but are in fact, a part of the system. It is convention, to assume that “a wind blew over the tree”. A true statement in the proper context if one is simply force diagraming the problem. However in the causality problem here, and by the new causal analysis I’m proposing, such convention is misleading. We know that the wind is more accurately understood as a vortex that was resultant from a system of nano-states, molecules absorbing heat, pushed to disequilibrium. Thus their macroscopic vibrations, led to higher order vortices, eventually building to form the wind that blew down the tree.  (17)

**It is true that the ordered motion of a vortex or wave, is a response of the system to dissipate energy, like diffusion spreads out a cluster of molecules. (that is far-from equilibrium dissipation [Prigogine, 1977]). What is not correct is to assume that this is more efficient” or “less efficient” as there is no “less efficient” possibility in the physics. We would not say that diffusion occurs because molecules “need” to spread out their energies uniformly. (18)
[(29) I updated 5.5.15 the expression above to be inclusive of the non-equilibrium state and show its broader and surprising implications to the sun's system (see comment 29)] 
 
On the other hand, evolution at least as a theory, is a term that is clearly conveyed and defined in biology . And there is little point in defining it here, except to say that evolution implies that an organism is changing in some way that is a response to its environment or to its competitors. And so although Dr. Bejan clearly is making the argument that a river delta “ages” over time and might even be “born”, this statement lacks physical evidence to suggest that the rocks and dirt and the stream itself, are anything physically different than they were at any other time point (with respect to their capacity to carry flow, which [we recall] is a self defined instrinsic property of the system in question. (19)
The "flow capacity" of a river is obtained by formula, but this capacity alters proportionately to other parameters that define the physics. We can see with the aid of microstate analysis I perform here, that the river only increases flow  capacity as the volume of water increases, not before and not after, its physical shape is dictated by fundamental laws). (15)
 Are we to believe as constructal theory claims, that a river delta “ages” and if so, what physically differentiates it at a “young” age vs a much older age in terms of flow? Of course constructal theory suggests that rivers increase in flow over time, they get larger, so size would be a factor, but the inherent problem with this suggestion is that we know when a river was “born” and even where it was born… And what a river is, meaning what its boundaries are. Unlike particles with finite mass, and radius, rivers are highly ambiguous. Does the mississipi river delta really only encompass certain states or does it include every tributary, minor tributary, and even the tiny etchings on a mountain sides? What is a rivers’ boundaries? Chaos theory comes to mind. Neither of these physical boundaries issues are even discussed in the paper. But that is the trap that anthropomorphic theories fall into. (20)

 

 [note](There are basic problems with so called "optimization theories" which relate to flow. Of course, it many not even be true that a given river we are observing is at optimized flow, if we are to accept that the context is a valid physical model. What if the river that particular week or year, sub-optimal in terms of run-off? There would be no guarantee that the volume of water is moving at its theoretical capacity, whatever that capacity might be. In reality, the same problems can be raised with other optimization theories, such as Dewar's Entropy Maximization Theory (Dewar, 2006) which proposes to measure the optimal heat dissipation of an ATP processing enzyme. The paper speculates on how the function of the ATP enzyme is specifically designed for maximum entropy generation. Maximized" carries with it the implication that there are less than "optimal" entropy productions of the ATPase, and it is not clear how one would make this assertion, except to assume that the maximal level is somehow already known or pre-dictated. (21)
That carries a strong anthropomorphic implication to a natural system, not to mention that it fails to explain why the entropy production is not indifferent to maxima or minima, to a theoretical state that the enzyme is not "aware" of. It is not clear why the values given for the entropy generation are not precisely the values that are generated by the system at any time t, neither optimal nor sub-optimal. Furthermore, I can provide several tests, as entropy is a universal property of all molecular systems, not just ATPases (but also not just molecular systems). (22)
I do not run a cell toxicity experiment and consider if a drug species is "optimized" for cell toxicity or not, such labels would have no physical basis in chemistry. Nor would I expect that the combination of a certain inorganic salt with water, a process that creates entropy in a fixed molar quantity, is at an optimized level. (23)
Is there a sub-optimal generation of entropy in the dissolution of calcium carbonate in water? Again, for the given experimental conditions, it is exactly what the system generates. If we consider the experimental tables of Dewar in his paper, are we to assume that some of the values calculated for replicate entropy generation of ATPase were "less optimized" whereas other values of the entropy were "more optimized"? By the physical analysis I employ with "Indifferent Time" a working hypothetical test, each of these data points would be a precisely what was generated, not a maximum or minimum, which implicitly assumes that they should in fact be some other value than they are. ) [4]

Based on my theory of “indifferent time” , I believe there is no physical difference between a river system a thousand years ago, and today, in terms of its expected flow or any other normal forces it encounters. And this is completely independent of what age one arbitrarily assigns to the river. (24)

Again, I have searched this paper (and others) for evidence to the contrary, but according to my time indifference argument,(time is “indifferent” as are the normal forces, to what state a physical system is in). A natural system at time t is “optimized” for maximum flow of all its components flowing through it, and is not more optimized at a later time t=t2, in other words it is optimized” at any time t for any flow material passing through it. (11)
It appears as though the trenches are deeper, but we cannot claim that this system is more “optimized” than a prior system. Why? Because of the rather obvious fact that the prior system was already optimized for the given flow requirements that it encountered. This derivation I provide, stems directly from the basic laws of motion. (15)
But mathematically, it is a sound argument since the net flow capacity would always be normalized to what the capacity is of the system at any time point. We note that the capacity of a river might increase, but mathematically, so does the potential of the system, in exact proportion. Unexpectedly, we might see that this is a product of the system, it is the system generating the flow potential.

When Bejan claims that a system has in fact reached an “optimized configuration”, as he states here…“Because the engines of engineering and biology are constructal, they morph in time towards easier flowing configurations. They evolve towards producing more mechanical power (under finiteness constraints), which, for them, means a time evolution towards less dissipation, or greater efficiency.”) does he believe that this “snapshot” or drawing of the system, is really somehow different than its state at some other time point? Is it really optimized” now, when in fact it wasn’t optimized before? More importantly, how do we know this? What physical measurements indicate that the system is in fact “better at flowing” because implicit in this assumption is that it needs to be better than it is.

When I hike a dry gulch in Southern Utah and gaze up at trees and rocks that have been deposited high above, in the now dry banks, I consider F=ma, not constructual theory. I do not imagine for a moment that the river is animate and this is somehow designing itself to carry more jetsome or flotsome. Nor can we imagine that it is “designing” itself to carry more water. According to my theory of indifferent time, it carries precisely the amount of water it carries. If the flood waters are diverted then this canyon will erode (the dry gulch will fill with sand, and it would appear that it is no longer "optimized" for carrying water, though in this case we have now mentioned a wholly different force  that is at work opposing so-called "flow optimization".) (25)
 If constructal theory were to actually hold, I believe that Newton’s F=ma would need to be restated, such that masses would “want” to collide at maximum efficiency. And that really does pose mathematical problems. (26)
We do not justify such a statement because it is clear that the collision is not at disequilibrium. We should not be surprised that the flow in a natural river is optimized for the water that is coursing down it. Any more than we should be not surprised that an incline is not “optimized” for rolling rocks downslope. None of these “optimizations” are really true, and "optimization" is a term that is being introduced artificially, into the equation.

There is another issue too, in the constructal thesis that our engines and other designs are “evolving” towards “less dissipation.” In reality this runs contrary to the accepted notions of thermodynamics, since for engines to exist, greater dissipation of entropy must occur outside these systems to compensate for the increased order. This would occur in the burning of fuels and disorder of other ordered systems to make (highly ordered) engines. That is, the engine is at such a high state of order, that the cost of this lowered entropy is great on the system around it. Dissipation of NET energy must be greater for the system in this case, not less. This is the principal already espoused by Schrodinger, and many others. For example, cells must pump entropy out of their systems in accordance with this theory, so they in fact are dissipating more heat.

So I return to an argument I made earlier (here) that constructal theory is making numerous factual arguments, about how a system at some time point, i.e., is not yet optimized, but perhaps at a later time point is optimized. And yet, if this was the case, we would see disequilibrium. Looking at the system in terms of microstates, we realize from Newton’s laws, that the water against the bank applies a force, but the bank in turn applies an equal and opposite force against the water, thus the “optimization” of forces is in balance at all times. (14,15)
At any time point, the system is already optimized in an absolute sense, to the flowing material passing through it. It will not change or alter itself until it is met by a force which causes a change, at which point it will be instantly “optimized” again. To imply or infer that a river delta system is somehow “doing” anything, other than being molded by forces that are acting in its immediate time frame, strains incredulity.

The constructal theory, (like other optimization theories) has obviously concluded that if a system is evaluated at a later point in time, it will be apparent that it has achieved an “optimized” level of flow that it might not have had at an earlier point in time. Yet there is no physical reason for believing that such evidence does exist to support this alternate, physical view of a system. Moreover, it would not seem possible to envision what kind of data this would be? As I’ve argued previously, there is a distinct lack of any units of measure in which to qualitatively or quantitatively evaluate how a system might be more optimized at one time point and less optimaized at another for the given flow that passes through it. When this theory is evaluated causally, in terms of vectoral diagrams these issues I believe become more obvious.
My theory: "Indifferent time" states that at any given time point the flow through the system, is indifferent (to the normal forces opposing it), it is neither optimized nor unoptimized in terms of maximal flow or minimal flow. (1) Indifferent time would hold that the premise of a system “optimizing itself” or evolving to a more perfected form, is not evidenced and mathematically is not possible. Indifferent time posits that at any time t, the normalized forces are in perfect equilibrium and thus the system is at perfect optimization. Any flow equation that we might establish, just like any other equation resembling F=ma, would be de novo generated from the system itself, and therefore normalized against it. It is neither too optimized nor too underoptimized. This would disprove the contention that a change in optimization is occuring or an evolution, since if both states (I) and (II) for example are already 100% optimized, how can one observe a change towards greater optimization?

Monday, April 6, 2015

Poem..The Edge Of Tomorrow


In the million mile journey
Poised on the edge of tomorrow
I'm surrounded by a sea of lights
..The emptiness of "What will be"
A pretty movie poster face stares into shadows.  Surveying Rooms filled with ghosts..yesterday's, tomorrow's crowds
Music drifts around me like water
Slot Machine noise unwinds on the great carossel. From here to there
And my life unfolds like an escalator
It's taking me to the  horizon
There is everything to concern me
And yet nothing to worry me
In the ambient rime
That shines smiling, vanishing like a broken sunset
Torn violently from a wall

Saturday, April 4, 2015

I question the thesis of an article "How Europeans Evolved white skin" presented by the American Association of Anthropologists


I decided to scrutinize a story, by an AAAS contributor for SCIENCE, itself based on a scientific article that appeared on an AAAS web site. The article was based on a study done by Iain Mathieson, and David Reich, and it is apparently in pre-publication at an archival server called bioRxiv. This is an excerpt from the AAAS article which I took issue with on the blog http://news.sciencemag.org/archaeology/2015/04/how-europeans-evolved-white-skin.

"Now, a new study from the same team drills down further into that remarkable data to search for genes that were under strong natural selection—including traits so favorable that they spread rapidly throughout Europe in the past 8000 years. By comparing the ancient European genomes with those of recent ones from the 1000 Genomes Project, population geneticist Iain Mathieson, a postdoc in the Harvard University lab of population geneticist David Reich, found five genes associated with changes in diet and skin pigmentation that underwent strong natural selection." -SCIENCE

I evaluated this paper based on causality analysis, and I believe that the central hypothesis that it is based on has serious issues. My disagreement is not with the genetic data itself, it is the interpretation of the data that I take issue with.

I was hoping to have a response from the Harvard authors of this study specifically, Iain Mathieson and population geneticist David Reich, but I ended up engaging a bunch of others in simultaneous debate.

And this is what I wrote (in italics below):

The thesis of the article's paper, however is more than simply (about) the data. It is the interpretation that the present genes sequenced are present because they conferred a selective advantage to their hosts. That, as I've said below, fails to acknowledge the selectability of the other genes, such as Bcl2 and P53, certainly present 40,000 years ago and found in all mammals. Skin color has no selectability for these genes specifically, and yet tthey co-develop along with the other 30,000 genes in the human genome.

I received some replies but nothing convincing to me that there is an answer to my questions. I'll just call some of the other responses "some other replies" and you can see them for yourselves on the actual blog but I'll spare readers details here:

A Reply:
A well meaning scientist who described himself as a quantitative geneticist, with a PhD, replied, and I'll paraphrase here, that "the author's in the article were somewhat "lazy" in not differentiating alleles from genes, (which implies that the Bcl2 and P53 are not selectable in this case as they are too large). He also stated in so many words, that I was unclear on the concept of what a polymorphism is, and thus, the two genes that I described above, would not be relevant to selection in skin specifically, as they are much larger genes and critically he argued, ANY slight change in these genes would be terminal.

Needless to say this thinking is simply not backed up by experimental evidence, which I'm fully aware of, but this is what I wrote:

I do understand the distinction you make about polymorphisms. A significant change to Bcl2 or P53 would be terminal whereas the genes [of skin pigmentation] discussed here are perhaps "less critical" they can vary much more in sequence without drastic consequences. However, I would disagree that these are entirely non-polymorphic, since Bcl2 in particular is believed to be directly responsible for cancer resistance in addition to mediating the onset of cancer in ways that aren't understood. P53 is a similar gene, and I'm speaking again about its cancer relatedness with respect to how it controls transformation. Because cancer is prevalent, afflicting 1 in three people, these are subtle polymorphisms would be selected for by a variety of factors. I don't agree with the "these genes are untouchable". Every gene or even allele has a history. The point is that skin cancer is intricately related to sun exposure, but also genetics and the operation of the tumor suppression capabilities of bcl 2 and P53, I could argue that a frequency of cancer would in fact be selectable. Skin cancer would be highly detrimental to fitness. My other point is why don't we all have cancer? a rather extreme view, but hypothetically a good question. You, a quantitative geneticist see function of genes, I see chemistry. But the fact that cancer is so complex and effects people differently, (has different triggers sun exposure, etc) says that genes like Bcl2 and P53 are mutating enough to create such divergence and hence fitness. Genes express proteins, they don't "know" if they're polymorphic or not.

You might ask OK what does polymorphic mean? So for readers, who aren't in the "know" what he's saying is actually a well known convention of evo theory, and that is to say that certain genes are generally "off limits" they're "safe" so to speak, not because they can't change, mind you, but because if they did even change even slightly, it would be terminal to that organism at birth or even before, so in other words the genes are never carried forward, neither would the modification to Bcl2 or P53.

I continued with that point in another response:

Those two genes I mentioned are specific to skin's function, like all other cells. Hence, they are relevant to the discussion. My point is that these other gene's presence in descendants (the ones you mention) are equally critical to the thesis that some factor such as vitamin D, caused their frequency to increase. Bcl2 and P53 are critical to skin cell's ability to avoid and fight cancer by regulation. The unanswered question that I have already posed is "Why aren't
these genes also mentioned in the paper?
" They are more critical to skin health and survival of their hosts than the genes discussed i.e. SLC24A5 and SLC45A2. So I would like an explanation as to how these genes were also selected for along with the genes mentioned in the paper.
You would not be reproducing without intact and highly active forms of these two genes, period. I've yet to have a reply from a scientist here on this point,which it seems you’ve missed entirely. We would not conclude that skin color was the advantaged trait, as the authors do, since these other genes which
confer no color or visible trait, (other than not being alive perhaps?) were obviously more important to vital function of skin cells and the organ and had to be inherited in any individual. Of course it would be ideal to have the authors of the paper, Iain Mathieson or David Reich provide an explanation on this specific point.




Another responder, (which I'll again paraphrase) provided an explanation for the change in pigmentation based again, on the already well accepted model that Vitamin D is a necessary nutrient, and thus, the possession in the skin of a gene which makes it, would be an advantage. He also made a comparison between this selection mechanism and that of bear's coats (white in Northern latitudes for camouflage/hunting advantage on ice) vs other bears "darker coats" in warmer regions. Of course, that part about Vitamin D, is exactly what the article is already stating.
This was my reply:

The argument that you present here is "smoking gun" for teleological, "bears have heavy coats because they 'must' stay warm in the winter." Dawkins in "selfish gene" theory avoids this argument by use of gene "selfishness". In nature there is no 'must' only chemistry and probability. The basic thesis of the article's paper, however is more than simply the data that specific genes were traced through varioius generations. It is the interpretation and CONCLUSION that the present genes sequenced are present because they conferred a selective advantage to their hosts. That is what is critical about this paper. That, as I've said below, fails to acknowledge the selectability of the other genes, also involved critically in skin tone survival, such as Bcl2 and P53, certainly present 40,000 years ago and also found in all mammals if not other vertebrates. Skin color has no selectability for these genes specifically, Bcl2, at least as stated in the paper, and yet tthey co-develop along with the other 30,000 genes in the human genome.



Many other commentators simply resorted to responses that were either meant to censor my posting or to drive me away from the site, and (for now) I won't bother reproducing here. So in reply to those types of posts, which are attempted to attack one's argument by "poisoning the well" this is basically where I left it:



I'm a PD/PI, that would be a professional scientist, commenting on the specific AAAS article above "How Europeans Evolved White Skin" by author Ann Gibbons (correspondent author for Science magazine) with a specific question relating to Bcl-2 and P53 gene function, which relate to the health of all cells, including those in skin, and which appear to be neglected in this referenced paper, and yet would be vitally important to the question of skin pigment development via their regulation of cellular mutation response. How does selection of Vitamin D account for them? Unfortunately, the only response to my question thus far, comes from a mutant troll on this site, who rambles on about the "bible" and who knows what else. So, are there any REAL scientists who would like to engage in a discussion about this AAAS referenced article? And if not, what is it that you fear about scientific questions? My question is for the moderator/editor Ann Gibbons. Let's raise it a level shall we?



In summary, the central thesis that the five genes, primarily genes relating to Vitamin D are somehow causative is what I am questioning in regards to the other critical genes Bcl2 and P53, which are never mentioned in their paper.

I did not receive a succinct response to my argument addressing the articles central thesis. And what I'd hoped might generate a "breakthrough" on this point, perhaps in a live forum of dialogue, fizzled. But I will update this post if a cogent response from the authors does come through.


Wednesday, April 1, 2015

Poem: Chemical illusions and The Enraptured Framed Within The Unenraptured


I think photos are very much illusions of a time, form and space they appear to capture.

I quote Steven Pinker, Cognitive Scientist: “Our mind’s eye is also sentenced to live in a world of time.  Just as we can imagine an empty space devoid of objects but cannot imagine a set of objects that aren’t located in space, we can imagine a stretch of time in which nothing happens but cannot imagine an event that doesn’t unfold in time or take place at a given time.  We can imagine time slowing down, speeding up, going backwards, or stopping altogether, but we can’t imagine time having two or three dimensions.  In fact, it’s not even clear that we do imagine time slowing down or stopping so much as we simulate those possibilities by imagining things moving at half throttle, or halting in freeze-frame, while time marches on as usual..You might wonder whether these features of our experience come from the design of the mind or from the nature of the perceptible universe” 

That last line really rings true for me. I think a book could be dedicated to exploring that idea.
 

A photograph might seem to be one thing, to the eye, as real as anything, but elements of time, space, and light, that compose it in the mind is very different from the reality that forms it.  Light is an aspect that is the most critical.  Light too, is important in chemistry in visualizing elements, and light is important in modulating mood.  And if the photos can be said to contain basic elements.., earth, sun, water, candle light, architecture, and beauties that traipse through them, then my attempt is to construct visual bonds between these elements, that hold them in ways that are interesting. Some I call “polymers”, like repeating units of an idea that vary slightly.  They are sparse, obvious, simple and true.  Like a model standing clearly before a vanishing horizon behind her on a sunny day, (stands in a world,) part reality and part illusion.  Or forms vanishing in shadow.  Science is about experiment. It is as much about what is found as what we didn’t find, and photos too are the uncaptured as well as the captured.  The positive and negative results are important in the shot.  The emptiness, spatial and time, is also an aspect.  There seems never enough time to take all the photos we want to take,  the second shot doesn’t always come, and that is what makes life so real and chaotic, and exciting.   The fleeting nature of time in a photo is also something interesting too. Time can rush by in big cities.  The sun comes up and sets in a place you’re not expecting. 

There are aspects of design but also of the nature, that compose the city, that I’d say make it different and beautiful.

 
The enraptured framed within the unenraptured , the sparse and dim places, the uninspired.  It is chemical art, where the photo becomes composed of the visual elements like carbon and oxygen, hydrogen, compose rings of cyclodextrins.  Like matter. Unassuming and candid.  I was just as interested in showing the effects of these photos as in exploring them deeper, their impact on photographer.  Less is more.  It took time to find words that would work for these.  Notes are not specific and deliberately so,. The noise is reduced as much as possible. They only speak to the places, or of the places as they should probably do,  but not the photos themselves.  And like a drawing of a molecule, it cannot really show how the molecule reacts, its nature, which is known to the mind’s eye.  I think they are superficial like chemistry drawings sometimes, they reveal very little of the beauty of what’s behind them.  Still this is an attempt to show but not show too much and preserve and enhance the mystery that is very natural and beautiful about this place. 

Photographs like paintings, can hang in mysterious galleries.  Places that are not always physical ones, in the mind’s eye, but places, even landscapes that contains so much more than simple objects.

I think that the rational mind can be hidden sometimes by emotion so that very obvious things that it should perhaps know are hidden from itself, The emotional lattice can’t be seen except like a shape through a foggy window.  But possibly too, we don’t expect the things we want most.  They are obvious and yet unreal because we refuse to accept the potential of their reality.  And we can’t see them either when emotion is deep.  They are invisible like ghosts.  That is because things in the mind’s eye are so much more real, than the objects and light and shapes that compose them, that confront the eye.  They have time.  Time confronts us with causality.  So too are paintings that reveal very little of where they came from, and yet this denied existence is more of what they really are.  Paintings that create the illusion of time and causality achieve something beyond their surface, their elements.  What they represent, in the mind’s eye, is more real than what we see.  And so is life. It is natural that  you would feel that way and if you have feelings about it, as I do, the reaction (to the feeling) might be very natural too.  after much time, feelings that are true, still exist.  And they are possibly unresolved, complex and naked” in that they are simply as they are, with nothing added and nothing taken away.
 

“light coming over the ocean”

 The unplanned nature of this wandering produced I think, a candid personal view of a city through my lens.  Many photos and words behind them are superficial to what lies beneath.  I think more natural photos are the best.  Shadows, disappearing horizons, night shots, architecture and beauties who would traipse through now and then made them more exciting.  I added some notes a year later not because I was trying at documentary, but because most are famous in this city, and should be noted.  So it’s superficiality is perhaps an illusion unseen things and stories that echo behind the images.  They are illusions of reality of life, and emotion.

There isn’t enough time to say everything and so it becomes superficial and most of the deeper elements go unsaid.

Shelley writes in “Hymn To Intellectual Beauty”

“Like moonbeams that behind some piny mountain shower,

It visits with inconstant glance

Each human heart and countenance”.

 

Photos visit us too with some unseen power.