Dear Marcel,

I am not a physicist. I hope Hanno will explain something to us in respect to the following: I dare to say that agglomerations of particles behave differently from singular particles for which the Heisenberg principle is relevant. We should not extend principles from the subatomic dimension onto larger dimensions. So we should not say that we cannot know what happens to macroscopic objects because of the uncertainty principle in relation to subatomic objects. There can always be an uncertainty (not "Unschärfe") for macroscopic objects, too, but not because of the Heisenberg Principle.

Grains of sand can consist of various materials.  We should not say that it thwarted our bill after accepting it in our experiment. I think we are working with some concepts that refer to very specific objects while other concepts refer to families of objects. Almost every scientific statement is such a combination of general and singular terms.

In relation to two oxygen atoms I would say that they are structurally the same even in combination with other atoms, but I am willing to learn.

Your question is, once more, a very interesting one. In the meantime I would like to recommend Nancy Cartwright’s How the laws of physics lie – She is homophonic with you in saying that individual measurements never display an outcome that is congruent with what was predicted by the laws.

She also writes about truth of statements in relation to laws and about correlation/causality.

Two phenomena can by definition not be physically expressed simultaneously at the same spatiotemporal moment. Interactions between phenomena and their environment should therefore also be unique in (perceived) physical expression.

Philosophers might claim that the greatest human scientific challenge will be to demonstrate that two phenomena are physically exactly the same at all scales of analysis or perception. Or not?

And if people do not agree, why?

Wikipedia statement: In modern philosophical use, the term 'phenomenon' has come to mean what is experienced as given. In Immanuel Kant's Inaugural Dissertation, On the Form and Principles of the Sensible and Intelligible World (1770), Kant theorizes that the human mind is restricted to the logical world and thus can only interpret and understand occurrences according to their physical appearances. He wrote that humans could infer only as much as their senses allowed, but not experience the actual object itself.

From scientific point of view studying a phenomena is not the same as doing exact the same thing or observing the same thing. As in fact such thing is not possible. It's more like playing a maze puzzle. The scientists observes causal relationships or correlations. I personally prefer the term correlation over causality.

Dear Nona,

people never do exactly the same thing or never observe exactly the same thing. This also implies they will never observe exactly the same correlation in at least one scale of analysis or perception. If people think otherwise, I would like to the arguments.

There's a sensibility to science that is recognized by those who practice a science of qualities.  That is, one can't deny that there is something the same about the same type of phenomenon such that we call it by a single name to the extent that many would agree.  So, I don't think you would find a group of experts practicing a particular discipline ever arguing over details of whether this molecule was in the same place during these two typhoons or whether these identical twins should get cancer at the same exact time.. 

Therefore, with respect to your question about replicability, it is understood that the goal is about choosing significant things.  Yet, neither is this considered simply a "human mental product disconnected from the true nature" nor is it a matter of scientists accepting "imprecisions" to make things replicable. That is, there exist forces outside of that investigator's control.  Skeptical minds will resist, the phenomenon, itself, will produce surprises if you're wrong.

"I call “truth” "predestinate opinion, by which I ought to have meant that which would ultimately prevail if investigation were carried sufficiently far in that particular direction."   C.S. Peirce

http://www.commens.org/dictionary/term/truth

Are 'replicable' phenomena as defined in science practice not more than human mental products disconnected from the true nature of nature? Scientists might for example accept 'imprecisions' when they define classes or groups of phenomena with common characteristics to make them 'replicable'. Do scientists invent artificial rules to make science practice workable from an empirical or mathematic point of view?

oops...that last bit was your words, clearly.

J

There is a difference between details in nature that might be useful for humans (e.g. to improve the living conditions that do not require many details concerning how the world functions) and the details that exist but simply ignored, e.g. because of time constraints/mental constraints/perception constraints.... If science ignores the last set of details because of X reasons what people call 'exact' science is not really 'exact' because of biased visions of the world....

Dear Marcel,

I am not a physicist. I hope Hanno will explain something to us in respect to the following: I dare to say that agglomerations of particles behave differently from singular particles for which the Heisenberg principle is relevant. We should not extend principles from the subatomic dimension onto larger dimensions. So we should not say that we cannot know what happens to macroscopic objects because of the uncertainty principle in relation to subatomic objects. There can always be an uncertainty (not "Unschärfe") for macroscopic objects, too, but not because of the Heisenberg Principle.

Grains of sand can consist of various materials.  We should not say that it thwarted our bill after accepting it in our experiment. I think we are working with some concepts that refer to very specific objects while other concepts refer to families of objects. Almost every scientific statement is such a combination of general and singular terms.

In relation to two oxygen atoms I would say that they are structurally the same even in combination with other atoms, but I am willing to learn.

Your question is, once more, a very interesting one. In the meantime I would like to recommend Nancy Cartwright’s How the laws of physics lie – She is homophonic with you in saying that individual measurements never display an outcome that is congruent with what was predicted by the laws.

She also writes about truth of statements in relation to laws and about correlation/causality.

Dear Martin,

yes, it would be nice to have additional comments from specialists in Physics!

Replication means repeatable. The replicate must not be exact, but it must be good enough, based on the given definition of good enough. An assembly line turns out replicas. Not one is exactly like the other. Each that is good enough is accepted, those that are not are rejected.

Science requires replication. The replicator must define good enough (subject to argument by peers).

A grain of sand cannot be like any other grain of sand, yet two may be close enough that we cannot tell the difference based on the method of comparison. We could call this replication within bounds. Twenty or 1000 grains of sand that are similar under the defined conditions might be used to confirm a scientific hypothesis. Someone wishing to replicate the test has to collect another 20 or 1000 grains of sand. The same collection method and bounds must be used.

Two oxygen atoms, both comprising the most common isotope of oxygen, are identical. We have no way at present of saying otherwise. We also have no theoretical basis for saying otherwise. The identity is good enough. Nevertheless, two oxygen atoms can be in different states. This can be measured. The two atoms are identical because all the same states are accessible to both. We can distinguish states, but the atoms are interchangeable. It is like identical twins, one may be outside and one inside. They are still identical.

Would specialists in Physics accept the idea that the trajectories of the electrons of two oxygen atoms are identical/exactly the same? They might say, 'no' but also think this level of variation is not interesting from a scientific point of view? Is this science? 

Yes, the two oxygene atoms are identical in all details. And the electron distributions of course are totally identical at least as long as you don´t disturb them by measurements or some other kind of interaction. These are the principles of quantum theory and I don´t see a reasonable way out.

Large systems like your grains can til now not be described or understood by quantum theory. We today only have the classical descriptions.

Dear Hanno,

But how you know this with 100% certainty accepting that atoms are (probably) always in interaction with something. In addition, two atoms are not at the same place, and therefore differ in environment, or not?

If I understood well, there is also a methodological problem: you can measure position or speed, not the two at the same time and everything electron is moving so fast... 

Dear Marcel,

here we start again the old discussion of quantum theory. Without interaction you dont know anything. But you have to accept the undefined status to explain the result after your interaction. Just remember the famous Schrödingers Katze or the double slit experiment with electrons.

Dear Hanno,

That's what I mean. Theory is often based on unverified assumptions... Theory is often based on 'believe'... (like religion?)

Dear Marcel,

I want to contradict. If you need a special assumption to explain a later result, the status of science tells us the theory is ok. But you are not thwarted as scientist to find better basics.

Dear Marcel,

I think it is a slightly different thing you are after. The poor cat reacts on poison that is released in a macroscopic device. This macroscopic device reacts on a subatomic state. It is not the cat that turned into a “Heisenberg thing” (a macroscopic object that is submitted to Heisenberg’s uncertainty). The cat is still an object with a measurable position and impulse.

Dear Martin,

Schrödingers cat is the famous paradoxon used in quantum theory to show that the status is only defined after the interaction. Of course, cats are macroscopic.

And when scientists observe a phenomenon, they interact with the phenomenon

Yes, observing is interaction. The question is, does this interaction change ascertainably the status of the object. Thats the case for microscopic atomic structures, it doesn´t happen for macroscopic systems like real cats.

The behavior of a cat changes when you observe a cat...

Only if the cat is able to observe your observation. Take a infrared camera 5 miles away or just listen to it´s meow.

PS: I don´t know which kind of cats you know. Most cats even don´t ignore you with one exception: fresh meal. ;-)

The cat is “between life and death” not because of some “cat properties” or some properties of our perception organs reacting on cats, but because it is part of a device that is going to kill her in reaction to a measurement of a subatomic state. I think we are not entitled to assume that a bird might be in a state of Heisenberg uncertainty only because we have not excluded that somebody construed a device that keeps the bird in a Schrödinger-situation.

But let’s assume the bird has been brought into a Schrödinger-situation: what would a mean scientist need therefore? He would need more than Marcel is assuming: he would need a device that makes a measurement on a subatomic scale plus an apparatus that can do something to the bird. Sense organs of a bird watcher would not be enough, right?

I agree with Hanno. Certainly we need approximations of physical reality. For macroscopic world these approximations work nicely. For microscopic realities the observer is incorporated to reality itself and thing become much more difficult. 

I should add that when we have probability uncertainty, then the experiments should be repeatable, otherwise probability should not be applied. In such cases we have non probabilistic methods to apply.  

We should consider also biological realities, where mathematics seems not to apply  easily. 

Dear Martin please read the wiki: http://de.wikipedia.org/wiki/Schrödingers_Katze. It´s time saving for our dispute, or if you prefer the english version with the same statements.

168O represents the most abundant isotope of oxygen. The structures of any 2 atoms of this isotope are exactly the same; they will have identical nuclei containing 8 protons & 8 neutrons and they will also have the same distribution of the 8 electrons in orbitals outside the nuclei. An orbital is a region in space where an electron is most probably found (i.e. we are not talking about a definite location but a most probable location). Uncertainty in pinpointing location of an electron is not something unusual since this tiny particle is always on the move & does not rest.

The structures of 2 oxygen atoms in the above example ought to be distinguished from their positions. When the factor of position is entered, then there will be variations in potential energies as simple as when one O atom is in a lab in the 3rd floor & the other one is in a lab in the 4th floor.

Turning to macro scale, when you & I make 2 pieces of soap then they may differ even if we followed the same procedure & used the same materials. This is the essence of batch production. But when the production of soap is done one a large scale in continuous manner, then the products ought to be uniform in all aspects. Every piece will be identical with every piece in various features. Any piece, that comes out unmatching the others, is considered as a defect & is rejected.

An example which explains better: when table salt is dissolved completely in pure water in a cup, the taste will be the same whether you take 2 or 3 or more sips. There is definite replication of sips & tastes since the solution is homogeneous from top to bottom.

Perhaps. Nobody verified all details because of perception constraints or time constraints. I know this is an easy argument, but I also think it is a fact

Dear Marcel,

I think perception constraints are not disputed. Let’s return to your question: Why would you, then, repeat the experiments? Are you hoping to cover different segments of an incomplete picture? Or do you stay with your claim of principally incomplete perception?

Please don´t confuse events with quantummechnical particles. Two totally different worlds.

Dear Martin,

I like the idea 'good enough'. Replication can be 'good enough' and accepted by science practice. As I said before, we do not require to know every tiny detail in nature to survive, to reproduce, to be happy, to be healthy, etc...

A Mathematician, a Biologist and a Physicist are sitting in a street cafe watching people going in and coming out of the house on the other side of the street. First they see two people going into the house. Time passes. After a while they notice three persons coming out of the house.

The Physicist: "The measurement wasn't accurate.".

The Biologist: "They have reproduced".

The Mathematician: "If now exactly one person enters the house then it will be empty again."

“The opinion which is fated to be ultimately agreed to by all who investigate, is what we mean by the truth, and the object represented in this opinion is the real.”  C.S. Peirce

Herbert Simon:

“The Scientist is a problem solver. If the thesis is true, then we can dispense with a theory of scientific discovery - the processes of discovery are just applications of the processes of problem solving.”

“Economic man deals with the "real world" in all its complexity.  Administrative man recognizes that the world he perceives is a drastic simplified model... He makes his choices using a simple picture of the situation that takes into account just a few of the factors that he regards as most relevant and crucial.”

“I don't care how big and fast computers are, they're not as big and fast as the world.”

“The world you perceive is drastically simplified model of the real world.”

__________

"It´s time saving for our dispute..."   Hanno Krieger

"Nobody verified all details because of perception constraints or time constraints."  Marcel Lambrechts

My friend Jerry,

The world is a reflection (and a perception perhaps) of the perfection of the Maker beyond  the limitations of time, space and matter  and their scientific and mundane constraints! 

Dear Jerry dear Marcel, dear Marwan,

Very wise. We could leave it. But there was Marcel’s question….I find it interesting to go on with the discussion for a special reason:

There are dozens of questions on RG suggesting that quantum effects rule our daily life. I would like to have a discussion about the tendency to assume that there is a big door open for us to cross the scales in both directions. I hope you will share the fun.

Dear Hanno,

Thanks for the link about Schrödinger’s cat. I’m impressed by mesoscopic cat states of 6 (separated) atoms. Nevertheless it is about spin up or spin down. So when you are joking about the smell of fresh cat food you are talking about phenomena in a different scale, right?.

I don’t want eternal discussions. Just one question: When I say to Marcel “Don’t wait for an atom or particle to come by and change something for a bird in the forest while you are watching it.” – Would you agree? Why should you?

1. To be closed off is not enough for an intervening observation to decisively change something that will be realized in the observation after the opening.

2. To be in a state in which it is not decided whether the spin is up or down is not enough to attract the cat once it is decided. (Well, we already know that most of the RG fellows like “ups”).

3. Why are we having the discussion right now? It was clear for hundreds of years that cats are attracted by certain smells without any discussion about the time point in which the cat is exposed to it.

The question was, "All phenomena are unique in perceived physical expression: what are the potential consequences for the definition of 'replicated' science practice?" The last sentence in the argument was, "Do scientists invent artificial rules to make science practice workable from an empirical or mathematic point of view?"

Each phenomenon is unique. Each phenomenon is perceived unique. These are two different statements. There is no possibility to replicate, if the philosophical perception of unique quantifies the definition of replication. There is no potential problem. No replication is possible. One person's philosophy may drive one's belief, but it does not change the scientific method for the rest of us. We all have our unique interpretation of the scientific method and that interpretation is subject to change. Nevertheless, the definition of replication as good enough or the scientific method as good enough does not constitute inventing artificial rules to make science practice workable. We deal with what we have until we invent a better way of doing it. A philosophical point of view of perfection and uniqueness is also subject to change. We deal with that point of view as necessary and keep redefining good enough.

Macroscopic phenomena defined on a quantum level may help with a description but does not hold at quantum dimensions. Quantum phenomena defined on a macroscopic cat are not applicable at cat-like dimensions. Knowing the exact location of a cat is an easy observation. Knowing the exact location of an electron is but a fleeting thing. I was once scratched by a cat. Last week I lost an electron, I am positive.

Martin

Do quantum effects rule our daily lives? An atom comprises a very dense nucleus and is surrounded by space that is sparsely populated by electrons. The volume of an atom is mostly empty space. The floor you are standing on is mostly empty space. Why do you not fall through? And you thought cats were strange. But then, they too are empty space. Do you expect a particle to come along and change it?

Sure, quantum effects rule our daily lives, but our daily lives are macroscopic.

Dear Jerry,

I know your jokes. But joking doesn´t help to find translations of our different aspects or common thoughts and models. But besides jokes, how shall we find a resolution?

Joseph,

Of course I am aware that quantum effects rule our daily lives in the sense that atoms and particles are what they are. I had better asked if it is reasonable to expect that the changing of a feature of a single particle (that is not separated) could be efficient enough to make Marcel see a different result in a repeated experiment. I guess this is not the case. I am not talking of domino effects or changed forces.

Dear all,

Yes, we should deal with replication.  If I may with another quote by Peirce:

“Different minds may set out with the most antagonistic views, but the progress of investigation carries them by a force outside of themselves to one and the same conclusion.”

The joke about physicists/biologists/maths above was to emphasize that different people bring different conceptions to a problem and they have different things they want to know.  Replication plays an important role in coming to agreement because we make a contract that if this experiment produces this result irrespective of who performs the experiment, then the conclusion is so and so.  In most circumstances of normal science in which the problem is already structured in an agreed-upon sense, we take many assumed parts of enthymemes (a syllogism in which we are still working out the details of premises, ie., abduction-in-progress) as being understood.  Yet, there are too many things we have to consider and, as Marcel pointed out, some of these may be relevant to the problem at hand.  We just don’t know, yet.

One problem arises when someone outside this framework comes in to the inquiry, who brings his own sensibility and standards of measurement.  This can lead to reproductions of old questions that have already been addressed, which will make the new person sheepish and embarrassed…or he may bring a novel perspective that needs to be addressed, which can make the establishment angry or dismissive.  Yet, some may actually take notice and further the inquiry.  Regardless, our challenge is to compose an elegant experiment to address the new sensibility.

The scientific method exposes such values in decision-making of what is relevant and what needs to be addressed…what is considered replicated or not.

Replication falls under the rubric of inquiry in which the measurement scales are more or less agreed-upon or in the complicated but ideal case, accepted/believed to be resolvable in the long-run.  A good working hypothesis will stimulate productive imagination, which facilitates truth construction.  New supportive information will feed back and give more confidence in this scientific method of knowing.  Exactness, therefore, becomes one of consensus opinion, a collective sensibility.

“…that mind into which the minds of utterer and interpreter have to be fused in order that any communication should take place … may be called the commens. It consists of all that is, and must be, well understood between utterer and interpreter, at the outset, in order that the sign in question should fulfill its function.”

Charles S. Peirce, 1906

Martin

There is no butterfly effect in quantum mechanics. Chaos theory postulates that the flutter of a butterfly wing in Brazil could lead to a tornado in Kansas. This is far from the truth, indeed, ridiculously far from the truth. It is used to explain that the starting point of a nonlinear system cannot predict the end point.

͕T̊rµe ph͝ysics looks at entropies and diversities.

Yes, indeed the need is to reduce to workable index and orders. But it is no longer correspondent to a raw construction of hierarchies and classes, and the unification is no more related to the objective of a mere "regulation". It is rather the effect of an approximation of sensitivities across the scales, indeed we would say "more true orders".

Marcel, some of your questions are well answered within the argument argued in the attached file [From Entropies twd Diversities].

—g

Replication, which is a necessary principle in investigating and studying things that are obscured or similar in some sense, should indeed be in terms of an existence of some mapping(s) between two physical or abstract things. In mathematics for instance we can differentiate two topological manifolds (or spaces ) as similar or topologically invariant, if one is continuously deformed to the other or simply if there is a  homeomorphism between the two topological spaces. In mathematical discourse therefore, the mathematics we do in one manifold or space is equivalently valid in a topologically isomorphic or homeomorphic space as well, which is not the case in non-homeomorphic spaces. Therefore to count different- ness,  it is non-homeomorphic spaces what are called different and distinct. 

For instance the mathematics performed in doughnut like spaces is exactly valid in a coffee mug like spaces.      

Dear Hanno,

Thank you for the wonderful question! 

“But joking doesn´t help to find translations of our different aspects or common thoughts and models. But besides jokes, how shall we find a resolution?”

Peirce starts to address your question in the Fixation of Belief.  First, he defines the contrast between doubt and belief:

“Doubt is an uneasy and dissatisfied state from which we struggle to free ourselves and pass into the state of belief; while the latter is a calm and satisfactory state which we do not wish to avoid, or to change to a belief in anything else.”

He then states that “the sole object of inquiry is the settlement of opinion. We may fancy that this is not enough for us, and that we seek, not merely an opinion, but a true opinion.”

He then discusses the different methods of fixing belief and judges them. 

In other works, he develops his idea of the scientific method more, which can be considered as reasoning correctly; the systematic application of abduction, deduction, induction/inference to the best explanation, repeat.  We discuss one example in our recent paper, which I believe to be a very special case. 

I was fortunate to stumble across Peirce at a time I was asking a simple why question.  It helped me to interpret much of what he was talking about, although I have only read a small piece of his work.  That is, my experience with a special number and my embedding in the current science environment helped to interpret the following so that it started to make some sense: “If you carefully consider the question of pragmatism you will see that it is nothing else than the question of the logic of abduction.”    (logic defined as how we ought to think).

One valuable thing I keep losing sight of is how embedded we all are in this complex culture of doing science and how dependent we are in that system.  His motivation to help us navigate this complexity of doing collective science is pervasive throughout his works. 

btw Marcel,

Many of the questions you posed on here, I struggled with while working on the manuscript (eg., on the precision of our questions and others...).  I would really appreciate your thoughts on it, if you have time.

Dear Jerry,

You say:

One valuable thing I keep losing sight of is how embedded we all are in this complex culture of doing science and how dependent we are in that system. His motivation to help us navigate this complexity of doing collective science is pervasive throughout his works.

For discussion:

It are these human-defined/culture-dependent standards that can make the science method human-acceptably repeatable or replicable. This does not mean they are truly repeatable/replicable in details ignored by human scientists, e.g. those details considered to be unimportant/irrelevant in a science framework. 

Marcel,

You're right, it doesn't mean that those details are strictly replicable right now because measurement depends on a lot of things.  But we can also talk about whether that will be true in the long run.  That is, we can imagine in some distant future, after we've had enough time to examine the problem in detail, to determine whether there will be a consensus between all who investigate, that such  experiments are replicated. 

To talk about whether that time will come requires faith and sensibility...a belief, a willingness to act.  I believe that if we all practice the scientific method correctly, at least in the systematic manner Peirce set up, then that convergence will happen.

Hello,

I think consensus is very important. Of course, there has been scientific consensus in the past which in the course of knowledge evolution that apparently was not always correct? Any examples?

Jerry

Replication in the scientific method is here and now. If we practice the scientific method correctly there is no need for convergence in the long run. Replication must be accomplished in an acceptable, well-defined manner within the confines of the measurement system. The confines of the measurement system determine if the replication was good enough.

There may different interpretations of the effect, but replication means replication.

Peirce talks about consensus opinion "fated to be agreed upon by all who investigate".  Therefore, it depends on what you mean by consensus and the difficulty of changing opinions in reality. 

97% of scientists agreeing on whether man is causing climate change means that there is consensus to those who believe (who would call it truth).  To the 3%, it means that there isn't a consensus (who would call it opinion).  Regardless of which, the important matter to those who investigate is NOT whether there is or isn't a consensus.  The part that matters is the values they have that influence the choice to believe or not and whether an argument can be constructed so that others will also believe. 

This is one example of embeddedness and it also gives an idea of how steering consensus opinion can be outside of ourselves.  But this doesn't necessitate that current consensus is the consensus at the limit. Something may happen tomorrow to push that number higher or lower, like your house burning down because of drought.  An important matter is whether we are willing to act on that belief.

Joseph, how would you respond to Marcel's point that consensus opinions change and that if we examine the details closely enough, one can say that the experiment has not been replicated?  

As an example, we can talk about all the problems with biological replication going on in the cancer and high throughput science community.  What standard would we agree upon to say that this microarray experiment replicates that?

In the context of doing science, I agree with you that there is a sensibility involved, a scientific temperament.  I also think that in that context, investigators will not fuss over details once the problem is framed clearly enough but people have been known to be crazy...and sometimes, crazy is creativity that isn't recognized by others.

...and importantly, not all problems are framed clearly, which would be a major difference between replication now and at the future limit.

I will repost a previous comment on scientific temper because of its relevance:

In the following video, Putnam equates temperament with sensibility.

https://www.youtube.com/watch?v=0pNXUVImSyM

Given the many things we could talk about, Richard Bernstein ascribes recognition of an important distinction to Putnam:

“good philosophy…combines two different sorts of things: vision, some type of vision with a certain amount of argumentative finesse.  And if you don’t have a sense of vision…it can turn into just pedantry.  And…if you just have argumentative finesse and all that, it can become terribly boring.  And the ought that makes the distinctive philosopher is the capacity to combine the two in an interesting kind of mix.”

Finally, Douglas Anderson says of William James,

"James once put it that the person you meet that has no philosophical temperament at all, is the most inauspicious of characters that you might want to hang around with...they're just uninteresting".

Jerry

Consensus is far different from replication. Consensus is driven by personalities, social and political pressure, funding, and years of repetition of the same beliefs. Replication means the ability to repeat an outcome whatever the consensus. Replication means replication and it could mean within the consensus.

On several occasions I have attempted to replicate a peer reviewed result. I performed the experiment in exactly the same way. I discussed the experiment with the authors to ensure that I was replicating the conditions of the experiment. I did not get the same result. On two occasions the original results were retracted. On others I received excuses.

Millikan measured the charge to mass ratio of the electron. No one was able to replicate his results, but no one admitted it until over twenty years later. The consensus was 'How could Millikan be wrong?' Millikan was not wrong, but  his instrument was improperly calibrated.

Yes. It is possible that consensus beliefs and practices can cause errors that later are corrected. Replication means replication no matter where you sit or stand. Improperly framed questions can lead to improper conclusions. Within the question replication means replication.

It is unfortunate that high throughput science can lead to a rush to judgement and to publication without replication. In a high throughput science, replication means replication. Note the level of non-replication in medical science.

97% consensus in climate change? Really? By whose count?

Hi Joseph,

Here's an interesting site.  I had no idea it existed as I recalled that number from a news column.  Does this change your attitude towards the truth of that number?

http://climate.nasa.gov/scientific-consensus/

In my opinion, replication can't be understood without respect to all three of the following: the sign, object and interpreter.  Biological measurement replicability can depend on the state of the tissues you're measuring, what age, what sex, at what state of stimulation, what part of the tissue, what thing in that tissue you're looking at, the measurement tool, the coarseness of the range, what the acceptable standards are with regard to that measurement, the purpose of taking the measurement in the first place with respect to what others have said about it, at different scales of attention, previous knowledge about the dynamics of activity (oscillations, plastic transformations) etc...

Therefore, one can perform the replication assay, get a completely different result, and the experiment can be said to have been replicated because it accurately reflects the same process at different stages of physiology/development.  Whether the experimenter taking that measurement is aware of all that must be known to represent what we'd like to know can also affect our decision to repeat the experiment and whether we accept that the experiment has been replicated.  Given the magnitude of what we'd like to know, we tend to satisfice because things are close enough to expectation for further inquiry.  The problem is that what we don't all have the same expectations, especially when the problem is not structured clearly.

Another confounding matter is how our decisions are affected by the labor-intensiveness, the costs, social pressures, how it fits in a story for publication, even...

Replication of methods versus replication of results of methods

How important is the impact of the observer in research replicated from a methodological point of view? Imagine that 100 observers have the same television placed at the same distance watching the same YouTube film, but the 100 observers are not in contact with each other to discuss what/where to look at. What are potential consequences (see example below).

Analysis of short wildlife films

A film lasting about four minutes on YouTube might illustrate examples of wildlife behaviour, like plant-animal interactions during pollination. The film can practically be subdivided into a large number of pictures on a screen of 1 m². Each individual picture of the film might also be subdivided into smaller or larger compartments. If one picture would be subdivided into a puzzle of 10.000 cm² and each 1 cm² is visualized and analysed separately, which part of the screen is required to get an idea about the information provided by the whole screen and the whole film? Doing this might result in a continuous flow of an uncountable number of potential hypotheses. Different people watching the whole film, a fraction of the film, or a fraction of the screen presenting one picture of the film will produce different hypotheses based on what they perceive and what they memorized in the past. Different potential hypotheses will definitely follow different probability distributions depending on who is watching the film and scales of analysis or perception involved. The probability that two observers will produce exactly the same hypothesis using the same wording and terminology will probably be very low. How many hypotheses might be formulated focusing on only 1 cm² from a screen of 1 m² and what will be the scientific approach used? Hypotheses and methods used to test them will definitely change with changes in scales of analysis and perception, e.g. going from 1 pixel to 1 cm² to 2 cm² up to 1m². Pixel analysis might focus on physics of colors whereas analyses of whole pictures might focus on physics of colors or color contrasts but also on other aspects, like how and why two filmed species interact. Moreover, how many mathematical equations will be required to describe film details concerned with pollination of flowers? If people only would have access to Mathematics describing the film they did not see before, how would they translate equations into film pictures? How would different mathematicians cope with 20 pages of mathematical equations to be transformed into visual pictures of which contents become accessible to citizens? All this illustrates that interactions between methods and hypothesis-testing involving people varying in background knowledge might potentially result in an uncountable number of hypotheses and related conclusions, evidently depending on scales of analysis or perception involved. It also implies that the same problem might be tackled in many different ways depending on who will start and conduct research, probably related to past biology-based experience of the researchers involved.

In this case, dear Marcel, I'm afraid we are NOT talking about the film and what it IS, in the first place, but about our responses and what they DO in us!

Dear Marwan,

Observer - method interactions that produce the results can never be truly replicated!

Experimental design can never be truly replicated because collaborators rarely or not visit set ups from other teams and set ups at a given place express uncontrolled dynamics

Examples (cf. example of tissues above)

Laboratory: There will always be at least one inaccessible scale of analysis or perception in laboratory experiments. Laboratory conditions will never be truly standardized from a practical or logistic point of view. A test cage or a laboratory harbouring a test cage consists of multiple visible and invisible characteristics (e.g. micro-organism communities and their dynamics) reflected in methods to clean cage environments, individual observer behaviour, material coming from multiple ‘uncontrolled’ external sources, etc.

Field experiments: Field conditions may scientifically never be truly standardized because of perception constraints, logistic constraints or continuous dynamics in nature. 

Marcel,

You said:  "The probability that two observers will produce exactly the same hypothesis using the same wording and terminology will probably be very low."

How do you calculate that probability?  Whewell, Peirce and Simon all talk about this weird ability we have, how the "human mind is akin to the truth in the sense that in a finite number of guesses it will light upon the correct hypothesis”  C.S. Peirce 

This, in spite of the fact that the possible problem spaces are immense. 

"Problem spaces, even those associated with relatively "simple" task environments, are enormous…The sizes of problem spaces for games like chess or checkers are measured by very large powers of ten—10 to the 120 power, perhaps, in the case of chess.  The spaces associated with the problem called "life" are, of course, immensely larger...

Problems with immense spaces inform us that the amount of search required to find solutions, making use of available structure, bears little or no relation to the size of the entire space.  To a major extent, the power of heuristics resides in their capability for examining small, promising regions of the entire space and simply ignoring the rest."   Herbert Simon and Allen Newell

I agree, but how do you know that what is examined is representative for the entire.... (e.g. study population representing more or less the target population)

Retrieving a concept from Jost (cit., 2006), what mathematics indexing considers as "deviation", is regarded as "diversity" and "community richness" within the biologists' indexes.

However, the level that both indexes are working :

#1. are certainly "consistent", if the functions to which they relate are both concave;

# 2. however, remain "limited" to the radius of each index.

In this sense, a diversity more "true" must be determined. And Jost finds that truth in Hill's effectiveness (1973).

I do not think we can agree with Hoffmann S, A,  (2006) when quoting Tim Thompson (Feb 2002), they try to upset that truth setting the concept of entropy in a relative dimension; of course, Thompson states his evaluation based on very solid arguments:

• “The easist answer to the question, What is entropy?, is […] :

Entropy is what the equations define it to be. You can interpret those equations to come up with a prosey explanation, but remember that the prose and the equations have to match up, because the equations give a firm, mathematical definition, […] that just won’t go away.”

but the basic architecture, in my opinion, ends up being Nietzscheanly perspectivist, if interposed as a limit to the final identification of more refined and approximating entropy. I do not think that, what Jost indicates as "true" should be understood in a subtractive sense ["selected”; "exclusive"]; but it is better understood in the sense of "closer" > "smoothing" > more approximating the various indices > more "prepared" to make fertile different karyotypes, each to the others.

It is something very evolutive, on my opinion: it makes smoother the transition from the "pixelization" of shapes in quantum indices, towards the unique design of an emergent identity — even if it was composed of anonymous pattern, all replicated.

It frees up the observer from the issue of his intervention on the nuclear object, returning to him a wider scale both non-deformable [for the single units] and receptive [for the whole item].

—g

Dear G.,

It remains human-made with all the perceptions constraints involved

I don't believe so, Marcel.

However, we could fall in the ancient dilemma whether mathematics and any other code are human constructs or natural entities in themselves. We do or we find an index?

—g

Dear G.,

Mathematics is obviously not more than a human-made language providing a very simplified vision of nature's complexity. Because humans belong to nature, maths as a language belongs to nature. This has been discussed in another question a while ago.

Yes, I'm aware of that very long thread, and I was bored from its reductionism. I just wrote a topic of few minutes, just to keep it in memory.

The fact is that both branches lead to the same condition [and it could not be otherwise]:

#1. codes are written by us, for the purpose of epistemological synthesis: well, our need is to refine more and more, because the goal is to resemble the truth;

# 2. codes are autonomous and natural, therefore our need is to understand more and more finely, because otherwise our understanding is not resembling the truth.

Because the nature, although complex, is true - and this assumption is useful and inviolable - it could not be otherwise. It's just different every time we build a new artificial mathematical, and any other artificiality.

But your quanta are natural, aren't they? The pixels of the screen you are referring to, are really happening in nature, or not?

So my point is to refine the closeness between different indexing, without confusing ontological and natural differences.

—g

The pixels of the screen are really happening in nature, but how the perception mechanism (e.g. the brain and its characteristics) biologically translates the pixels in what is seen by the observer might be defined as an 'illusion' not necessarily reflecting the true nature of the pixels. In addition, what we perceive are light emission patterns of the pixels, not the pixels per se.

Yes, I do agree. But it seems to me that you come to my way.

To avoid all the possibile falses in the mirroring of "items~ligands~receptors", we need to deepen into truth.

By the contraty, If we would stay helpless against the entity that lives by itself, we would have a world of incoherent self-atoms, a kind of schizophrenic madness.

—g 

Perhaps. Anyway, if brains would result from natural selection placed in an evolutionary framework, we do not have to know the true nature of pixels to survive, to reproduce, to be happy, to be healthy, do we?

An expert opinion that supports earlier views on how our experience with natural systems constrains our hypothesis making:

Vanag and Epstein, Pattern formation mechanisms in reaction-diffusion systems, Int J. Dev Biol, 2009:

"If a handful of inorganic chemicals can already generate such an immense variety, the range of possibilities available to the molecules of life seems almost unimaginable. Nevertheless, the results obtained in our “simple” systems and their striking similarity to living patterns suggest that chemistry may have much to teach us about the constraints that ultimately determine the range of biologically accessible patterns."

Marcel, to answer your question on how I "know" "that what is examined is representative for the entire..", it is a belief. 

Simply imagine yourself doing theoretical chemistry and developmental patterning with others who have decades of experience talking to one another and trying to act as rational agents, ie., to provide systematic explanations to why questions, which focuses attention.  How would you convince them that what you see is important enough to continue further inquiry and use of resources?  You basically would need to provide justification for your argument...and so goes the world...

From Of Minds & Language:  A dialogue with Noam Chomsky in the Basque-Country, Piattelli-Palmarini, Uriagereka and Salaburu:

Participant:  Could I ask you to deal a little bit with Peirce’s theory of abduction, and the importance of an abductive instinct?

Chomsky:

"Peirce posed the problem of abduction in lectures which I think are from about a century ago, but as far as I know, nobody ever noticed them until about the 1960s.  When I found them and wrote about them then, I couldn’t find any earlier discussion of them.  Those were pre-electronic days when you couldn’t do a real database search, but I couldn’t find any reference to Peirce’s theory of abduction.

Now, the term abduction is used, Jerry Fodor has spoken about it and others, but it is a different sense;  it is not Peirce’s sense.  Peirce’s sense was very straightforward and, I think, basically correct.  He says you want to account for the fact that science does develop, and that people do hit upon theories which sort of seem to be true.  He was also struck by the fact, and this is correct, that at a certain stage of science, a certain stage of understanding, every tends to come to the same theory, and if one person happens to come to it first, everyboy else says, “Yes, that’s right.”  Why does this happen?  You take any amount of data and innumerable theories can handle them, so how come you get this kind of convergence in a straight pattern through even what Thomas Kuhn called revolutions?"

From 

“Binary Synthesis”: Goethe’s Aesthetic Intuition in Literature and Science R. H. Stephenson

“There can be no such thing as an eclectic philosophy, but there can be eclectic philosophers. But an eclectic is anyone who, from whatever exists and is happening round about, appropriates the things he or she finds congenial to her or his nature; and this context validly includes all that can be called culture and progress in a theoretical and practical sense. It follows that two eclectic philosophers could turn into the greatest opponents if they are antagonistic to one another, each picking out whatever suits him or her in every traditional system of philosophy."

(Goethe, Wilhelm Meister’s Journeyman Years)

Yes indeed!

Marcel, scientists postulate hypotheses that are brought to the attention of the scientific community in general. That is the foundation of SCIENCE. Tested these hypotheses are accepted or rejected according to their "degree" of explanation of the phenomenon itself. This "degree" involves a series of repeatable "situations" in levels of uncertainty and bounded, who are defining the "viability" of the hypothesis. All "uniqueness" of the tested phenomenon is relative and subject to technical reliability margins vary according to the progress of civilization. In other words, the "objective reality" exists independently the know or not. And every time we are closer subjectively as individuals to know in depth. This "degree" of acceptance is the approach (for each species) from the subjective to the objective, and it is what varies continuamente.-

Dear Marcelo /Dear All,

For more discussion:

The degree to which hypotheses are formulated in exactly the same way:

If 1000 people would observe the same phenomenon ‘C’ and be asked to formulate a hypothesis ‘C’ to explain phenomenon ‘C’, what fraction of the observers would formulate hypothesis ‘C’ in exactly the same way, for instance with the same words expressed in the same order? Can the same hypothesis be represented with different oral or written expressions? This is apparently the case when different publications dealing with the same science topic are compared. Liberty in writing is advisable from an aesthetic point of view, but should it be allowed from a scientific or philosophical point of view?

The degree to which a single hypothesis is accepted by different people differing in back-ground information:

Different people that test the same hypothesis 'C' apparently accept or reject it with different degrees. Some people might, for instance, state that hypothesis ‘C’ is true with a probability of 75% whereas others do not believe hypothesis ‘C’ can work. Different people have different background information available definitely causing people to believe more or less in a given hypothesis. The scientific challenge then will be to identify reliability in individual-specific background information to judge claims from those that have more or less confidence in hypothesis ‘C’. Is it important to define historically interconnected chains in background information to ultimately support or reject a given hypothesis with higher or lower probability? Those that possess more historical information should be more efficient in hypothesis-testing when a scale of analysis is adequately defined.

Marcel:

If 1000 people would observe the same phenomenon ‘C’ and be asked to formulate a hypothesis ‘C’ to explain phenomenon ‘C’, what fraction of the observers would formulate hypothesis ‘C’ in exactly the same way, for instance with the same words expressed in the same order?

This formulation is incomplete, should be also taken into account the time dimension. Well, for example the hypothesis of the phenomenon "lightning" is not the same in prehistory and today. For in that time dimension increases the technification level of the "species" which interprets the phenomenon, regardless of the number of people who watch it.

Can the same hypothesis be represented with different oral or written expressions?

Yes, including with "mental models" different can arrive at the same conclusion. .

Hello again,

If 1000 specialists working in the same research field observe the same phenomenon 'C' and be asked to formulate a hypothesis 'C' without interacting with the fellow specialists, what fraction of the specialists would formulate hypothesis 'C' in exactly the same way, either orally or written?

Let's say the hypothesis is written with the same type of computer to control for the techniques used....

Hi all,

To be more precise, it should be hypothesis (A).  That is, according to Peirce:

The surprising fact, C, is observed.

But if A were true, C would be a matter of course.

Hence, there is reason to suspect that A is true.

We visited Peircean abduction in our latest report.  In it, we describe a phenomenon/vision/observation C and provide an explanation/mechanism A. 

In filling out what C and A are, we proposed

The surprising fact, the phi spiral (C), is observed.

But if our FEM model (A) were true, C would be a matter of course.

Hence, there is reason to suspect that A is true.

Prior to our work, the observation was not the phi spiral, rather it was "a spiral".  This means that because there are an infinite number of curves between a circle and a line that fit the term "spiral", the problem as posed was ill-structured.  Moreover, there was no strong consensus on what the mechanism should be without a clear statement of the relevance relation. 

"That is, we choose the working hypothesis (phi, FEM model), in contrast to rest of contrast-class X (i.e., Netlogo model), because A (deduction of logarithmic spiral, relevance relation) [21]. Adopting the hypothesis that the phi spiral describes the global state of the system proved valuable for structuring the abduction, which then allowed simple performance evaluation via resemblance during induction (CP 7.218), sc., inference to the best explanation [99]."

You can judge for yourself whether our choice of the phi spiral over a 21deg logarithmic spiral (M51) is a good one and imagine how it should be modified after further testing.  That is, the FEM model is expected to be adjusted and refined based on future consequences. 

Promoting convergence: the phi spiral in abduction of mouse corneal behaviors.

Dear Jerry,

What is your opinion concerning how/why (A) and C are related? Can you give a simple example concerning daily life to illustrate your point of view? 

Hi Marcel,

I think you’re asking me what makes for a good explanation and more specifically, what makes for a good scientific explanation.

This is a very complicated problem but I think van Fraassen gives a wonderful treatment in “The Scientific Image”.  He argues that you need at least three things, the topic, a contrast-class and a relevance relation.  The contrast-class determines the context and the context determines relevance.  Why questions are further influenced by presuppositions…

As an example of how complicated why-questions can be, he provides a simple case:

“Consider the question

3. Why did Adam eat the apple?

This same question can be construed in various ways, as is shown by the variants:

3a. Why was it Adam who ate the apple?

3b. Why was it the apple Adam ate?

3c. Why did Adam eat the apple?

In each case, the canonical form prescribed by Bromberger (as in 2 above) would be the same, namely

4. Why (is it the case that) (Adam ate the apple)?

yet there are three different explanation requests here.  The difference between these various requests is that they point to different contrasting alternatives. For example, 3b may ask why Adam ate the apple rather than some other fruit in the garden, while 3c asks perhaps why Adam ate the apple rather than give it back to Eve untouched. So to 3b, ‘because he was hungry’ is not a good answer, whereas to 3c it is. The correct general, underlying structure of a why-question is therefore

5. Why (is it the case that) P in contrast to (other members of) X?”

He gives other nice examples (“Compare ‘Why does the blood circulate through the body?’ answered (1) ‘because the heart pumps the blood through the arteries’ and (2) ‘to bring oxygen to every part of the body tissue’) and sums up his theory with:

"Summing up then, the why-question Q expressed by an interrogative in a given context will be determined by three factors:

The topic Pk

The contrast-class X = {P1, . . ., Pk, . . .}

The relevance relation R

and, in a preliminary way, we may identify the abstract why-question with the triple consisting of these three   Q = (Pk, X, R):

A proposition A is called relevant to Q exactly if A bears relation R to the couple (Pk, X)  "

So, going back to your question, framing the observation C clearly will help evaluate the goodness of the contrast class of hypotheses/mechanisms that can explain C. 

I should add, though, that justification depends on a lot of other information that may not be obvious to everyone discussing case examples.  Lipton discusses nuances of "inference to the loveliest explanation" in his works on IBE. 

All this determined by biology-based processes: abilities to communicate, abilities to write, what has been memorised in the past, the environment of the past, the perception mechanism that treats information, etc.....

From BBC World today:

The weird and wonderful world of quantum mechanics reveals that nature is at heart probabilistic. Nothing can be predicted with any certainty.

.. where physicists don't agree is about how these facts should be interpreted....

This would implies that more complex constructions built from quantum mechanic principles (atoms, molecules, tissues, rocks, organisms, etc...) should at heart also be probabilistic. No physical structure can be predicted with any certainty  

Quantum mechanics does not say

Nothing can be predicted with any certainty.

In deed, quantum mechanics says atomic phenomena are predicted with high certainty. Popular interpretations of quantum mechanics and relativity include interpretations beyond the reach of the models and a good dose of hyperbole.

Dear Joseph,

Take a look at BBC World (Science/Environment) in the article dealing with multiple universes (Cox). 

Does high certainty still belong to the probabilistic world?

Well-said, Marcel!

Marcel

The current model of quantum mechanics is the Copenhagen Interpretation. Schrodinger's cat was a bad example for explaining the observation phenomenon. A similar bad, but popular, example of a phenomenon is 'if a tree falls in the forest and no one is there to hear it, does it make a sound?' It makes sound waves. Does sound mean only the conscious perception of the sound waves? One must define the terms before the question is asked. Schrodinger was attempting to simplify the argument and ask, 'Is this what we want to say?' The answer is yes for the electron, but no for the cat.

The Copenhagen Interpretation is not exact, but it is good enough. Like all inexact theories it requires patches here and there. There have been many attempts to apply the big patch, a new, complete theory. Find the hidden variables is one. Another is to bring back the de Broglie - Einstein interpretation. Many universes is another try.

Brian Cox might have said, 'Nothing can be predicted with any certainty.' He might have been misquoted. He might have been making a Schrodinger-like over statement. Nevertheless, the Copenhagen Interpretation is what we have to work with right now. Atomic phenomena are predicted with a high degree of certainty and that is good enough to explain and predict sub-atomic and macro-atomic (several to many molecule) events. I would welcome an even better model than the Copenhagen Interpretation, but I am happy with the results thus far.

Should you refer to medical statistics when you ask, 'Does high certainty still belong to the probabilistic world?' I would say, 'The many universe explanation is the only viable model.'