Evolution through the Back Door

Various | 6/15/2003 | Alamo-Girl

[PatrickHenry]

Have you read Deutsch?

No. What does he have to say? Got some links to save time? (A search on "deutsch" is rather hopeless.)

[Nebullis]

...people expect perfect randomness, where randomness in actuality is constrained in some fashion?

The constraints just mean limitations of the area over which an event is unpredictable ("perfectly random"). Let me give you an example. Aflotoxins cause DNA mutations by binding to parts of guanine residues resulting in a G to T transversion. The toxin is very biased in this affinity, because it only binds to G and not to other nucleotides. At the same time, the toxin has no affinity for one available G over another G. It is constrained by chemistry, not by a directed or goal-oriented process, and, as such, it is still unpredictable within those constraints.

[unspun]

Extant phenomena in biology arrived there via extremely biased pathways and with the help of many external variables.

Yes, tell us about those miraculous biases that come along the way of mindless evolution, Mr. Ad Hominem.... We're all ears. Tell us how mindless nature makes such wild leaps over and over again, despite the inabilities to demonstrate scientifically.

BTW, what arm of the pseudo-science chair do you lean on?

[unspun]

The constraints just mean limitations of the area over which an event is unpredictable ("perfectly random"). Let me give you an example. Aflotoxins cause DNA mutations by binding to parts of guanine residues resulting in a G to T transversion. The toxin is very biased in this affinity, because it only binds to G and not to other nucleotides. At the same time, the toxin has no affinity for one available G over another G. It is constrained by chemistry, not by a directed or goal-oriented process, and, as such, it is still unpredictable within those constraints.

And this proves what?

[Nebullis]

And this proves what?

It's not intended to prove anything.

[unspun]

It's not intended to prove anything.

An apt non-intention, thank you.

[Ichneumon]

To measure the date we use carbon dating.

We also use many, many other methods, all based on wildly different methodologies, measurements, and premises. And yet, for the most part results of all the differently determined dating methods agree with each other. (And when they disagree, there are well-understood reasons why.) How do you explain this if you believe they are unreliable?

Furthermore, most items of evolutionary interest are *not* dated via "carbon dating", because Carbon-14 dating can only be used for items up to about 50,000 years old. Most items of evolutionary interest have ages measured in millions of years, and other methods are used. Carbon dating is primarily of use for items within the range of human history and early pre-history.

Yet can you answer with certainty the amount of carbon at any given time? As in, were the levels constant? The answer is no.

Very wrong. The answer is yes. There are many, many samples of known age (e.g. tree rings, arctic ice layers, lake bottom layers, etc.) which can be used to multiply and independently determine how much carbon-14 was in the atmosphere in any given year, and thus be used to calibrate Carbon-14 dating methods.

For a quick article on one such study, see http://more.abcnews.go.com/sections/science/dailynews/carbon0220.html

A much more technical treatment: Atmospheric Radiocarbon Calibration to 45,000 yr B.P.: Late Glacial Fluctuations and Cosmogenic Isotope Production

Such studies produce calibration results such as the following:

If the amount of Carbon-14 in the atmosphere had been exactly constant throughout time (and no one expects that it has been), then the results would fall on the straight diagonal line. Instead, the wiggly line indicates how much the actual amount of C-14 in the atmosphere deviated from the "base" amount, and from this we can know how much C-14 was actually present in any given year in the past 50,000 years.

Note that the above graph includes C-14 data from *two* completely independent sources (Lake Suigetsu varves, and ocean corals), and yet the results overlap beautifully, confirming each other. There is similar match from C-14 studies based on tree-ring data and other sources.

From this, we can build a Carbon-14 dating calibration or "correction" curve which can be used to confidently produce an accurate date from a given Carbon-14 measurement. These calibration curves look like this:

There are many databases available which are used to compile massive amounts of data to ensure the proper calibration of carbon-dating. For just one example, Marine Reservoir Correction Database.

Other methods are used to cross-check and calibrate other dating methods to ensure accuracy.

So we can get approximate dates, but relative to how close in terms of the universe?

Quite close.

If we can take a leaf from a tree and date it as being 10,000 years old, yet it was just removed and is still green,

"If"... Feel free to document that this is actually possible.

, then how can we rely on this?

Because the various dating methods give consistent results which have been repeatedly determined to be reliable and accurate.

Science goes out of its way to try to disprove the existance of God.

No, it really doesn't.

More so than to try and prove evolution.

You are extremely mistaken. There are multiple heavy monthly journals which consist of nothing but studies of evolution [one sample]. I can't think of a single article published in any peer-reviewed science journal which even attempted to "disprove the existence of God" (although you might find a few in the Philosophy department).

To deny a "supreme being" without proving "his" non-existance conclusively, is a fundemental error.

So... Since Shiva and Zeus and Odin haven't had their "non-existence conclusively proven", is it a "fundamental error" to deny them as well?

To prove "evolution" wihtout complete proof, such as all missing "links" is also an error.

You misunderstand how science works. Science does not deal in proofs.

However, by your own argument, if it's a "fundamental error" to "deny" something without "proving its non-existance conclusively", then aren't you making a "fundamental error" if you deny evolution without conclusively proving its falseness?

I think your thesis needs a bit more work. Meaning that the evidence, as more is gathered seems in direct contradiction to itself.

Feel free to present your alleged examples.

Leave anit-religious agendas out of science and deal with the facts found. But sadly it seems most science attacks religion

Speaking of agendas...

The Bible if nothing else, has proven things archeologically and including the existance of Peter. His house, and his name carved upon a stone. In the fishing village he was from. When you use the evidence found in the pages of the Bible and things start to add up, more truth upon more truth it is hard to deny the "whole" when the sum of its parts turn out to be real.

History and archeology teach us that the Civil War really happened, there really was a general named Sherman who burned Atlanta, there really were battles at certain places and times, etc., and that there was a woman named Margaret Mitchell. Does this make *all* of "Gone With The Wind" necessarily true?

Science has yet to find life on another planet. Yet they keep trying in this.

Because the only way to find out, *either way*, is to keep looking.

So they seem to have their own faith.

Yes, they have faith in the value of making efforts to keep learning more about the universe we live in.

But have yet to prove it to the world.

Nothing can be "proven" (there's that word again) without information. Science believes in gathering as much information as possible, so that when conclusions are made, they are based on real information, and not philosophical or religious dogmas or "sound-good-isms". And in gathering further information so that past conclusions can be further reality-checked. Science and the scienific method is, in a nutshell, all about doing frequent reality-checks of beliefs.

[gore3000]

2. If there was a chemical necessity to any particular scheme, we would be seeing that certain possible combinations do not occur. Instead we see all 64 possible combinations of the three bit code appearing in living things.-me-

What you are saying is not strictly true, but the point is minor enough that it doesn't really change things one way or the other.

If it is not accurate, let me know how it is innacurate, don't leave me guessing. I like to be as accurate as possible.

More importantly, DNA doesn't "do" anything, merely providing a template.

That is a terrible analogy for what DNA does. Sure, DNA needs the rest of the cell to accomplish its work and even the entire organism, but to call it a template is like calling a program a bit of nonsense in a computer. Like a program without which a computer is just a piece of junk, without DNA a body would be just food for scavengers. Like a program, DNA is information, essential information for the human body, just as a program is essential information to make a computer work.

Building proteins off that template is an extremely biased system

If you mean by the above that it takes a lot of fiddling to get the protein to come out correct, you would be right, however it is DNA itself that sets out how it is to be fiddled with with stop codons, homeoboxes, specific RNA's for specific genes, sets up a control system to tell how much protein is to be produced and when, and much more. So you are totally degrading the tremendous job which DNA does in the organism.

we expend a fair portion of our supercomputing power today figuring out what protein conformations are probable under certain circumstances and which aren't.

If you are trying to make a better protein than nature or to modify it in any way you certainly will need a lot of work to accomplish it which like the rest of your post pretty much verifies what Alamo-Girl's sources have been saying - that it is virtually impossible to create a single functional gene at random. Such a miracle occurring once would be possible though extremely unlikely. However to propose that such a miracle could have occurred not just once but millions and millions of times with the numerous species we have on earth is certainly impossible.

[gore3000]

What sort of evidence is there for "pre programmed adapation capability"?

The Hox genes, all of them:

What do humans have in common with worms, flies and rodents? If you said, "not much," you're right. But not as "right" as you might think. During the early 1980s, scientists discovered that most of the genes in fruit flies that control the identity of different body parts -- a head, wing, or other structure -- are remarkably identical. The genes contain short sequences of deoxyribonucleic acid (DNA), which is found in every living cell and forms the "blueprint" for all organisms. Surprisingly, researchers discovered that the DNA sequence they had found in flies, called the homeobox, was common to genes that direct development of body structure in virtually all animals, including worms, flies, birds, mice and humans. "Homeo" is derived from the Greek word for similar; "box" refers to the clearly defined sequence, as though in a box.

Since the homeobox sequence stayed very similar during millions of years of evolution in many species, scientists suspected it must be important to life. They soon learned that the part of the protein it encodes can bind to DNA in a way that turns other genes on and off.

Even more surprising, scientists found that many genes containing the homeobox sequence, called hox genes, are lined up in clusters along chromosomes -- large strands of genetic material -- in an order that parallels the body part they control. On a fly chromosome, hox genes closest to one end control formation of the head, while the next ones in line control the upper body. At the other end of the cluster are genes controlling abdomen formation. When all these genes work correctly, the proteins they produce act together to ensure that each organism's body parts are made in correct locations. Hox genes also control development of parts of the central nervous system, including different regions of the brain.

Researchers concluded that hox genes are "master regulators" for the organization of the body. When the function of one of these genes is changed due to a genetic mutation or other factor, the wrong body part will develop in a given place. A fly, for example might grow a leg in the middle of its head.

A brief note, all the genes which evolutionists call 'pathways' are from multi-cellular creatures which arose during the Cabmrian explosion. The Hox genes are obviously a necessary requirement for multi-cellular organisms, that such a universal set of genes could have arisen in such a short time to become the basis of just about all multi-cellular animals, and that they could serve as building blocks for future species functions, shows pretty well that they could not have arisen either at random or due to 'selection' but could only have arisen by design.

[unspun]

You misunderstand how science works. Science does not deal in proofs.

Let's review what science actually is and what the scientific method actually does. (When one does, one realizes how far from science are conjectures of macroevolution, how far from scientifically validated are any descriptive hypotheses of how evolution is supposed to work, and how far from scientific theory is any patchwork model of the process of evolution.)

I'll present the information in roughly an order of very summarized to more detailed, so you can best decide where to stop.

1/4. from:  http://www.soci.niu.edu/~phildept/Dye/method.html 
          Selected texts bolded in green, by unspun

Socratic Method and Scientific Method

Socratic Method	Scientific Method
1. Wonder. Pose a question (of the "What is X ?" form).	1. Wonder. Pose a question.
2. Hypothesis. Suggest a plausible answer (a definition or definiens) from which some conceptually testable hypothetical propositions can be deduced.	2. Hypothesis. Suggest a plausible answer (a theory) from which some empirically testable hypothetical propositions can be deduced.
3. Elenchus ; "testing," "refutation," or "cross-examination." Perform a thought experiment by imagining a case which conforms to the definiens but clearly fails to exemplify the definiendum, or vice versa. Such cases, if successful, are called counterexamples. If a counterexample is generated, return to step 2, otherwise go to step 4.	3. Testing. Construct and perform an experiment which makes it possible to observe whether the consequences specified in one or more of those hypothetical propositions actually follow when the conditions specified in the same proposition(s) pertain. If the experiment fails, return to step 2, otherwise go to step 4.
4. Accept the hypothesis as provisionally true. Return to step 3 if you can conceive any other case which may show the answer to be defective.	4. Accept the hypothesis as provisionally true.Return to step 3 if there other predictable consequences of the theory which have not been experimentally confirmed.
5. Act accordingly.	5. Act accordingly.

Copyright © 1996, James Dye

Last Updated 8 January, 1996

2/4. from: http://www.ldolphin.org/SciMeth2.html

Steps in the Scientific Method

by Lambert Dolphin
Email: lambert@ldolphin.org
Web Pages: http://ldolphin.org/ May 1992.


3/4. from:  http://teacher.nsrl.rochester.edu/phy_labs/AppendixE/AppendixE.html
           Selected texts bolded in green, by unspun

APPENDIX E: Introduction to the Scientific Method

• Introduction to the Scientific Method
  • I. The scientific method has four steps
  • II. Testing hypotheses
  • III. Common Mistakes in Applying the Scientific Method
  • IV. Hypotheses, Models, Theories and Laws
  • V. Are there circumstances in which the Scientific Method is not applicable?
  • VI. Conclusion
  • VII. References

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Introduction to the Scientific Method

The scientific method is the process by which scientists, collectively and over time, endeavor to construct an accurate (that is, reliable, consistent and non-arbitrary) representation of the world.

Recognizing that personal and cultural beliefs influence both our perceptions and our interpretations of natural phenomena, we aim through the use of standard procedures and criteria to minimize those influences when developing a theory. As a famous scientist once said, "Smart people (like smart lawyers) can come up with very good explanations for mistaken points of view." In summary, the scientific method attempts to minimize the influence of bias or prejudice in the experimenter when testing an hypothesis or a theory.

I. The scientific method has four steps

1. Observation and description of a phenomenon or group of phenomena.

2. Formulation of an hypothesis to explain the phenomena. In physics, the hypothesis often takes the form of a causal mechanism or a mathematical relation.

3. Use of the hypothesis to predict the existence of other phenomena, or to predict quantitatively the results of new observations.

4. Performance of experimental tests of the predictions by several independent experimenters and properly performed experiments.

If the experiments bear out the hypothesis it may come to be regarded as a theory or law of nature (more on the concepts of hypothesis, model, theory and law below). If the experiments do not bear out the hypothesis, it must be rejected or modified. What is key in the description of the scientific method just given is the predictive power (the ability to get more out of the theory than you put in; see Barrow, 1991) of the hypothesis or theory, as tested by experiment. It is often said in science that theories can never be proved, only disproved. There is always the possibility that a new observation or a new experiment will conflict with a long-standing theory.

II. Testing hypotheses

As just stated, experimental tests may lead either to the confirmation of the hypothesis, or to the ruling out of the hypothesis. The scientific method requires that an hypothesis be ruled out or modified if its predictions are clearly and repeatedly incompatible with experimental tests. Further, no matter how elegant a theory is, its predictions must agree with experimental results if we are to believe that it is a valid description of nature. In physics, as in every experimental science, "experiment is supreme" and experimental verification of hypothetical predictions is absolutely necessary. Experiments may test the theory directly (for example, the observation of a new particle) or may test for consequences derived from the theory using mathematics and logic (the rate of a radioactive decay process requiring the existence of the new particle). Note that the necessity of experiment also implies that a theory must be testable. Theories which cannot be tested, because, for instance, they have no observable ramifications (such as, a particle whose characteristics make it unobservable), do not qualify as scientific theories.

If the predictions of a long-standing theory are found to be in disagreement with new experimental results, the theory may be discarded as a description of reality, but it may continue to be applicable within a limited range of measurable parameters. For example, the laws of classical mechanics (Newton's Laws) are valid only when the velocities of interest are much smaller than the speed of light (that is, in algebraic form, when v/c << 1). Since this is the domain of a large portion of human experience, the laws of classical mechanics are widely, usefully and correctly applied in a large range of technological and scientific problems. Yet in nature we observe a domain in which v/c is not small. The motions of objects in this domain, as well as motion in the "classical" domain, are accurately described through the equations of Einstein's theory of relativity. We believe, due to experimental tests, that relativistic theory provides a more general, and therefore more accurate, description of the principles governing our universe, than the earlier "classical" theory. Further, we find that the relativistic equations reduce to the classical equations in the limit v/c << 1. Similarly, classical physics is valid only at distances much larger than atomic scales (x >> 10^-8 m). A description which is valid at all length scales is given by the equations of quantum mechanics.

We are all familiar with theories which had to be discarded in the face of experimental evidence. In the field of astronomy, the earth-centered description of the planetary orbits was overthrown by the Copernican system, in which the sun was placed at the center of a series of concentric, circular planetary orbits. Later, this theory was modified, as measurements of the planets motions were found to be compatible with elliptical, not circular, orbits, and still later planetary motion was found to be derivable from Newton's laws.

Error in experiments have several sources. First, there is error intrinsic to instruments of measurement. Because this type of error has equal probability of producing a measurement higher or lower numerically than the "true" value, it is called random error. Second, there is non-random or systematic error, due to factors which bias the result in one direction. No measurement, and therefore no experiment, can be perfectly precise. At the same time, in science we have standard ways of estimating and in some cases reducing errors. Thus it is important to determine the accuracy of a particular measurement and, when stating quantitative results, to quote the measurement error. A measurement without a quoted error is meaningless. The comparison between experiment and theory is made within the context of experimental errors. Scientists ask, how many standard deviations are the results from the theoretical prediction? Have all sources of systematic and random errors been properly estimated? This is discussed in more detail in the appendix on Error Analysis and in Statistics Lab 1.

III. Common Mistakes in Applying the Scientific Method

As stated earlier, the scientific method attempts to minimize the influence of the scientist's bias on the outcome of an experiment. That is, when testing an hypothesis or a theory, the scientist may have a preference for one outcome or another, and it is important that this preference not bias the results or their interpretation. The most fundamental error is to mistake the hypothesis for an explanation of a phenomenon, without performing experimental tests. Sometimes "common sense" and "logic" tempt us into believing that no test is needed. There are numerous examples of this, dating from the Greek philosophers to the present day.

Another common mistake arises from the failure to estimate quantitatively systematic errors (and all errors). There are many examples of discoveries

Another common mistake is to ignore or rule out data which do not support the hypothesis. Ideally, the experimenter is open to the possibility that the hypothesis is correct or incorrect. Sometimes, however, a scientist may have a strong belief that the hypothesis is true (or false), or feels internal or external pressure to get a specific result. In that case, there may be a psychological tendency to find "something wrong", such as systematic effects, with data which do not support the scientist's expectations, while data which do agree with those expectations may not be checked as carefully. The lesson is that all data must be handled in the same way.

Another common mistake arises from the failure to estimate quantitatively systematic errors (and all errors). There are many examples of discoveries which were missed by experimenters whose data contained a new phenomenon, but who explained it away as a systematic background. Conversely, there are many examples of alleged "new discoveries" which later proved to be due to systematic errors not accounted for by the "discoverers."

In a field where there is active experimentation and open communication among members of the scientific community, the biases of individuals or groups may cancel out, because experimental tests are repeated by different scientists who may have different biases. In addition, different types of experimental setups have different sources of systematic errors. Over a period spanning a variety of experimental tests (usually at least several years), a consensus develops in the community as to which experimental results have stood the test of time.

IV. Hypotheses, Models, Theories and Laws

In physics and other science disciplines, the words "hypothesis," "model," "theory" and "law" have different connotations in relation to the stage of acceptance or knowledge about a group of phenomena.

An hypothesis is a limited statement regarding cause and effect in specific situations; it also refers to our state of knowledge before experimental work has been performed and perhaps even before new phenomena have been predicted. To take an example from daily life, suppose you discover that your car will not start. You may say, "My car does not start because the battery is low." This is your first hypothesis. You may then check whether the lights were left on, or if the engine makes a particular sound when you turn the ignition key. You might actually check the voltage across the terminals of the battery. If you discover that the battery is not low, you might attempt another hypothesis ("The starter is broken"; "This is really not my car.")

The word model is reserved for situations when it is known that the hypothesis has at least limited validity. A often-cited example of this is the Bohr model of the atom, in which, in an analogy to the solar system, the electrons are described has moving in circular orbits around the nucleus. This is not an accurate depiction of what an atom "looks like," but the model succeeds in mathematically representing the energies (but not the correct angular momenta) of the quantum states of the electron in the simplest case, the hydrogen atom. Another example is Hook's Law (which should be called Hook's principle, or Hook's model), which states that the force exerted by a mass attached to a spring is proportional to the amount the spring is stretched. We know that this principle is only valid for small amounts of stretching. The "law" fails when the spring is stretched beyond its elastic limit (it can break). This principle, however, leads to the prediction of simple harmonic motion, and, as a model of the behavior of a spring, has been versatile in an extremely broad range of applications.

A scientific theory or law represents an hypothesis, or a group of related hypotheses, which has been confirmed through repeated experimental tests. Theories in physics are often formulated in terms of a few concepts and equations, which are identified with "laws of nature," suggesting their universal applicability. Accepted scientific theories and laws become part of our understanding of the universe and the basis for exploring less well-understood areas of knowledge. Theories are not easily discarded; new discoveries are first assumed to fit into the existing theoretical framework. It is only when, after repeated experimental tests, the new phenomenon cannot be accommodated that scientists seriously question the theory and attempt to modify it. The validity that we attach to scientific theories as representing realities of the physical world is to be contrasted with the facile invalidation implied by the expression, "It's only a theory." For example, it is unlikely that a person will step off a tall building on the assumption that they will not fall, because "Gravity is only a theory."

Changes in scientific thought and theories occur, of course, sometimes revolutionizing our view of the world (Kuhn, 1962). Again, the key force for change is the scientific method, and its emphasis on experiment.

V. Are there circumstances in which the Scientific Method is not applicable?

While the scientific method is necessary in developing scientific knowledge, it is also useful in everyday problem-solving. What do you do when your telephone doesn't work? Is the problem in the hand set, the cabling inside your house, the hookup outside, or in the workings of the phone company? The process you might go through to solve this problem could involve scientific thinking, and the results might contradict your initial expectations.

Like any good scientist, you may question the range of situations (outside of science) in which the scientific method may be applied. From what has been stated above, we determine that the scientific method works best in situations where one can isolate the phenomenon of interest, by eliminating or accounting for extraneous factors, and where one can repeatedly test the system under study after making limited, controlled changes in it.

There are, of course, circumstances when one cannot isolate the phenomena or when one cannot repeat the measurement over and over again. In such cases the results may depend in part on the history of a situation. This often occurs in social interactions between people. For example, when a lawyer makes arguments in front of a jury in court, she or he cannot try other approaches by repeating the trial over and over again in front of the same jury. In a new trial, the jury composition will be different. Even the same jury hearing a new set of arguments cannot be expected to forget what they heard before.

VI. Conclusion

The scientific method is intricately associated with science, the process of human inquiry that pervades the modern era on many levels. While the method appears simple and logical in description, there is perhaps no more complex question than that of knowing how we come to know things. In this introduction, we have emphasized that the scientific method distinguishes science from other forms of explanation because of its requirement of systematic experimentation. We have also tried to point out some of the criteria and practices developed by scientists to reduce the influence of individual or social bias on scientific findings. Further investigations of the scientific method and other aspects of scientific practice may be found in the references listed below.

VII. References

1. Wilson, E. Bright. An Introduction to Scientific Research (McGraw-Hill, 1952).

2. Kuhn, Thomas. The Structure of Scientific Revolutions (Univ. of Chicago Press, 1962).

3. Barrow, John. Theories of Everything (Oxford Univ. Press, 1991).

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Send comments, questions and/or suggestions via email to wolfs@nsrl.rochester.edu.

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4/4.  from:  http://phyun5.ucr.edu/~wudka/Physics7/Notes_www/node5.html
Next: What is the ``scientific Up: Introduction Previous: Overview

The scientific method

Science is best defined as a careful, disciplined, logical search for knowledge about any and all aspects of the universe, obtained by examination of the best available evidence and always subject to correction and improvement upon discovery of better evidence. What's left is magic. And it doesn't work. -- James Randi

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It took a long while to determine how is the world better investigated. One way is to just talk about it (for example Aristotle, the Greek philosopher, stated that males and females have different number of teeth, without bothering to check; he then provided long arguments as to why this is the way things ought to be). This method is unreliable: arguments cannot determine whether a statement is correct, this requires proofs.

A better approach is to do experiments and perform careful observations. The results of this approach are universal in the sense that they can be reproduced by any skeptic. It is from these ideas that the scientific method was developed. Most of science is based on this procedure for studying Nature.

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• What is the ``scientific method''?
• What is the difference between a fact, a theory and a hypothesis?
• Truth and proof in science.
• If scientific theories keep changing, where is the Truth?
• What is Ockham's Razor?
• How much fraud is there in science?
• Are scientists wearing blinkers?
• Why should we worry?

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Jose Wudka
9/24/1998

[tortoise]

If you are trying to make a better protein than nature or to modify it in any way you certainly will need a lot of work to accomplish it which like the rest of your post pretty much verifies what Alamo-Girl's sources have been saying - that it is virtually impossible to create a single functional gene at random.

That isn't really a valid analysis -- apples and oranges. You completely missed what I said, so I'll try again. "Difficult to compute" and "improbable" are completely orthogonal to each other. I can trivially compute molecular interactions that are virtually impossible in a real molecular system (as shown by the computation). Computing a particular conformation has the same cost no matter how probable or improbable its actual occurence is.

What we are trying to do (and straining our computational abilities as we do it) is compute the probabilities of an entire molecular phase space. Not just what happens in a specific instance, but what could happen under what conditions and the probability pertaining thereto. The easy case is taking a particular starting point and seeing what the outcome is. Even worse, we often attempt do an inverse computation i.e. given a certain protein outcome, what are the possible starting points that would give that result. Quite frankly, our computers are pretty taxed doing the forward computation, and doing the inverse computation is largely beyond our computational abilities. It is not a symmetric computation, in the same way factoring large composites is vastly more difficult than multiplying the primes that make up the composite.

Biochemistry is computationally probable for the most part, and we can compute specific results with relative ease. Computing the inverse case so that we can manipulate protein systems at will is nigh intractable. Nature just follows the probable pathways. Computing what probable pathways can get you to a specific endpoint is extraordinarily difficult no matter how "common" and probable the protein interaction is. The extremely difficult inverse computation is important because it allows us to thoroughly explore biochemistry (both the probable and improbable), and despite the computational expense, it is often cheaper to do the modeling on computers than actually testing and sifting the astronomical number of permutations in a lab.

In short: difficult to compute is utterly unrelated to probability. We aren't just analyzing what happens from a specific known starting point, we are reverse engineering the entire phase space of possible starting points and possible end points. A vastly different problem, that.

[gore3000]

This is one of those profound differences between things that are "designed" and things arising through evolution. Living things have an enormous economy in their blueprints.

Indeed there is a tremendous economy in living things. For example, when the genome project was done, scientists were surprised that there were only some 30,000 odd thousand genes in humans because they had already identified some 100,000 different proteins used in human organisms. The reason is that genes can be made to make more than one protein by using very sophisticated code reuse. Some genes can make more than 50-60 proteins! Code reuse is definitely a sign of intelligence. It takes hard thinking to figure out how to take code from here and there to make it do something else you need done. This cannot be done by dumb luck.

[unspun]

Thank you for allowing me to eaves drop on this conversation about that 'maxim' of Yockey's. I root for it being applicable only where evidence should be demonstrably compelled to reveal its little head, but doesn't.

(I confess I didn't read where it go to be "too many notes" though.)

--holy roamin' empirer (though not a scientist)

[gore3000]

On top of all that, we already know, with massive amounts of supporting evidence, that natural selection that acts on variation exists. Any change, however it is induced, is subject to selection.

Evolutionists often speak as if natural selection changes the odds of something occurring. It does not. Selection only works after the event occurs so it has no influence in the occurrence of a particular event. If the chances of an event occurring are 1 in 10^60 chances without selection they are 1 in 10^60 with selection. Selection does not create anything, it does not work before the fact which is what would be needed for it to change the odds. What it does do is leave a trail of death which makes the finding of the correct change virtually impossible. That is why selection is an agent of stasis not of evolution.

[tortoise]

Code reuse is definitely a sign of intelligence.

Or efficient expression, which happens all the time in nature absent intelligence because it is favored by thermodynamics.

This relates back to the point that "entropy" has a much deeper meaning than the simplistic (and often incorrect) thermodynamic definition that is the extent of most people's understanding of the word.

[gore3000]

I can trivially compute molecular interactions that are virtually impossible in a real molecular system (as shown by the computation).

Since the discussion is about biological evolution not of computing per se, you are agreeing with my statement (and Alamo-Girls - and Yockey's!) about the virtual impossibility of creating functional genes.

Biochemistry is computationally probable for the most part, and we can compute specific results with relative ease.

No. You have just gone through a long exegesis on how the computing faculties are strained trying to find a simple change. Unlike with computers which work fast and do not die if they do not find the answer, organisms do not reproduce at megabytes per second. They also die if they get the wrong answer.

Further the computers have been given intelligent directions which cut down the number of tries required to get success. This is not the case in nature.

To change at random a single DNA bit correctly will take numerous tries. This claiming that there are 'pathways' which cut down the chances is not correct because there is no chemical reason for the sequence of DNA. What the 'pathways' do is exclude out of hand a tremendous amount of possible changes, it does not cut down in any way the random tries it takes to achieve those changes. You are indulging in the usual evolutionist fallacy of the future predicting the past. When put this way it is obvious nonsense. When put as 'pathways' determine the outcome, it does not sound as silly but it is the same logic - that what will be successful in the future is the cause for the events in the past.

In short: difficult to compute is utterly unrelated to probability. We aren't just analyzing what happens from a specific known starting point, we are reverse engineering the entire phase space of possible starting points and possible end points.

You are again giving support to my statement above. What you are speaking of is the reverse of how things actually happen. The future does not determine the past (except in the Terminator movies!).

[gore3000]

Code reuse is definitely a sign of intelligence.-me-

Or efficient expression, which happens all the time in nature absent intelligence because it is favored by thermodynamics.

Just because something happens in nature, does not mean that it is due to evolution, in fact this is what the whole evolution/creation debate is about - how did things in nature come about.

Now gene expression is determined by DNA. You surely are not claiming that the laws of thermodynamics get into our genome and change our DNA so that it will be in conformance with it do you??????????

[tortoise]

Selection does not create anything, it does not work before the fact which is what would be needed for it to change the odds.

You are sort of right, but you completely missed the point nonetheless. Evolutionary theory proscribes some large number of small steps between two points. At step(n), selection(n) does not alter the odds of step(n) occurring. In this you are correct. The point you miss is that selection(n) constrains the possible phase space for step(n+1), thereby altering the probabilities for all step(n+k) where k>0 (a recursive feedback loop that reduces the number of possible outcomes at each step, increasing the odds of any one of those outcomes of happening).

This is why the aggregate probabilities are not a multiplicative function of simple combinatorics. You cannot assert the probabilities at each step until the selection function has been applied to the previous step which actually limits the number of possibilities at each step. You have to use the aggregate probabilities of each step post-selection from the previous step which makes each subsequent step far more probable than if you assumed the phase space was unconstrained (which is what you do).

Time for dinner...

[Alamo-Girl]

Thank you so much for the information on the Hox gene!

It looks like the trend may be that many of the regulator genes appear from the earliest, e.g. like pre-programmed adaptation ability.

Are the Hox genes conserved across phyla like the eyeness gene, i.e. between human and mouse, 100% identical and between human and drosophilia, 94%? This is evidently the astonishing observation; IOW, it puts more emphasis on pre-programmed adaptation capability and less on random mutation branching away from the common ancestor(s).

[tortoise]

Just because something happens in nature, does not mean that it is due to evolution

I never said that. I said that code reuse is not a sign of intelligence ipso facto, contrary to what you asserted. Evolution versus design is a false dichotomy. There are other plausible mechanisms that can create speciation (such as complexification in automata systems). System dynamics offers a number of possibilities, so-called "evolution" is just one possible mechanism described, and one fixated on because some famous dude wrote a book on it many years ago. In fact, it rather annoys me that people remain stubbornly ignorant about the fact that evolution is only one of a myriad of plausible explanations for speciation that come out of systems theory.

If I say "does not imply design", it does not equal "implies evolution". It could be any one of a number equally plausible mechanisms. As I said, evolution versus design is a false dichotomy, mostly due to ignorance and an unhealthy fixation on evolution that exists for historical reasons. No one has, for example, even attempted to refute molecular automata theories, which are actually increasingly popular in many biological circles. I'm not sure what the creationists would do if all the evolutionists switched teams to automata theory.