Comment #2797

Posted by ~DS~ on May 25, 2004 09:23 AM (e) (s)

TY, that was excellent!

Comment #2799

Posted by charlie wagner on May 25, 2004 10:18 AM (e) (s)

Pim wrote:

Since we have seen some poorly argued claims about entropy and its relevance to evolution, I will explore the concepts of entropy as they apply to genome evolution and will show that the evidence shows how simple processes like variation and selection are sufficient to explain the evolution of complexity or information/entropy in the genome.

Unfortunately, neither entropy, complexity or information has anything at all to do with evolution. So I guess you could call this a “red herring”.
  If you explained the evolution of *organization* (not order), now that would really be something!

As for the rest of your post, very interesting. Instead of answering each point, allow me to refer you to my prior responses to this issue:

http://tinyurl.com/2sk5c…

  The search term is “Nelson’s Law”

Comment #2802

Posted by Pim van Meurs on May 25, 2004 10:31 AM (e) (s)

Contrary to Charlie’s suggestions that the issues are a red herring let me point out that it is the ID movement who is claiming that evolutionary mechanisms cannot explain the origin of information and complexity. Is Charlie suggesting that we blame Dembski for introducing the concept of entropy/information? Or in this case is Charlie arguing that Jerry’s comments are irrelevant?

As far as organization is concerned, scale free networks, gene duplication all help understand such issues as modularity, degeneracy, robustness, evolvability.

The real red herring may be the suggestion that the issue is one of ‘organization’. But let’s focus on the issue at hand in this thread which addresses the arguments by ID proponents about information/entropy.

Comment #2804

Posted by Jim Anderson on May 25, 2004 10:40 AM (e) (s)

Unfortunately, neither entropy, complexity or information has anything at all to do with evolution. So I guess you could call this a “red herring”.

Thermodynamics has nothing to do with biology?  Call me an uninformed, ignorant layman—and you should, because I am—but that bald assertion strikes me as more than a little, um, radical.

Comment #2805

Posted by Jim Anderson on May 25, 2004 10:41 AM (e) (s)

Oh, and replace “biology” with “evolution.”  Duh.

Comment #2807

Posted by charlie wagner on May 25, 2004 11:01 AM (e) (s)

Pim wrote:

let me point out that it is the ID movement who is claiming that evolutionary mechanisms cannot explain the origin of information and complexity.

  I don’t represent the “ID movement”, I don’t speak for the “ID movement”, I don’t defend anyone’s views but my own. I don’t know Bill Dembski, I’ve never read his books and I could care less what he thinks. I speak on my own behalf, and I defend what *I* say.

Comment #2808

Posted by Pim van Meurs on May 25, 2004 11:07 AM (e) (s)

charlie and Nelson's law wrote:

Which is exactly why I have put forth Nelson’s Law. It separates out  this problem and allows it to stand alone on it’s own merits. Nelson’s  law involves logical entropy and separates it from thermodynamic  entropy. It measures the disorder of a system and is a pure number, with  no units. Life can be described as organization and Nelson’s Law states  that “things do not organize themselves”. The evolution of life involves  in increase in organization, a decrease in logical entropy. Nelson’s law
forbids this. Things cannot organize themselves without input from  outside. You cannot seek refuge from this dilemma by taking advantage of
the confusion between the two forms of entropy.

Nor can one take refuge from the logical and practical answer to Nelson’s law namely that the input from outside is exactly what natural selection is all about. In fact the entropy in the genome can be shown to be linked to the correlation between the genome and the environment and natural selection tends to increase this correlation, thus reducing the entropy.

Simply arguing that it looks like a machine and that it requires input from the outside does not help eliminate evolutionary processes as ‘designers’. In fact it strengthens the proposed evolutionary mechanisms.

Nelson’s law is nothing much different from appeal to entropy with the same fallacies. Its ‘prediction’ that complex machines require intelligent design are meaningless when intelligent design cannot exclude natural processes as its designer.

Comment #2809

Posted by Pim van Meurs on May 25, 2004 11:12 AM (e) (s)

charlie wrote:

I don’t represent the “ID movement”, I don’t speak for the “ID movement”, I don’t defend anyone’s views but my own. I don’t know Bill Dembski, I’ve never read his books and I could care less what he thinks. I speak on my own behalf, and I defend what *I* say.

That is all nice but this thread is *not* about Charlie and all about the confusions exhibited by ID proponents when it comes to entropy and evolution. If you want to be included, fine and I appreciate that your comments help make my point that ID proponents such as Dembski and Jerry are ‘misguided’?

Comment #2820

Posted by zed on May 25, 2004 02:13 PM (e) (s)

I was fairly amazed by Chronos’ assertion that “With every generation in homo sapien, entropy increases in the genome.”

Now my thermodynamics is a bit rusty, but wouldn’t that mean our offspring would progressively degenerate into piles of primordial goo?  Isn’t the continued presence of life predicated on at the least a zero net change in “entropy”?

And does anyone actually take this seriously?

Comment #2825

Posted by Panda Bear on May 25, 2004 02:47 PM (e) (s)

A good explanation of problems with common creationist arguments based on the SLOT can be found here or here

Comment #2826

Posted by charlie wagner on May 25, 2004 03:21 PM (e) (s)

Pim wrote:

Nor can one take refuge from the logical and practical answer to Nelson’s law namely that the input from outside is exactly what natural selection is all about. In fact the entropy in the genome can be shown to be linked to the correlation between the genome and the environment and natural selection tends to increase this correlation, thus reducing the entropy.

With all due respect, this is not true. How do you measure the entropy in the genome and how do you demonstrate that natural selection reduces this entropy?
  There is no evidence that natural selection can “design” anything. All it can do is change the frequency of already existing variation.

Its ‘prediction’ that complex machines require intelligent design are meaningless when intelligent design cannot exclude natural processes as its designer.

There is no empirical evidence, either observational or experimental that supports the idea that natural processes are capable of design.

Comment #2827

Posted by chris on May 25, 2004 03:32 PM (e) (s)

I think I have to agree that the issue of entropy in evolution is a bit of a red herring.  First of all (and most importantly), the
order of nucleic acids in the genome is not actually subject to the laws of thermodynamics.  It certainly has aspects that bear a resemblance to familiar concepts in thermo but others are unfamiliar.  A current major area of research in physics is to develop a framework to describe certain nonequilibrium phenomenon (of which evolution is an example) with familiar concepts of thermodynamics and statistical mechanics.  I want to be clear that I’m not saying there isn’t some definition of “entropy” that applies to evolution and maybe it always increases or decreases or whatever - I think the hope is that there *is* such a thing, actually - I’m only saying that you can’t just lift thermodynamics and apply it to anything you want.

Besides which, increasing entropy is not really associated with increasing disorder at all.  That’s just an analogy.  There are several famous examples of situations where increasing entropy INCREASES ORDER.

Comment #2828

Posted by Town Crier on May 25, 2004 03:40 PM (e) (s)

There is no empirical evidence, either observational or experimental that supports the idea that natural processes are capable of design.

For the love of aliens, Charlie, could you at least make the slightest effort to express your own beliefs accurately?

Numerous people have gone around the bend with you numerous times regarding the same issue.

What Charlie really means to say is “No evidence shown to me, alone or in combination with any or all other evidence, will convince me that natural selection is responsible for the diversity of organisms and structures, including all known extinct organisms and all known living organisms.”

This statement, Charlie, unlike yours, is honest and forthright.

The statement you made, highlighted above, merely begs numerous questions, such as what you mean when you use terms such as “empirical,” “evidence,” “observational,” “experimental,” “natural processes”  and “design.”

Woe be unto those who would ask you to define these terms in an effort to understand how anyone could be so deluded to assert that **no evidence exists** to support evolution by natural selection.

Woe be unto those!!!

Comment #2829

Posted by Pim van Meurs on May 25, 2004 03:49 PM (e) (s)

Charlie wrote:

There is no empirical evidence, either observational or experimental that supports the idea that natural processes are capable of design.

Of course this is an argument based on personal incredulity contradicted by the actual empirical evidence that shows how natural selection and variation (in other words natural processes) are capable of ‘design’. Charlie may surely argue that he is unfamiliar with the scientific evidence but that is hardly of any interest to me.

Charlie continues his strawman wrote:

There is no evidence that natural selection can “design” anything. All it can do is change the frequency of already existing variation.

Charlie, until you accurately represent evolutionary processes that is variation AND selection, your comments have to be rejected. In fact your argument supports my claim namely that by changing the frequency of already existing variation natural selection does increase the correlation of the genome with the environment.

So yes there is theoretical, empirical and observation and experimental evidence to support these claims.

Chris wrote:

I think I have to agree that the issue of entropy in evolution is a bit of a red herring.  First of all (and most importantly), the  order of nucleic acids in the genome is not actually subject to the laws of thermodynamics.

Which is why I use the Shannon entropy.

chris wrote:

There are several famous examples of situations where increasing entropy INCREASES ORDER.

I would be interested in some references to these famous examples. But he discussion is not about order but rather about information/complexity and the claims made by ID proponents as to the limitations of natural processes to increase information/complexity.

Comment #2831

Posted by Ben on May 25, 2004 04:21 PM (e) (s)

Thank you, Town Crier. I was just about to slash my wrists. Christ I’m sick of this “design” crap.

Comment #2833

Posted by Jim Harrison on May 25, 2004 04:55 PM (e) (s)

Unless the designer of  ab organism can suspend the laws of nature, he or she remains subject to the Second Law. If naturally evolved organisms are impossible because of thermodynamic considerations, designed organisms are no less impossible.

Comment #2834

Posted by Reed A. Cartwright on May 25, 2004 05:06 PM (e) (s)

There is much confusion that in Shannon information theory entropy/uncertainity is a measure of information.  However, in reality “information” is defined as “a measure of the decrease of uncertainty at a receiver.”  (See here and here.)

Imagine that we are in communication and that we have agreed on an alphabet. Before I send you a bunch of characters, you are uncertain (Hbefore) as to what I’m about to send. After you receive a character, your uncertainty goes down (to Hafter). Hafter is never zero because of noise in the communication system. Your decrease in uncertainty is the information (R) that you gain.

Since Hbefore and Hafter are state functions, this makes R a function of state. It allows you to lose information (it’s called forgetting). You can put information into a computer and then remove it in a cycle.

Many of the statements in the early literature assumed a noiseless channel, so the uncertainty after receipt is zero (Hafter=0). This leads to the SPECIAL CASE where R = Hbefore. But Hbefore is NOT “the uncertainty”, it is the uncertainty of the receiver BEFORE RECEIVING THE MESSAGE.

Comment #2835

Posted by Art on May 25, 2004 05:08 PM (e) (s)

About “Nelson’s Law”:

From the URL (and its “destinations”) - “Life can be described as organization and Nelson’s Law states that “things do not organize themselves”. The evolution of life involves in increase in organization, a decrease in logical entropy. Nelson’s law forbids this. Things cannot organize themselves without input from  outside. “

I don’t know what “Nelson’s Law” really is, but Charlie (or anyone else reading this) can refute the characterization seen in this thread in their own kitchen.  Pour some salad oil in a bottle, add some water (or vinegar), and mix thoroughly.  Then let the mixture (which should be the disorganized state that “Nelson’s Law” predicts will be the final state) sit - untouched, completely isolated from all influences.  (Heck, we can be really anal and put it in total darkness.)

We all know what will happen - the completely disorganized mixture will spontaneously, completely of its own accord, without any input of energy, information, design, or any other influence, organize into two perfectly-separated phases.  The “thing” will most definitely “organize itself”.  It’ll happen each and every time, without fail. 

What’s really neat is that the same chemical principles underlie the majority (IMO, at least) of organization in biology.

Comment #2839

Posted by Reed A. Cartwright on May 25, 2004 05:25 PM (e) (s)

Art,

Nelson’s Law is a tautology that Charlie came up with and named after his middle name.

Comment #2840

Posted by charlie wagner on May 25, 2004 05:34 PM (e) (s)

Art wrote:

We all know what will happen - the completely disorganized mixture will spontaneously, completely of its own accord, without any input of energy, information, design, or any other influence, organize into two perfectly-separated phases.  The “thing” will most definitely “organize itself”

  I don’t expect that you’ve read *all* of the messages I wrote in talk.origins, but if you had, you would have seen that I carefully explained the difference between “order” and “organization”. These terms are sometimes interchanged and some confusion occurs, which is why I carefully defined what I meant. Your example with the oil and vinegar is an example of an increse in order, which can and does occur naturally, as you point out, without intelligent intervention. In this case, order is defined as “a condition of logical or comprehensible arrangement among the separate elements of a group”. Ther are many such examples, from ice crystals forming to the separation of immiscible liquids by density.
  But organization is another matter. I define it as “a system made up of elements with varied functions that contribute to the whole and to collective functions of the system”.

Here are two examples of my views:

  “The only difference I see is between living systems and non-living
systems. Non-living systems do not adapt means to ends, they do not
adapt structure and process to function and they do not self-organize.
And one must be careful not to confuse organization with order.
There’s a lot of talk about ordered systems in the non-living world,
snowflakes, tornadoes, etc. but this is not the issue. Living systems
are beyond order, which is simply a condition of logical or
comprehensible arrangement among the separate elements of a group.
Like putting files in alphabetical order or using a seive to separate
items by size. Organization is a much different structure in which
something is made up of elements with varied functions that contribute
to the whole and to collective functions, such as exist in living
organisms. Ordered systems can result from non-intelligent processes,
as has been seen many times and cited by the examples given. But
organized systems require intelligent guidance. They need to be put
together with intent and their assembly requires insight. They need to
be the product of intelligence because it is necessary to determine if
they are functioning properly and that can only be acheived by
insight. Since living systems display organization, they display means
adapted to ends and structures and processes assembled to perform
specific functions, it becomes self-evident that they are the product
of a higher intelligence.”

And,

  “a mousetrap has a quality
called organization, which is much different from complexity or order.
Each part of the mousetrap, the platform, the holding bar, the spring,
the hammer and the catch each have specific functions. And each of
these functions are organized in such a way that they support the other functions and the
overall function of the mousetrap, which is to catch mice. The
function of the platform is to hold the parts, but it’s there
ultimately to facilitate the process of mouse catching. The function
of the spring is to exert a force on the hammer, but it’s ultimate
goal is to enable the process of mouse catching. All of the parts have
functions that not only support the other functions, but ultimately
support the overall function of the device. This type of organization
is not obtainable without insight, and insight always requires
intelligence. There is no way that these parts could be assembled in
such a manner without insight.
  A mousetrap is a simple machine, made up of several structures and
processes and exists for a purpose. The construction of the mousetrap
was initiated with intent, and fashioned for a purpose. Living
organisms are similarly machines, with structures and processes that
work together to create a function. In fact, all complex, highly
organized machines in which means are adapted to ends are the product
of intelligent design. The important point is that the adaption of
means to ends, the adaption of structure and process to function
requires insight.
  A moustrap is unevolvable without intelligent input, not because you can’t take it
apart without it losing it’s function, it’s unevolvable because you
can’t put it together in the first place using only random,
non-directed, accidental occurrences. The selection of the parts, the
configuration in which they’re aligned, the assembly into one unit all
require intelligent decisions at every step of the way. Similarly,
living organisms show the same characteristics. It’s not that you
can’t remove parts and lose total function, it’s that you can’t
explain why these particular parts were selected, why they’re
integrated together in just such a way and how they were assembled
from raw materials without invoking an intelligent agent.”

Comment #2842

Posted by charlie wagner on May 25, 2004 05:41 PM (e) (s)

Reed wrote:

Nelson’s Law is a tautology that Charlie came up with and named after his middle name.

  Go to my website and scroll down to the very bottom, right corner where you will find my middle name. It is not Nelson. Marshall Nelson is  my pen name. I did, in fact, name the Law after myself. And Nelson’s Law is NOT a tautology, it is a falsifiable scientific law.

Comment #2843

Posted by Town Crier on May 25, 2004 05:57 PM (e) (s)

Charlie said:

Organization is a much different structure in which
something is made up of elements with varied functions that contribute
to the whole and to collective functions

Ah, such a clear and useful definition of “organization”!  Come to think of it, Charlie, you never were able to explain why Great White Wonder’s swimming hole didn’t satisfy your definition of “organization.”  Would you like to take a stab at that now? 

Or you could simply endorse what I stated in my earlier post and spare us the backpedaling.

Comment #2846

Posted by Reed A. Cartwright on May 25, 2004 06:12 PM (e) (s)

Charlie wrote:

Go to my website and scroll down to the very bottom, right corner where you will find my middle name. It is not Nelson. Marshall Nelson is  my pen name. I did, in fact, name the Law after myself.

My bad, when looking on T.O. I thought I saw you say that it was after your middle name.

And Nelson’s Law is NOT a tautology, it is a falsifiable scientific law.

It is so a tautology: (to paraphrase your logic) “Everything that we’ve observed made by mankind did not arise without intelligent input.”

Your use of “falsifiability” is also flawed.  “Falsifiability” does not make something true, only testable.  Only after repeatedly failing to falsify a “falsifiable” claim is it considered valuable.  I have yet to see “Nelson’s Law” tested on biological entities.  Therefore, your attempts to say “Nelson’s Law prevents X” are invalid.

Comment #2847

Posted by charlie wagner on May 25, 2004 06:23 PM (e) (s)

Reed wrote:

It is so a tautology: (to paraphrase your logic) “Everything that we’ve observed made by mankind did not arise without intelligent input.”

  Reed, that’s an incorrect characterization of my “logic”. Perhaps it would be better to just quote me, rather than trying to paraphrase my logic.
  I said:

Nelson’s law is not an abstract conceptualization, it has clear and easily
observable qualities, chief among which is the adaptation of means to
ends. It also includes the relatedness of structure and function and
the adaptation of structures and processes for the purpose of
accomplishing the function. All of the aspects of a refrigerator meet
these criteria, The physical construction of the cabinet, compressor,
heat exchanger, etc. exist for the purpose of carrying out the cooling
function. The process of compression and expansion of gases in the
refrigerator are adapted to the function of cooling as well. All of
these aspects are assembled in such a way as to work together, each
part and process performing a specific function that contributes to
the overall goal of cooling. All known entities that we have observed,
that have the above mention qualities, are the products of intelligent
design. Living organisms also have these qualities and possesss the
same inherent properties as a refrigerator, or any other functional
machine. My conclusion, therefore, is that they also were designed for
a purpose. Nelson’s Law clearly states that entities of this nature,
fitting this description, and having these properties and qualities,
do not create themselves without the benefit of intelligent
intervention.

Comment #2851

Posted by Town Crier on May 25, 2004 06:40 PM (e) (s)

Nelson’s law is not an abstract conceptualization, it has clear and easily
observable qualities, chief among which is the adaptation of means to
ends. It also includes the relatedness of structure and function and
the adaptation of structures and processes for the purpose of
accomplishing the function.

Charlie, you are clearly refusing to address the fact that your definition of organization means that swimming holes and beaches are intelligently designed (even those without tire swings or showers).

Your refusal to answer can only be taken as an admission that your theory is, at best, half-baked.

Comment #2857

Posted by Reed A. Cartwright on May 25, 2004 07:29 PM (e) (s)

Charlie wrote:

Reed, that’s an incorrect characterization of my “logic”. Perhaps it would be better to just quote me, rather than trying to paraphrase my logic.

Here is what you state in your quote:

All known entities that we have observed,
that have the above mention qualities, are the products of intelligent
design.

Your “all know entities” that you cite are human creations.  Thus “Everything that we’ve observed made by mankind did not arise without intelligent input.” is an accurate paraphrase of your logic.

Comment #2859

Posted by Nomen Nescio on May 25, 2004 08:11 PM (e) (s)

does it seem to anyone else that naming a made-up “law” after one’s own self-assigned nickname is an even more pretentious social faux pas than simply naming it after oneself?

not, of course, that that alone is any argument against the “law” in question. nonetheless, bad taste, n’est pas?

…

as for the “law” itself, i cannot say with certainty that it is flawed - frankly, it’s too vaguely and verbosely stated for me to make a whole lot of sense of it. however, it does occur to me that - if it is to be of any use - it really ought to be able to determine whether or not the Oklo  reactors were intelligently designed could anybody with a better sense of what Charlie’s trying to say perhaps take a stab at working out if it does or not?

Comment #2860

Posted by Art on May 25, 2004 08:22 PM (e) (s)

Charlie,

Thanks for the clarification (I think).  But I don’t buy your distinction between “order” and “organization”.  At least in its entirety.

But even if I did - I think its easy to see how storms (tornadoes, hurricanes, et.c) are organized according to some of your rules (those that do not reduce your terminology to tautology), and I could probably dissect the oil-water system into an organized, as opposed to ordered, one as well.

So, either way, I don’t see how “Nelson’s Law” is of any particular use, except as a vehicle to wander into semantic hair-splitting.  It’s much easier (and more correct) to accept that “SLOT’s”, regardless of their derivation, simply cannot rule out evolution.

Comment #2862

Posted by Jerry Don Bauer on May 25, 2004 09:09 PM (e) (s)

LOL…This has got to be the silliest thing I’ve ever seen posted on the Net on “thermodynamics“— To start with it’s genetics and has nothing to do with anything I have ever discussed concerning devolution of the genome.

What’s even more telling is the rest of the forum is like cool, go man, go…..we are really doing some science here. PvM hasn’t done a thing here with this nonsensical ‘math’ and I’ve seen him laughed out of other forums with this same stuff. Observe:

*******The approach is very simple first assume a genome with site i which has the following probabilities for the four nucleotides involved******

I did not assume ANY genome. I introduced a study by evolutionary biologists where all deleterious mutations were already identified. There is no probability involved with that. Sheeeze.

[img]http://www.pnas.org/content/vol97/issue9/fulltext/4463/img00…[/img]

******One can show that the entropy for this site can be calculated to be******

LOL…OK, what is it, PvM? People he didn’t calculate any entropy. He threw out an empty formula with no numbers in it and thinks he has calculated entropy. And everyone else: Hey good job, man. I understand this now.

[img]http://www.pnas.org/content/vol97/issue9/fulltext/4463/img00…[/img]

*****And the entropy tendency or information can be defined as*****

You didn’t define anything and again you didn’t calculate anything because there are no numbers in your formula.

[img]http://www.pnas.org/content/vol97/issue9/fulltext/4463/img00…[/img]

******Now sum over all sites i and you find that the complexity or information is given by******

You cannot sum over anything! You don’t have any figures in this formula to sum over.

[img]http://www.pnas.org/content/vol97/issue9/fulltext/4463/img00…[/img]

Of course, he then graphs all of this stuff he never calculated to start with and he does this before he doesn’t calculate anything.

LOL…You people don’t know he is just cutting and pasting stuff he doesn’t even understand?

Comment #2864

Posted by Jerry Don Bauer on May 25, 2004 09:37 PM (e) (s)

******I was fairly amazed by Chronos’ assertion that “With every generation in homo sapien, entropy increases in the genome.”*******

Don’t believe anything Francis (PvM, the very confused YECer) posts. He’ll have you so confused you won’t know whether you’re coming or going because he is totally confused.

This came not from me (Chronos) but from a peer reviewed study submitted in Nature by two well respected evolutionary biologists name Eyre-Walker of Sussex University and Keightley of EdinBurgh.

http://homepages.ed.ac.uk/eang33/…

They found in this study that in man’s evolutionary walk from Chimp, the genome devolved at the rate of 1.6 deleterious mutations per generation AFTER natural selection had weeded out other of these mutations. This is the number that accumulate in the genome. But normally when we discuss this study, the figures are rounded off to two.

Here is the abstract:

High genomic deleterious mutation rates in hominids.

Eyre-Walker A, Keightley PD.

Centre for the Study of Evolution and School of Biological Sciences, University of Sussex, Brighton, UK.

It has been suggested that humans may suffer a high genomic deleterious mutation rate. Here we test this hypothesis by applying a variant of a molecular approach to estimate the deleterious mutation rate in hominids from the level of selective constraint in DNA sequences. Under conservative assumptions, we estimate that an average of 4.2 amino-acid-altering mutations per diploid per generation have occurred in the human lineage since humans separated from chimpanzees. Of these mutations, we estimate that at least 38% have been eliminated by natural selection, indicating that there have been more than 1.6 new deleterious mutations per diploid genome per generation. Thus, the deleterious mutation rate specific to protein-coding sequences alone is close to the upper limit tolerable by a species such as humans that has a low reproductive rate, indicating that the effects of deleterious mutations may have combined synergistically. Furthermore, the level of selective constraint in hominid protein-coding sequences is atypically low. A large number of slightly deleterious mutations may therefore have become fixed in hominid lineages.

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&d…

Those who don’t care to read through the science can find a good read here:

http://www.open2.net/truthwillout/evolution/article/evolutio…

Comment #2865

Posted by Pim van Meurs on May 25, 2004 10:07 PM (e) (s)

It should be obvious by now that Jerry, is in ‘over his head’.

jerry wrote:

I did not assume ANY genome. I introduced a study by evolutionary biologists where all deleterious mutations were already identified. There is no probability involved with that. Sheeeze.

I was responding to your ‘calculations’ of entropy which you concluded were positive and thus showed a tendency to disorder. This incorrect application of mathematics is what I am addressing here. And contrary to your claims that

P1: With every generation in homo sapien, entropy increases in the genome.

P2: Complex macroevolution requires that the genome have a lower entropy over time through the generations.

Therefore, complex macroevolution did not occur

I argued that not only have you failed to provide for support for P1 and P2 but I also showed that mutation and variation actually can be shown to decrease the entropy in the genome.

Not only can it thus be shown that no support for Jerry’s P1 and P2 claims exist but also that actual evidence contradicts Jerry’s conclusions.

All because Jerry seems to be unable to apply the correct concepts.

Jerry wrote:

What’s even more telling is the rest of the forum is like cool, go man, go…..we are really doing some science here. PvM hasn’t done a thing here with this nonsensical ‘math’ and I’ve seen him laughed out of other forums with this same stuff. Observe:

I understand that your only response to solid mathematics is ridicule. But we often ridicule that which we do not comprehend. In fact not only is this math not nonsensical but it is also supported by actual examples (did Jerry miss the graphs) which show the evolution of entropy under the influence of mutation and selection.

Of course Jerry seems easily confused by abstract mathematics

You didn’t define anything and again you didn’t calculate anything because there are no numbers in your formula.

It is trivially simple to replace the parameters in these formulas with actual values which is what was done to create the graphs.

Jerry ironically comments: LOL…You people don’t know he is just cutting and pasting stuff he doesn’t even understand?

So far the only person who does not seem to understand is you Jerry. And that by your own comments. Remember you are the person who confused the positive value of entropy with its tendency. People are ISCID are still rolling their eyes on that one.

Jerry then quotes an article by Walker without doing ANY calculations to show that entropy has in fact increased. If Jerry’s argument is not about entropy but about the rate of deleterious mutations then why all his nonsensical postings to introduce these concepts?
Are you saying that when you spammed this board with your nonsensical articles about entropy you were not really arguing entropy at all?

Can we say back pedaling Jerry?

SO Jerry, what part of my introduction to Shannon entropy confused you?

Or shall we consult a scientist on these matters rather than rely on your ‘claims’? Let’s see

How do genetic systems gain information by evolutionary processes? Answering this question precisely requires a robust, quantitative measure of information. Fortunately, fifty years ago Claude Shannon defined information as a decrease in the uncertainty of a receiver. For molecular systems, uncertainty is closely related to entropy and hence has clear connections to the Second Law of Thermodynamics. These aspects of information theory have allowed the development of a straightforward and practical method of measuring information in genetic control systems. Here this method is used to observe information gain in the binding sites for an artificial `protein’ in a computer simulation of evolution. The simulation begins with zero information and, as in naturally occurring genetic systems, the information measured in the fully evolved binding sites is close to that needed to locate the sites in the genome. The transition is rapid, demonstrating that information gain can occur by punctuated equilibrium.

Tom Schneider “evolution of biological information”

To explain for Jerry’s sake the implications: Schneider has shown how under the simple processes of mutation and selection the information in the genome can increase. Since information increase means entropy decrease, it should be obvious that evolutionary processes can and do in fact decrease entropy and increase information.

But let’s continue with how real scientists address these issues of entropy and the genome

To make a case for or against a trend in the evolution of complexity in biological evolution, complexity needs to be both rigorously defined and measurable. A recent information-theoretic (but intuitively evident) definition identifies genomic complexity with the amount of information a sequence stores about its environment. We investigate the evolution of genomic complexity in populations of digital organisms and monitor in detail the evolutionary transitions that increase complexity. We show that, because natural selection forces genomes to behave as a natural “Maxwell Demon,” within a fixed environment, genomic complexity is forced to increase.

Adami, Ofria and Collier evolution of biological complexity

Jerry’s postings and arguments are no match to the reality.

Comment #2866

Posted by Pim van Meurs on May 25, 2004 10:12 PM (e) (s)

As far as Charlie is concerned, his appeal to personal incredulity combined with a lack of any supporting argument makes his Nelson’s law quite meaningless and forcing him to ignore the empirical data, experimental data and theoretical arguments that disprove his claims. Until Charlie can show that he can correctly represent evolutionary theory, his claims have to be rejected due to their strawman nature and unproven and in fact fallacious assumptions.

Comment #2867

Posted by Pim van Meurs on May 25, 2004 10:19 PM (e) (s)

Some more relevant data

The assumption of an increase of conformational
order and structural stability in the course of evolution was tested using a comprehensive molecular morphospace defined by the metrics of base-pairing propensity (P), mean length of helical stem (S) and the Shannon entropy of the base-pairing probability matrix (Q) (defined by Schultes et al., 1999). Evolved sequences had larger P and S, and lower Q values that their corresponding permuted cohorts obtained by sequence randomization (generated by permutation
using heteropolymer randomization algorithms).
These results follow those recently reported for several classes of functional RNA (Schultes et al., 1999), confirming that evolved sequences were more ‘ordered’ than randomized derivatives.

1. Novel strategies to study the role of mutation and nucleic acid structure in evolution Plant, G. Caetano-Anolles,  Cell, Tissue and Organ Culture 67: 115–132, 2001.

Note that Jerry has yet to present any entropy calculations that show that entropy of the human genome increase (P1) not to mention any evidence to support P2.

Comment #2868

Posted by Pim van Meurs on May 25, 2004 10:37 PM (e) (s)

Me: Note that Jerry has yet to present any entropy calculations that show that entropy of the human genome increase (P1) not to mention any evidence to support P2.

And this is not a non-trivial calculation since Eyre-Walker looked only at slightly deleterious mutations, ignoring thus beneficial mutations.

And as far as P2 is concerned, it seems that these findings fall within the realm of evolutionary explanations. Perhaps P2 was just a wishful thinking argument?

A bit of quote mining, a lot of nonsensical and irrelevant claims about entropy all to show that there is a significant slightly deleterious mutational load in humans.

But what about the entropy Jerry? And what about the fact that the study only considered slightly deleterious mutations?

Shoddy Jerry, shoddy.

Not surprisingly Eyre-Walker presents the answer to this problem

Work has also started to elucidate the role of adaptive evolution at the DNA sequence level. Several studies have recently estimated that a substantial fraction of the amino acid substitutions in higher primates (30) and Drosophila (24, 31, 32) are a consequence of adaptive evolution rather than random genetic drift. However, inferring the number of advantageous mutations is difficult because the number of substitutions is a function of both the mutation rate to advantageous mutations and the strength of selection favoring them. We do not currently have independent estimates of either of these quantities.

Estimating the distribution of fitness effects from DNA sequence data: Implications for the molecular clock, Gwenaël Piganeau and Adam Eyre-Walker PNAS 2003 vol. 100 no. 18 10335-10340

Comment #2869

Posted by Pim van Meurs on May 25, 2004 10:49 PM (e) (s)

Let’s add to this the following data

Fitness effects of advantageous mutations in evolving Escherichia coli populations
Marianne Imhof and Christian Schlötterer

The central role of beneficial mutations for adaptive processes in natural populations is well established. Thus, there has been a long-standing interest to study the nature of beneficial mutations. Their low frequency, however, has made this class of mutations almost inaccessible for systematic studies. In the absence of experimental data, the distribution of the fitness effects of beneficial mutations was assumed to resemble that of deleterious mutations. For an experimental proof of this assumption, we used a novel marker system to trace adaptive events in an evolving Escherichia coli culture and to determine the selective advantage of those beneficial mutations. Ten parallel cultures were propagated for about 1,000 generations by serial transfer, and 66 adaptive events were identified. From this data set, we estimate the rate of beneficial mutations to be 4 × 109 per cell and generation. Consistent with an exponential distribution of the fitness effects, we observed a large fraction of advantageous mutations with a small effect and only few with large effect. The mean selection coefficient of advantageous mutations in our experiment was 0.02.

and

The Distribution of Fitness Effects Among Beneficial Mutations  H. Allen Orra

We know little about the distribution of fitness effects among new beneficial mutations, a problem that partly reflects the rarity of these changes. Surprisingly, though, population genetic theory allows us to predict what this distribution should look like under fairly general assumptions. Using extreme value theory, I derive this distribution and show that it has two unexpected properties. First, the distribution of beneficial fitness effects at a gene is exponential. Second, the distribution of beneficial effects at a gene has the same mean regardless of the fitness of the present wild-type allele. Adaptation from new mutations is thus characterized by a kind of invariance: natural selection chooses from the same spectrum of beneficial effects at a locus independent of the fitness rank of the present wild type. I show that these findings are reasonably robust to deviations from several assumptions. I further show that one can back calculate the mean size of new beneficial mutations from the observed mean size of fixed beneficial mutations.

Comment #2870

Posted by Jerry Don Bauer on May 25, 2004 10:51 PM (e) (s)

*****With all due respect, this is not true. How do you measure the entropy in the genome and how do you demonstrate that natural selection reduces this entropy?*****

The thread would do well to stay away from vague concepts such as Nelson’s law and go with the well proven work of Boltzmann and Feynman. Of course, Boltzmann was the first to term the W in his S = K log W as “the opposite of information” but Feynman refined this into formula without Boltzmann’s constant messing with Joules and degrees Kelvin which really just clutters everything.

Feynman honed this down: “So we now have to talk about what we mean by disorder and what we mean by order. … Suppose we divide the space into little volume elements. If we have black and white molecules, how many ways could we distribute them among the volume elements so that white is on one side and black is on the other? On the other hand, how many ways could we distribute them with no restriction on which goes where? Clearly, there are many more ways to arrange them in the latter case. We measure “disorder” by the number of ways that the insides can be arranged, so that from the outside it looks the same. The logarithm of that number of ways is the entropy. The number of ways in the separated case is less, so the entropy is less, or the “disorder” is less.”

http://www.panspermia.org/seconlaw.htm…

Feynman also gave us the formula with which we could calculate this: S = log2(W) where S is entropy and W is “those numbers of ways” or the total possible microstates of any given system.

We can find W, because the researchers tell us is there are about 100 million possibilities that could mutate, so four mutations is not that big a number, relatively speaking. (please read the BBC article I previously posted for this figure) But this will be positive entropy, thus we can surmise that entropy has risen in each, or at least most, generations for the last six million years and there is no evidence at all to suggest it hasn’t been this way throughout the entire 2 billion year process.

S = log2W, S = log2(100,000,000), S = 26.5754247590989, therefore S is positive showing a positive tendency of disorder as we would expect.

But this is only statistical entropy and if we are to figure reactional entropy, we will have to calculate actual deleterious mutations from generation to generation.

We can view the deleterious mutations as actual entropy because, in this case, this is the actual disorganization. Eyre-Walker tells us that the human genome is estimated to carry 1000 negative mutation, so let’s get that entropy S = log2 W = S = log2 1000 S = 9.96578428466209 —

Now let’s calculate the entropy after two more genes mutate S = log2 W S = log2 1002 S = 9.96866679319521 —

It is here that we do that subtraction you so badly wanted to do: deltaS, the actual change in entropy is: deltaS = S2 - S1 — deltaS = 9.96866679319521 (-) 9.96578428466209 = deltaS = 0.00288250853312

Questions, comments, or just ignorant trolls, its up to you guys.

Comment #2871

Posted by Jerry Don Bauer on May 25, 2004 11:32 PM (e) (s)

NOTE: I’m going to answer exactly one more of your ignorant posts, Francis. So after this one, you sum it all together and know that you had your chance to debate this. You somehow seem to have become one of my groupies. Go troll Mike Gene or something.

*****I was responding to your ‘calculations’ of entropy which you concluded were positive and thus showed a tendency to disorder. This incorrect application of mathematics is what I am addressing here. And contrary to your claims that
P1: With every generation in homo sapien, entropy increases in the genome.
P2: Complex macroevolution requires that the genome have a lower entropy over time through the generations.
Therefore, complex macroevolution did not occur*****

No, you are not answering ‘my calculations’ or my ‘claims.’ I’m sending you to papers by reputable scientists. You will not read them even when I post them verbatim for you and you always go back to Jerry claims this and that. Will you pull your head out of your arse and know that its not me saying this stuff but scientific studies? These calculations are just math describing them.

*****I understand that your only response to solid mathematics is ridicule. But we often ridicule that which we do not comprehend. In fact not only is this math not nonsensical but it is also supported by actual examples (did Jerry miss the graphs) which show the evolution of entropy under the influence of mutation and selection.******

LOL…Solid mathematics? Is this a joke? You calculated nothing. This is the stupidest forum I’ve ever been in as no one bothered to muse…well gee, what were the conclusions? Um..is there actually any figures in those formulas? What were the entropic conclusions and the sums? Nah….Its just, well gee whiz, this seems anti—Id. Let’s run with it. And look at all the PhDs listed as the sponsors. Unbelievable. You people you are just deceiving yourselves. The American public is nowhere near as stupid as you have become.

******It is trivially simple to replace the parameters in these formulas with actual values which is what was done to create the graphs.*****

Oh. This should be good. Let’s see you do it. And how did you create the graph without trivially using actual values? <;0)

The rest of your post is typical Francis the YEC/atheist turned I don’t know what the crap I am drivel who spouts Bible scripture while espousing atheism in the same posts conundrum.

You get one more post, troll. Make it good, dude. (or dudette, you post under female names as well)

Comment #2872

Posted by Steve on May 25, 2004 11:45 PM (e) (s)

Slowly I’m learning to come here and read the posted articles, but not the comment sections. Reading 7000 words of arguing with IDers who are using information theory and thermodynamics like a monkey would use an oscilloscope is just not valuable for me. I still read them sometimes out of a macabre fascination, though.

The articles are damned good, btw, kudos to the contributors. I hope a cool article in the future will explain to me how IDers fail to understand what it means that evolution-based research results in more papers in PNAS, Science, and Nature alone every week than I can even read the abstracts of, while IDers never get any research published. How can they think so much about the topic, and not realize their ‘science’ doesn’t produce publishible results? That’s really more of a psychology topic than a biological one, though.

Comment #2874

Posted by steve on May 25, 2004 11:58 PM (e) (s)

I have a request, too—articles about antibiotic resistence. For some eventual research on the physics of Syntaxin mutants, I’ve been hip-deep in e. coli DH5a, plasmids, pcr, sequencing, etc., and there’s really some very cool stuff involved in growing bacteria which is resistant to a specific antibiotics like kanamycin, in kanamycin, to prevent contamination. It’s a subject laypeople might enjoy hearing about. Just a few months ago I had no idea about the subtle evolutionary bits involved.

Comment #2876

Posted by Jerry Don Bauer on May 26, 2004 01:28 AM (e) (s)

****I have a request, too—articles about antibiotic resistence.*****

Here’s the only article you will ever need on it. Certain organisms in any species will always be more  susceptible than others to an antibiotics and some will be resistant to it. As more antibiotics are used, the ones that are susceptible are killed off and the ones who live will be the ones who have offspring.

These offspring are then also resistant to that antibiotic.

Others might take a book to explain this. But there you go and that’s the truth.

Comment #2879

Posted by Jack Krebs on May 26, 2004 03:47 AM (e) (s)

Steve writes, “Slowly I’m learning to come here and read the posted articles, but not the comment sections. Reading 7000 words of arguing with IDers who are using information theory and thermodynamics like a monkey would use an oscilloscope is just not valuable for me. I still read them sometimes out of a macabre fascination, though.”

I hope that the quality of the comments section improves, Steve.  Don’t give up.

Comment #2893

Posted by Navy Davy on May 26, 2004 09:25 AM (e) (s)

The reason the comment section often degenerates is actually a STRUCTURAL failing on the part of Panda’s Thumb. Observe the dynamic:

1. Poster tries to makes a point, imbued with scorn and ad hominem, which often specifically NAMES Jerry Don Bauer as the subject;

2. But poster refuses to engage JDB (ask civil questions, respond to civil questions posed);

3. JDB responds, fending off 5-10 persons sniping from sidelines, sometimes with ad homimen in response and sometimes over-enthusiastically;

4. Thread peters out. Few are satisfied.

Of course, I have offered to mediate a civilized, debate, where advocates actually get to TEST their propositions, and we get to learn something. JDB has pledged to participate and abide by standard debating rules. Kudos, Jerry.

But, alas, the “higher-ups” at PT cannot spare a solitary thread for such an orderly debate.

I thought scientists were, you know, into (1) evidence, (2) testing, (3) prediction, (4) logic. 

I guess not. Let the brawlin’ continue!

Cheers,

Navy Davy

Comment #2894

Posted by Pim van Meurs on May 26, 2004 09:34 AM (e) (s)

Jerry continues to exemplify his lack of understanding when he states: herefore S is positive showing a positive tendency of disorder as we would expect.

This whopper was in depth debunked on ISCID. That Jerry still repeats this silly notion almost verbatim is quite fascinating.

Jerry wrote:

The rest of your post is typical Francis the YEC/atheist turned I don’t know what the crap I am drivel who spouts Bible scripture while espousing atheism in the same posts conundrum.

Yes Jerry, ad hominem is all that you have left. Thank you for showing your ‘true colors’. And while we all hope that the quality of Jerry’s postings would improve, the opposite seems to have happened.

If Jerry cannot even understand the simple mathematical foundations for Shannon entropy as they apply to the genome, it does not come as a surprise that he fails to comprehend how one can calculate the actual entropy from abstract formulas.

Let me know what part of the derivation of Shannon entropy or the calculations based upon these formulas confuse you Jerry.

As I have shown, real scientists, have applied these concepts and shown how entropy in the genome could decrease under the workings of variation and selection.

And then there is Jerry who cannot even calculcate the entropy in the genome to show support for P1 (entropy in the human genome always increases).

Comment #2895

Posted by Jack Krebs on May 26, 2004 09:34 AM (e) (s)

How about taking your idea to ARN, where you or  Jerry would be free to start a post and propose details of this debate?

Comment #2896

Posted by Andrea Bottaro on May 26, 2004 09:44 AM (e) (s)

Here’s the only article you will ever need on it. Certain organisms in any species will always be more  susceptible than others to an antibiotics and some will be resistant to it. As more antibiotics are used, the ones that are susceptible are killed off and the ones who live will be the ones who have offspring.

These offspring are then also resistant to that antibiotic.

Others might take a book to explain this. But there you go and that’s the truth.

Ah, but that’s just a statement of fact, and explains little or nothing.  The real questions are, why will certain individuals always be more susceptible, or resistant, to antibiotics than others?  And why is it so hard to come up with an antibiotic that kills all individuals, preventing the onset of resistance?  And why does taking suboptimal doses of antibiotics increase the chances of inducing resistance?

Comment #2897

Posted by Pim van Meurs on May 26, 2004 09:47 AM (e) (s)

Navy, why not take Jack Krebs’ idea and implement such a discussion on ARN, which would be an excellent place for Jerry to discuss his ideas.

To suggest that I refuse to engage Jerry or that Jerry is asking questions can be easily shown to be wrong. Jerry started spamming other threads with his nonsensical ideas about entropy. And now we find out that it was all about detrimental mutations and not about entropy at all.

I guess we will never see Jerry support his claims. His application of mathematics does not seem to extend beyond

therefore S is positive showing a positive tendency of disorder as we would expect.

Of course S is positive, it always is positive. That Jerry confuses positive with a tendency of disorder is just totally nonsensical.

Jerry still fails to apply the correct formulas in a useful manner. Subtracting nonsense from nonsense will lead to a nonsensical conclusion. The dangers of using mathematics without understanding how to correctly apply is quite real in discussions of the second law of thermodynamics. Mostly because people confuse a mutation with an increase in entropy. In fact when a mutation happens and gets fixed in a population, entropy will decrease. Even if the mutation is a slightly detrimental mutation.

Surprised? I bet Jerry is. But as I said these are nontrivial concepts and often somewhat counterintuitive. So let me try to explain.

Originally lets assume that the nucleotide at the location of the mutation has an equal probability of being A, C, T or G. This means that this location has maximum entropy. After the mutation if the probability of the nucleotide becomes 1 for one of the 4 bases and zero for the others because the mutation becomes fixed in the genome, the entropy drops to zero. Not surprisingly when one understand the concept of Shannon entropy. Before the mutation and fixation there was maximum confusion as to which nucleotide would be found at the location or in other words maximum disorder. After the mutation got fixated, there is full predictability of the basepair at this location or maximum order.

Don’t believe me ? Do the calculations using the correct formulas
I provide the outline for how to calculate Shannon entropy.

Comment #2902

Posted by Nate Barrister on May 26, 2004 11:36 AM (e) (s)

This was good.

Comment #2908

Posted by Whistle Blower on May 26, 2004 01:30 PM (e) (s)

Navy Davy, an alleged lawyer, casts his judgment as follows:

I thought scientists were, you know, into (1) evidence, (2) testing, (3) prediction, (4) logic. 

I guess not.

For the record, Navy Davy, where do you find an indication in Pim’s posts that he is uninterested in any of the four categories you listed?  I’m particularly interested in where you find problems with the evidence or logic Pim used.

Your honest response will be greatly appreciated and recorded for future use, as appropriate.

Finally, the record will show that your statement re:

“poster refuses to engage JDB (ask civil questions, respond to civil questions posed”

is demonstrably false as pointed out by Pim.

In the future, please try to avoid distorting the record by making false, facially inaccurate, or dishonest statements in your posts.

Cheers,
WB

Comment #2915

Posted by Navy Davy on May 26, 2004 02:42 PM (e) (s)

Pim,

Navy, why not take Jack Krebs’ idea and implement such a discussion on ARN, which would be an excellent place for Jerry to discuss his ideas.

Not a bad idea, I might do that.  But, you POSTED here an attack specifically on Jerry (not simply his ideas on entropy). I quote:

Jerry Don Bauer a.k.a. Chronos has shown some interesting confusions as to the concept of entropy…..

So, for the life of me, I cannot understand why the Evolution proponents would rather snipe from the sidelines at ID folks, rather than directly engage their ideas in a civil manner.

To me, it just seems like a wasted opportunity. Particularly, because I see a whole lotta intellectual acumen here that, if channelled properly, would really be influential and informative.

Cheers, Navy Davy

Comment #2917

Posted by Whistle Blower on May 26, 2004 03:02 PM (e) (s)

Navy Davy attempts to defend himself, telling Pim —

you POSTED here an attack specifically on Jerry (not simply his ideas on entropy). I quote:

Jerry Don Bauer a.k.a. Chronos has shown some interesting confusions as to the concept of entropy…..

Navy Davy, please refrain from distorting and mischaracterizing the record.  Let me know if you need definitions for the terms “distorting” or “mischaracterizing” and I’ll be happy to provide them to you.

In your “summary” of Pim’s post, you failed to mention that Pim has provided substantial (indeed, conclusive) evidentiary support for his conclusion that Chronos had “shown some interesting confusions.”  Therefore, obviously, Pim’s statement cannot reasonably be construed as an “attack” on Chronos (aka JDBauer), at least not by a reader without substantial biases.

The record shows, Navy Davy, that you have alleged that you are free of such biases.  Please let us know if, in fact, you are retracting your earlier statements (e.g., “I don’t have a dog in this fight,” etc., etc.).  Some of have expressed doubts as to the honesty of those statements so we not be surprised or particularly disappointed if you retracted them.

Alternatively, Navy Davy, you are welcome to state where you believe that Pim has unfairly taken Jerry Don Bauer’s words and distorted them, such as would render Pim’s conclusion about Jerry Don’s “interesting conclusions” unsubstantiated.

As always, your honest and courteous responses are greatly appreciated.  For the record, we note that such responses from Navy Davy are few and far between.

Cheers,
WB

Comment #2918

Posted by Navy Davy on May 26, 2004 03:24 PM (e) (s)

Whistle Blower,

I give you a resounding, “Ho-hum.”

Comment #2921

Posted by Jerry Don Bauer on May 26, 2004 03:44 PM (e) (s)

******Jerry continues to exemplify his lack of understanding when he states: herefore S is positive showing a positive tendency of disorder as we would expect.
This whopper was in depth debunked on ISCID. That Jerry still repeats this silly notion almost verbatim is quite fascinating.******

I didn’t just posit this, unlike you I actually calculated it. And Francis, why don’t you quit sending people to other forums hoping they won’t read all the posts. If this whopper were debunked by you before, you wouldn’t have much trouble doing again here, would you?

*****If Jerry cannot even understand the simple mathematical foundations for Shannon entropy as they apply to the genome, it does not come as a surprise that he fails to comprehend how one can calculate the actual entropy from abstract formulas.****

Oh, I think I understand Shannon/Weaver entropy just fine. I at least understand that you have to put some math into a formula in order to get something out of it.

*******Let me know what part of the derivation of Shannon entropy or the calculations based upon these formulas confuse you Jerry.******

You didn’t do any calculations. Not one. You only threw ought empty formulas that you cut and pasted hoping to confuse people. Works, don’t it. ;)

******And then there is Jerry who cannot even calculcate the entropy in the genome to show support for P1 (entropy in the human genome always increases).******

But I did calculate it. Did you not read the posts? Now quit beating around the bush hoping this will go away. Refute the math or admit you cannot.

Comment #2922

Posted by Jerry Don Bauer on May 26, 2004 04:11 PM (e) (s)

*****Originally lets assume that the nucleotide at the location of the mutation has an equal probability of being A, C, T or G. This means that this location has maximum entropy.*****

LOL……No it doesn’t. You think something has maximum entropy just because it exists? All things with microstates such as this have statistical entropy and Feynmann would calculate it as S = log2(4) = S = 2. But this is not maximum entropy because if a deleterious mutation happened here, disorder can go up. Think these things through before you post them, Francis.

******After the mutation if the probability of the nucleotide becomes 1 for one of the 4 bases and zero for the others because the mutation becomes fixed in the genome, the entropy drops to zero.******

Entropy drops to zero? Calculate this for us. And haven’t we just left the second law and went to the third?

Third law of thermodynamics: “The third law of thermodynamics states that the entropy of a pure perfect crystal is 0 at 0 K: � S(0K) = 0. At 0K the atoms in a pure perfect crystal are aligned perfectly and do not move. Moreover, there is no entropy of mixing since the crystal is pure. For a mixed crystal containing the atomic or molecular species A and B, there are many possible arrangements of A and B and there is therefore entropy associated with the arrangement of the atoms/molecules.”

Quick people, back away from the table. Francis’ human genome just froze solid!

*****Before the mutation and fixation there was maximum confusion as to which nucleotide would be found at the location or in other words maximum disorder.*****

And how do we calculate this maximum confusion?

*****After the mutation got fixated, there is full predictability of the basepair at this location or maximum order.******

You just flunked the genetics test too. You don’t understand the word ‘fixated.’ This applies only to populations, not individual genomes. Nothing is fixed in an individual because of a mutation. The reason is that this same nucleotide can always mutate again. In fact, it may even be a beneficial mutation.

Comment #2933

Posted by Pim van Meurs on May 26, 2004 05:31 PM (e) (s)

Jerry in the same breath claims he understands Shannon entropy and shows confusion of said entropy with thermodynamical entropy when he states

Entropy drops to zero? Calculate this for us. And haven’t we just left the second law and went to the third?

I will show in a follow up posting how to calulcate this but it is trivial since p_i log p_i will be zero for this site since either p_i is zero or log p_i is zer (p_i = 1)

Jerry still seems to be confused about entropy being a positive number (which it always is) and entropy having a tendency to disorder because it is positive. As Gedanken and various others have shown, this is a meaningless and erroneous concept. That Jerry continues his claims in spite of the facts is further evidence that Jerry may have some problems with entropy, and the mathematics surrounding this at the surface simple concept but oh so tricky in the hands of creationists.

Jerry wrote:

You only threw ought empty formulas that you cut and pasted hoping to confuse people.

I apologize for presenting a mathematical foundation for my claims and thus confusing you with ‘empty formulas’ but no worry, not only will I walk the ‘confused people’ through how to apply Shannon entropy but it will also support what I have already shown using data from Schneider and Adami, namely that entropy decreases under the influence of mutation and selection.

jerry wrote:

And how do we calculate this maximum confusion? [/url]

I thought you understood Shannon entropy? Well, let me try to explain. Maximum confusion means that no nucleotide was prefered or in other words that the probability for the nucleotide being one of (A,C,T,G) is equal to 1/4. Applying the formula for Shannon entropy we find that for uniform distribution of probabilities, entropy is maximum.

It should be clear by now that not only do the facts contradict Jerry but that Jerry has failed to show that the entropy of the genome of humans increases continuously. Which is of course quite impossible using the limited data presented by Eyre-Walker on slightly deleterious mutations. In other words, Jerry ignores most data that shows fixation of benificial mutations. But in the end shows that his application of entropy is but a strawman version of how real science calculates entropy.

Nothing wrong with that perse, we are here to educate and help out when issues of confusion arise and in a soon to be released posting I will gently walk through these straightforward and, yet to some confusing, calculations to show further support for my thesis.

And just for good measure, what does Jerry mean when he states

[quote]
I at least understand that you have to put some math into a formula in order to get something out of it.

math into a formula? Or does Jerry mean, actual values? If that is the case, could Jerry apply these formulas to his example? As I have shown, if, as Eyre-Walker argues, slightly deleterious mutations become fixated in the human genome then by all measures of entropy, the entropy will decrease.

But we already knew that disorder, entropy and information do not really say anything much about the nature of the fixated mutation. After all this should be obvious to anyone familiar with Shannon entropy.

I do admit that this sounds confusing and perhaps counter intuitive but intuition and entropy never have been good friends.

Comment #2940

Posted by Jerry Don Bauer on May 26, 2004 08:18 PM (e) (s)

What is this deal with you writing posts about me rather than to me? <:0)

******Jerry in the same breath claims he understands Shannon entropy and shows confusion of said entropy with thermodynamical entropy when he states
Entropy drops to zero?

I will show in a follow up posting how to calulcate this but it is trivial since p_i log p_i will be zero for this site since either p_i is zero or log p_i is zer (p_i = 1)*******

LOL….I don’t want formulas, I want math. Do some with real figures. But I do want to know how you can mathematically show your genome as being frozen solid. And if you show statistical entropy as zero in a system with microstates, you will have just revolutionized, science, my friend. Deleterious mutations become impossible and genetic defects are just a myth of science.

You’ll never have to buy a new car again the rest of your life. Just sit your old one out in the sun and according to your math, it will magically regress into a new one. And you will have just refuted the second law of thermodynamics.

****Jerry still seems to be confused about entropy being a positive number (which it always is) and entropy having a tendency to disorder because it is positive.*****

It is not always positive. Sure, statistical entropy in a system with microstates is, and it grows larger when we are considering more microstates. But wouldn’t you expect it to be? The second law states that with any spontaneous reaction entropy will tend to increase. I’m showing this mathematically.

But statistical entropy is not reactional entropy. And in chemical reactions entropy can go down and often does.

*****As Gedanken and various others have shown, this is a meaningless and erroneous concept. That Jerry continues his claims in spite of the facts is further evidence that Jerry may have some problems with entropy, and the mathematics surrounding this at the surface simple concept but oh so tricky in the hands of creationists.*****

LOL….What does this mean and aren’t you a YEC? Stick to the subject, sheeze.

*****I apologize for presenting a mathematical foundation for my claims and thus confusing you with ‘empty formulas’ but no worry, not only will I walk the ‘confused people’ through how to apply Shannon entropy but it will also support what I have already shown using data from Schneider and Adami, namely that entropy decreases under the influence of mutation and selection.*****

Apology accepted. Now quit trying to dodge the subject and go back and tackle the math I gave you. Remember I gave you real figures in formulas. Not just the formulas. And how do you ever hope to defeat my math using something other than my formulas?

****Well, let me try to explain. Maximum confusion means that no nucleotide was prefered or in other words that the probability for the nucleotide being one of (A,C,T,G) is equal to 1/4. Applying the formula for Shannon entropy we find that for uniform distribution of probabilities, entropy is maximum.*****

So you mean by this that before your genome was frozen it pretty much became delirious? And gee…I’m rather shocked to learn that the probabilities of one out of four nucleotides mutating is 1:4.

*****Jerry ignores most data that shows fixation of benificial mutations.*****

And this information is found where in that paper? They only considered deleterious mutations. Cut and paste all of this. You’re good at that.

****we are here to educate and help out when issues of confusion arise and in a soon to be released posting I will gently walk through these straightforward and, yet to some confusing, calculations to show further support for my thesis.*****

You probably ought to write a thesis that refutes my thesis, don’t you think?

****math into a formula? Or does Jerry mean, actual values? If that is the case, could Jerry apply these formulas to his example? As I have shown, if, as Eyre-Walker argues, slightly deleterious mutations become fixated in the human genome then by all measures of entropy, the entropy will decrease.*****

As they say in Arkansas, “Do what?”

*****But we already knew that disorder, entropy and information do not really say anything much about the nature of the fixated mutation. After all this should be obvious to anyone familiar with Shannon entropy.******

You don’t even know what Shannon/Weaver entropy is. You are trying to apply entropy that deals with the loss of signal and the addition of noise added into a telephone line to the genome. Oh, you water it down into some genetics you don’t understand. And remember that I was personally present when Bill Dembski, a math PhD actually examined this stuff and told you personally that nothing you are cutting and pasting is even germane to the subject. You, my friend, are as full of crap as a Christmas turkey and you spoil the truth of science for both sides.

Well, you trolled me for a debate and since you seem to be the highest intellect I can find on this forum: Your turn.

Comment #2941

Posted by Frank Schmidt on May 26, 2004 08:19 PM