The Big Bang Theory

[gentu]

Thanks Frum for pointing that out, you're right, I did use the wrong word. I meant to use "increases" instead of "decreases" in my original post, and have edited it accordingly. Jeptha, sorry for the confusion, It was just a typographical error. Thanks for all the personal attacks though, they're really appreciated!

 

[gentu]

Alright, I did some digging into the earlier pages of this thread, not wanting to pull a Donny (For those of you who have seen the Big Lebowski) and I believe the reason we're all discussing thermodynamics, Jep, is because you said in the middle of page 6 that the 2nd Law of Thermodynamics would be violated in the grand scheme of organic evolution. Now, this doesn't have anything to do with the Big Bang, the topic of this thread, but I'd be happy to discuss it elsewhere if you're inclined.

 

[Aradia]

JEP: "SLOT does not discriminate between forms of entropy; it governs them all, doesn’t it? But we have to discriminate between the forms or we will never understand what is happening in the system we are studying."

Discriminating is not the same as ignoring. You cannot legitimately ignore those forms which are increasing simply to show that one particular form is decreasing in order to counter my argument. Fallacy of exclusion.

JEP: "We will also need to insure that we define our systems and subsystems correctly. This is the first step to understanding thermo and what it is doing. For example, it wouldn’t do me much good to label the universe as my system when I’m studying a bacterium, would it?"

We're not studying bacterium. False analogy.

Aradia: "If you wish to prove me wrong, you'll have to show evidence that net entropy in the universe decreases due to complex macroevolution"

JEP: "Why? Since my argument is just the opposite."

If your argument is that "net entropy in the universe [increases] due to complex macroevolution" (the opposite of the statement you replied to), then complex macroevolution does not break SLOT. You lose.

 

[lucaspa]

10th April 2003 at 11:14 PM Jeptha said this in Post #92

“1. The reason SLOT can apparently be overcome is that the entropy of you and car, the ice and the fridge, increases. It's not the "energy" per se, but a decrease in entropy of the system under study (car, water) is accompanied by an increase in entropy in the system and the surroundings.”

JEP: Only if you are dealing with thermodynamical entropy, Lucaspa. Heat. In the case of a car aging, we are not dealing with thermodynamical entropy but logical entropy. Order/disorder.

Doesn't matter.  When you are fixing your car, you are using chemical energy and generating heat -- increased entropy.

”2. Seeds, cocoons, etc do not have all the chemicals, vitamins, etc. to get you to maturity. You have to ingest food to get there.”
JEP: No. They get me from conception to birth.

But that still doesn't get you there. Unless you want to tell us you didn't grow in your mother's womb and take in all those nutrients from her.

”3. Aging and withering are still a decrease in entropy.”

JEP: So you think that aging, wilting and death actually brings more order to an organism? That’s just wrong. Nobel winning physicist Erwin Schrodinger teaches us that death, perfect equilibrium, is maximum entropy.

Death is, but we are talking about "aging and withering". As long as you live, you are a decrease in entropy compared to death.

Schrodinger’s book “What is Life’ is online if you care to read it. Here’s an excerpt from chapter 8: “Every process, event, happening—call it what you will: in a word, everything that is going on in Nature means an increase in entropy of the part of the world where it is going on. Thus a living organism continually increases its entropy—or as you might say, produces positive entropy—and thus tends to approach the dangerous state of maximum entropy, which is death.”

Schrodinger was a good physicist, but a poor biologist.  As long as an organism is alive it must decrease entropy compared to its surroundings in order to stay alive.  What we call "aging" is not an increase in entropy, but a change in the genes expressed and the biochemical reactions taking place.  The entropy is the same, but the biological manifestations of that change.

“As long as you live, you are a decrease in entropy due to the chemical reactions that make new proteins, DNA, carbohydrates, etc. Upon death these chemical reactions cease and entropy increases.”

JEP: This is not correct either. The only way an organism reduces its thermodynamical entropy is by releasing heat into the atmosphere of earth.

And what do those chemical reactions do? Release heat, of course.

The chemical reactions that turn sugars into phosphates (ATP) actually increase thermodynamical entropy in the organism. That’s the very reason that research from the thirties forward have shown that a starvation diet will keep you alive longer.

The increase the thermodynamical entropy of the surroundings, not the organism.  You are concentrating only on one phase of metabolism -- catabolism.  You are forgetting anabolism that builds proteins, DNA, and carbohydrates.  Yes, the entropy of the organisms and  the surroundings increase (waste heat), but the entropy of organism alone decreases.  Come on, you have to admit that you are more organized that a solution of proteins, lipids, and DNA in water. 

And your comment about research on a calorie restricted diet is wrong. The reason it keeps you alive longer is that it produces less reactive oxidant species and slows the formation of oxidation products in the cells.  People in my department are engaged in this research so I get updates about once a month on the status of the field.

Also please do not confuse entropy with energy. Energy can only be entropy if it is not available to perform work. Gibbs free energy does not meet this criterion.

Look at the deltaS term in Gibb's free energy. That is change in entropy. 

 

[lucaspa]

10th April 2003 at 11:55 PM Jeptha said this in Post #97

“Several posts earlier you stated that input of energy can overcome SLOT. That's not exactly correct but, for now, let's assume you are right.”

JEP: That is exactly correct. Go fill up an ice tray, put it into the freezer and watch what happens. The electricity will do the work, your water will turn to ice, order, and entropy will decrease.

”Earth is a sub-system of a main system: the solar system.”

JEP: Yep. You nailed that one.

“And organisms are a subsystem of Earth.”

JEP: Also correct.
“Energy comes into both earth and organisms.”

JEP: Yes it does. And when this energy comes into the human system, it serves to actually increase thermodynamical entropy. I know this is hard to understand, but I’ll walk you through the chemical reactions if you wish.

“All of this provides energy which, you say, can overcome SLOT.”

JEP: All that you have shown thus far is that the photosynthetic process reduces entropy in plants. Yes it does and I’ve said this from the get-go. It does not at all in humans, however. This food does provide Gibb’s free energy to run the cell, but this does not lower thermodynamical entropy, it raises it.

What humans and other animals do is take the chemicals produced by plants -- sugars mostly -- and use that as their source of energy to overcome SLOT in themselves.

They break down the sugars into (eventually) ATP, CO2, H2O, and heat.  Now, ATP is a high energy compound that can transfer its energy (do work) to other chemical reactions such as peptide bond formation, nucleotide bond formation, and C-C bond formation in lipids and carbohydrates.  That energy in turn makes deltaH bigger than the -TdeltaS term in Gibbs free energy and the reaction proceeds even tho the entropy of the proteins, DNA, lipids, and decreases relative to the component amino acids, nucleotides, sugars, etc.  deltaS in the Gibbs free energy equation decreases but the reaction takes place.

Now, the total entropy of the organism and the surroundings does increase.  There is all that waste heat released by oxidative phosphorylation and the hydroysis of ATP.  That heat is an increase of entropy.  But, the system that is the organism decreases in entropy.

No violation of SLOT.

Now, for the lurkers, Jeptha is using the "shell game" tactic of constantly shifting claims.  He acknowledges that input of energy from the sun will decrease entropy by the chemical reactions in plants.  What he then does is try to say that sunlight itself won't decrease entropy in humans.  That's correct, but is irrelevant. No one has ever claimed that sunlight directly decreases entropy in humans. Instead, humans and all other organisms use the chemicals of decreased entropy made from the energy of sunlight to couple the combustion of those chemicals to synthetic processes that decrease entropy in the organisms.

When looking at the total entropy of the solar system, it increases.  Looking at the entropy only in living organisms, entropy decreases, but not by enough to be greater than the total entropy increase of the solar system.

Now, macroevolution is based on the chemical reactions that take place in biological organisms.  Since those reactions can take place with input of energy to decrease entropy, so too can input of energy be used to increase the complexity of the individuals that compose a population. What Jeptha calls "macroevolution."

IOW, by the processes that Jeptha acknowledges to be true and accurate, Jeptha has shown that macroevolution doesn't violate SLOT.

 

[SLP]

11th April 2003 at 09:45 PM Jeptha said this in Post #116

“Why don't you tell the nice folks at THIS board all about entropy and heat as it pertains to biological organisms.

If you are too shy, and don't want to impress us too much, I can go ahead and post your thoughts on this matter, whihc I have archived.”

JEP: Well paint me red and call me a barn. I would recognize those two sentences anywhere. Ladies and gentlemen, please welcome the distinguished Dr. Scott Page a biology professor at Norwich University (Mr. moderator: Neither Scott nor myself care about keeping our true identities secret on the Internet).

Scott likes to follow me around the Internet and collect my writings. He once actually featured the dum kreationist Jep on the home page of Norwich University but I think they made him take it off.

1. As has been pointed out, I joined this board many months ago, so I could not possibly be "following" you anywhere.
2. Please do not speak for me on ANY topic.
3.This is the second time that Jerry Don has mentioned this bizarre fantasy of his. No, Jerry, you were never significant enough to mention on my website. Ever. And no, nobody has mademe take anything off of my site. I collect your rantings in order to throw them back in your face when you make bombastic, fantasy-based claims. Indeed, the genesis of this latest fantasy of yours is in fact that you complained about me mentioning another creationist lunatic (who is now, interestingly, an evolutionist) on my website. Take our OCW 'debate' - the one in which you insisted thart unless I supplied you with the full-text documents for the references I used they should be considered invalid. The debate wherein you insisted that because water fleas inbreed, molecular phylogenetics methods are invalid. I will be poutting that on my website and linking to it so all can see what an utter waste of time 'debating' with you is and how little sense you actually make. Then, of course, there was the scientific calculator fiasco...

Scott is really confused in the realm of science and he so misunderstands my musings on thermodynamical entropy that he thinks we ought to be able to take the temperature of a baby and an 80 year old man and observe a massive temperature change. Why don’t you go into that for the forum, Scott.

I am astonished that you would want to reveal your ignorance on yet another forum.
Actually, jerry Don, what I wrote was in response to YOUR claim. YOU claimed that entropy builds up in an organism over time. It was YOU that equated entropy with heat. It was YOU that claimed that this build-up is what causes organisms to die. I challenged you to test this claim. It is you that is very very confused on many issues. Later, I will post lots of evidence of this. YOU claimed that organisms die because of a build up of heat. I challenged you to test this claim. It is, afterall, laughably false.

More later.

 

[lucaspa]

11th April 2003 at 05:09 PM Jeptha said this in Post #118

JEP: Although there are a few beneficial mutations we can think of, by and large most mutations are harmful ones. Dr. Eyre-Walker of Sussex University (I think) recently completed a study that shows the human genome to be degrading at the rate of about two harmful mutations per generation:

http://abcnews.go.com/sections/science/DailyNews/mutation990127.html

What this means is that the human genome is disordering rapidly and will in the future become so disorganized that homo sapien will no longer be able to function. 

You should read the article you quote.  The article starts out saying that each individual has 4 mutations.  It then states "On average, about 1.6 of them are bad enough that evolution and natural selection will eventually weed them out. "

1.6 is less than half of 4.  Less than 50% doesn't justify a statement of "by and large most mutations are harmful ones". 

The article concludes: "To determine the rate of bad mutations, they compared the number of mutations in sections of DNA that encode proteins with those that don’t encode proteins. Only the former can have deleterious effects. “Usually if you change the protein, it’s bad for you, and those individuals get eliminated,” Eyre-Walker says.
    Only rarely is a mutation beneficial — such as better disease resistance or higher intelligence — although those rare ones are the ones that drive evolution along new paths. "

Now, the authors are also judging "good" and "bad" on their terms, not the environment's.  Other, more rigorous studies have shown that the deleterious mutation rate is about 2.6 per thousand mutations.

 

[SLP]

12th April 2003 at 05:18 AM Jeptha said this in Post #135

"You're exactly right,if you're only talking about a system in isolation and not its surroundings. Useful energy must be utilized to fuel an endothermic reaction. Because no process of generating energy is 100% efficient, the overall entropy of the Universe decreases."

JEP: It increases! Have all the scientists left this debate? I'm not going to take you back to 10th grade science. I simply don't have the time. Your posits in this post are simply asinine.

Funny, I have felt the same way whenever I see your child-like claims.

What is the evidence that mutations increase entropy of any kind?

Please provide the full-text references, lest they will be considered invalid.

 

[SLP]

Jeptha has burst onto the scene with his usual overconfident bluster. He will imply - or say outright - that he is right on nearly every topic he writes about, while others in those fields are, of course, all wrong. Below is a post from ARN (the link appears to be dead, but I believe it is still available in their archives) in which Jep "informs" a poster named Pixie all about entropy and how it relates to evolution. I find this post to be quite informative as to Jeptha's actual level of undersanding of the things he writes about. Couching ignorance in technical-sounding jargon, propped up with bluster and confidence, is still ignorance. Emphasis mine:

quote:
--------------------------------------------------------------------------------

http://www.arn.org/ubb/Forum3/HTML/000090.html

Hi Pixie:
Present in the physical laws of our universe is an effective law of decay.
Energy and energy exchange is the driving force of our universe. And order to disorder is the governing principle of this energy as it interacts within the universe. Fires burn out, they never become bigger over the course of time as they deplete their energy. Batteries exhaust their energy supply, they don’t recharge themselves through usage. Air escapes from a tire when it is punctured, it never concentrates itself into the tire on its own. The gas tank of your car cannot fill itself as you drive. You will always run out of gas if you do not manually refill the tank.
The sun will burn out over time, not get bigger and brighter through infinity. Organisms wane old and die, never will they get younger and healthier as they age. Shiny new cars will eventually end up as a pile of rust in the junkyard. Pristine new homes will always deteriorate as they age with time, if left alone.
Throughout nature we see this collective directive in effect that governs our universe in the process of new to old, order to disorder with almost every energy exchange. This law is one of the most fascinating laws of science and is called the Second Law of Thermodynamics, henceforth known as SLOT.
The measurement of this law, is called entropy. Entropy is perhaps one of the least understood words in the realm of science. If SLOT dictates that entities in the natural world age and die, go from new to old, wear out and break down, then since entropy is a measurement of this law, entropy is also the measurement of disorder. The more entropy we have in a system, the more disorder we have in it. If entropy decreases, then something can be said to have ordered. But entropy is not ALWAYS disorder. It just is in the way that I will use the term during the course of this debate.
SLOT may be defined accordingly: With any spontaneous reaction or event, entropy will tend to increase.
There are three entropies that affect the human organism. Thermodynamic entropy always deals with heat, and rises in the organism slowly but steadily, until it eventually kills the organism. Thermodynamic entropy affects the individual organism, but not necessarily macroevolution in the population.
Logical entropy is just along for the ride considering the organism. Logical entropy has nothing to do with heat and is just order/disorder. Logical entropy actually decreases as the organism matures through the growth cycle. Because the organism orders and grows. It then begins to increase as the organism ages, dies and decomposes. Logical entropy really has more to do with macroevolution than the individual organism, because SLOT forbids complexity from forming over time via spontaneous reactions as would have had to occur during complex macroevolution.
Finally, it is informational entropy that pumps the silver bullet deep into the heart of complex macroevolution. Genes are code--genetic information. For this process to have happened, the human genome would have had to grow extremely complex, both quantitatively and qualitatively, over a period of millions of years. The genome would have had to increase itself from a unicelled organism with under 500 genes into what we see today, a complex organism called Homo Sapien with between 33,000 and 75,000 genes.
Yet, SLOT through another measurement called informational entropy, tells us that as information is spread, it will degrade, not order. And when our scientists look at the human genome today, they see stark degradation, not complexity. Why is this, and how could complex macroevolution ever occurred in violation of the Second Law of Thermodynamics? The conclusion is that it is impossible for complex macroevolution to have occurred. It would have violated perhaps the most well tested and most universal law of science: the Second Law of Thermodynamics.
Thank you, Pixie. You may now counterpoint and point



--------------------------------------------------------------------------------

The number of gems in there is significant. I proposed a simple test of Jep's assertions:
Take the temperature of an infant and an adult. If the adult's temperature is not significantly higher than the infant's, then Jep's claim is falsified. As I recall, Jep hemmed and hawed and said he meant something else etc...

 

[Jeptha]

JEP: First, Thanks for sticking in there. Had to go out of town and get some business done.

”Doesn't matter. When you are fixing your car, you are using chemical energy and generating heat -- increased entropy.”
JEP: This is irrelevant. I’m going to have to get this thread to understand the distinct difference between the three types of entropy we are discussing. We are not considering heat—thermodynamical entropy—here; but logical entropy—or simple order/disorder. The fact that you may find an example of some heat in the system is irrelevant. What if I DON’T fix my car and just send it to the junkyard??

”Death is, but we are talking about "aging and withering". As long as you live, you are a decrease in entropy compared to death.”

JEP: An organism increases in all three entropies as it ages and dies, other than decreased logical entropy during the maturity cycle. I’m not aware of any scientist that would disagree with this.

Schrodinger’s book “What is Life’ is online if you care to read it. Here’s an excerpt from chapter 8: “Every process, event, happening—call it what you will: in a word, everything that is going on in Nature means an increase in entropy of the part of the world where it is going on. Thus a living organism continually increases its entropy—or as you might say, produces positive entropy—and thus tends to approach the dangerous state of maximum entropy, which is death.”


”And your comment about research on a calorie restricted diet is wrong. The reason it keeps you alive longer is that it produces less reactive oxidant species and slows the formation of oxidation products in the cells. People in my department are engaged in this research so I get updates about once a month on the status of the field.”

JEP: Hmmm…you hit the nail on the head with this one. I will go into more detail in my post to Scott below. Perhaps we can take this argument home.

”Look at the deltaS term in Gibb's free energy. That is change in entropy.”

JEP: It doesn’t matter. You still cannot confuse entropy with energy in the same system. I’ve never said that entropy and energy are not related and one must calculate energy in order to calculate entropy. But they are two very distinct critters.

I figured you were going into the common misconception that the intake of food decreases entropy in an organism. What food does is form free energy to operate a cell. But it does not decrease entropy. They simple are not the same thing.

 

[Jeptha]

¡¨What humans and other animals do is take the chemicals produced by plants -- sugars mostly -- and use that as their source of energy to overcome SLOT in themselves.

They break down the sugars into (eventually) ATP, CO2, H2O, and heat. Now, ATP is a high energy compound that can transfer its energy (do work) to other chemical reactions such as peptide bond formation, nucleotide bond formation, and C-C bond formation in lipids and carbohydrates. That energy in turn makes deltaH bigger than the -TdeltaS term in Gibbs free energy and the reaction proceeds even tho the entropy of the proteins, DNA, lipids, and decreases relative to the component amino acids, nucleotides, sugars, etc. deltaS in the Gibbs free energy equation decreases but the reaction takes place.

Now, the total entropy of the organism and the surroundings does increase. There is all that waste heat released by oxidative phosphorylation and the hydroysis of ATP. That heat is an increase of entropy. But, the system that is the organism decreases in entropy.¡¨

JEP: Well, I was going to save this to address Scott¡¦s silly assertion that I think heat rises in an organism from birth through old age. But you seem to be a biologist (forgive me if I¡¦m wrong, but I converse with a lot of scientists around the Web); and you have a good grasp of cellular respiration, so I¡¦ll go there with you.

Dr. Denham Harman of the University of Nebraska has been called the father of aging by his peers because he has done so much research into rising entropy within the organism that is proving to be true in today¡¦s research.

Dr. Page (SLP) believes I am postulating that it is heat rising in the organism over time. It is not heat rising, it is entropy, which is not always heat--that rises from conception forward.

Here is a good read on this:

¡§As Roth sees it, aging is a reduction in the amount of order in living systems, which require a high degree of order. He says that more energy, in the form of more calories, creates more disorder (which scientists call entropy).¡¨

http://whyfiles.org/057aging/radical2.html

Let¡¦s look at why Roth posits this. There are two paramount reasons, biologically, that the human organism ages and dies. The first has to do with logical entropy within the cell. This logical entropy is similar to the entropy we see in a fire using up its fuel and dying out and coming to perfect equilibrium¡Xmaximum entropy.

On the ends of the chromosomes are little structures called telomeres that govern cellular division. These telomeres serve as biological clocks in that they grow shorter with each cellular division. Once the telomeres are used up (at around 50 divisions) the cell can no longer divide and dies (I¡¦m talking about the normal, healthy human cell. Not cancer cells that have gone nuts). So this would be increasing logical entropy in the form of FULL„³EMPTY. See why Dolly the clone aged very rapidly? The cells they cloned her from would have already depleted some or much of its telomeres.

The other form is a direct result of the food we eat and the manner that it is transformed into ATP/ADP the cell can use in the form of direct energy derived from the breaking of bonds as the phosphates dance back and forth.

In this reaction: C6H12O6 + 6O2 -------------------> 6CO2 + 6H2O + 38 ATP heat is given off at the rate of 7 kcal per mole of ATP produced.

This reaction is exothermic and its coupled reaction within the cell is endothermic. So we are talking about reactions that involve heat and would be quite correct in terming the entropy that results from these reactions: thermodynamical entropy.

But it is not heat rising in the cell that we are seeking to find our entropy in. This excess heat is simply emitted into the atmosphere raising the entropy of planet earth, then the solar system; and finally the universe.

This entropy is aging as a direct result of the above reaction. Many times when this reaction occurs, it goes haywire, emitting highly unstable charged oxygen particles called free radicals that you mention in a previous post.

These molecules will grab other molecules from whatever healthy tissue that is nearby, damaging this healthy tissue resulting in aging. This is why people eat a steady supply of antioxidants in the form of Vitamins C, E, Beta Carotine, etc. to stay younger and healthier longer.

The problem is that antioxidants usually cannot make it to the place where this reaction occurs, the mitochondria of the cell.

Heres a good read on that:

http://www.lef.org/magazine/mag95/95jun3.htm

Note that the article states that when the research was done (50s 60s, I believe) that this was slightly controversial. But today it is not! Some of the latest papers in show that aging is a result of this reaction and begins via damage of mitochondrial DNA. Can you now see why I¡¦ve postulated that the more food we eat, the quicker we will die??

In fact, the Merck Manual defines this destruction of tissue, cellular necrosis, as an entropic phenomenon: ¡§Cell death may occur by necrosis or apoptosis. Necrosis is due to physical or chemical insults (eg, metabolic inhibition, ischemia) that overwhelm normal cellular processes and make the cell nonviable. In necrosis, loss of ion gradients across the cell membrane leads to an influx of calcium and other ions, which triggers proteolysis and rupture of organelle membranes. Necrosis is a purely entropic phenomenon due to loss of the cell's ability to transform external energy.¡¨

http://www.merck.com/pubs/mm_geriatrics/sec1/ch1.htm

¡§Now, for the lurkers, Jeptha is using the "shell game" tactic of constantly shifting claims. He acknowledges that input of energy from the sun will decrease entropy by the chemical reactions in plants. What he then does is try to say that sunlight itself won't decrease entropy in humans. That's correct, but is irrelevant. No one has ever claimed that sunlight directly decreases entropy in humans.¡¨

JEP: Yes they have. Several of them have. Please re-read the posts.

¡§Instead, humans and all other organisms use the chemicals of decreased entropy made from the energy of sunlight to couple the combustion of those chemicals to synthetic processes that decrease entropy in the organisms.¡¨

JEP: No. This is backward. Please see above. Again. I think you are confusing entropy with Gibb¡¦s Free Energy.

¡¨When looking at the total entropy of the solar system, it increases. Looking at the entropy only in living organisms, entropy decreases, but not by enough to be greater than the total entropy increase of the solar system.¡¨

JEP: This is not correct either. If you believe this to be true, then please show me how it happens as I just did you, above.

¡¨IOW, by the processes that Jeptha acknowledges to be true and accurate, Jeptha has shown that macroevolution doesn't violate SLOT.¡¨

JEP: *chuckle* That¡¦s a good one. You¡¦ve got a long row to hoe to get me there. But good luck!

 

[Jeptha]

“I am astonished that you would want to reveal your ignorance on yet another forum.”

JEP: I’m quite proud of my ignorance, Scott. It took years to get here. ;~)

”Actually, jerry Don, what I wrote was in response to YOUR claim. YOU claimed that entropy builds up in an organism over time. It was YOU that equated entropy with heat.”

JEP: Please read my post to Lucaspa and perhaps you’ll understand my argument a bit better. Then again, perhaps you won’t. And again, you do not understand that entropy is not energy. Heat is not entropy, its energy. Yes, heat can be used to figure entropy in heat systems. But it is not itself, entropy. And you teach this stuff at the PhD level??

All you would have to do to understand this is look at Clausius’ most basic formula. DeltaS = deltaQ/T –- S is entropy, Q is heat and T is the absolute temp of the system. See?? Heat and entropy are two different critters. S and Q.

BTW: After debating with you for a time period I’m now counting by years, has it ever occurred to you that we do not have to hate one another just because you are an evo and I am a creo??

 

[Jeptha]

You should read the article you quote. The article starts out saying that each individual has 4 mutations. It then states "On average, about 1.6 of them are bad enough that evolution and natural selection will eventually weed them out. "

1.6 is less than half of 4. Less than 50% doesn't justify a statement of "by and large most mutations are harmful ones".

JEP: You’ve either misunderstood me or the article; or perhaps I haven’t made myself clear. It is harmful mutations they are referring to. About four of them occur per generation, but only 1.6 of these harmful mutations are weeded out by natural selection. The rest accumulate in the genome and will lead to extinction of the human race. In fact, here is a nut (I don’t agree with him) that has calculated the demise of the human race to be 2065. Don’t have any grandkids!

http://www.worthynews.com/evolution-impossible.htm


”Now, the authors are also judging "good" and "bad" on their terms, not the environment's. Other, more rigorous studies have shown that the deleterious mutation rate is about 2.6 per thousand mutations.”

JEP: Sorry. I don’t believe this.

 

[Frumious Bandersnatch]

Jeptha,

What specific step required for macroevolution is prevented by the second law of thermodynamics?

You can't answer this question because no step required for macroevolution violates the second law.  Your claim that complexity in speciation is a step that violates the second law is just nonsense.  How is complexity in speciation a step? What is "complexity in speciation"? Why should anyone think that some nonsense term you made up indicates a violation of the second law. Either speciation can occur or it can't.  Speciation has been shown to occur so your claim is false.

All your ramblings about entropy , complexity,  energy and aging are just meaningless attempts to distract attention from the fact that you can't actually show that evolution violates the second law of thermodynamics.

The Frumious Bandersnatch

 

[lucaspa]

Yesterday at 04:54 PM Jeptha said this in Post #151

Dr. Denham Harman of the University of Nebraska has been called the father of aging by his peers because he has done so much research into rising entropy within the organism that is proving to be true in today¡¦s research.

I did a PubMed search on Harman. He advocates the free radical theory of aging that I discussed in a previous post.  He never mentions thermodynamics in his 31 papers available on PubMed.  (BTW, others in aging research have far more papers, your attempt to get Harman to be the "father of aging" is an appeal to authority, an invalid form of argument.)

This quote from his 1998 PNAS paper is typical: "Accumulating evidence now indicates that the sum of the deleterious free radical reactions going on continuously throughout the cells and tissues constitutes the aging process or is a major contributor to it."

Not thermodynamics, but free radicals.

Dr. Page (SLP) believes I am postulating that it is heat rising in the organism over time. It is not heat rising, it is entropy, which is not always heat--that rises from conception forward.

Here is a good read on this:

¡§As Roth sees it, aging is a reduction in the amount of order in living systems, which require a high degree of order. He says that more energy, in the form of more calories, creates more disorder (which scientists call entropy).¡¨

http://whyfiles.org/057aging/radical2.html

LOL! The article is on free-radicals and aging.  From the paragraph above your quote:
"It's not clear why reducing caloric intake should reduce the amount of free radicals produced in cells, although there are some candidate explanations. But George Roth, who heads the National Institutes of Aging study on calorically restricted monkeys, suspects that free radicals are part of the more general story of aging."

Roth is advocating a different theory. Now, looking at Roth's publications on PubMed I find 194 references to Roth and aging. But when I search Roth and aging and thermodynamics I get only 3 papers.  It would appear that, in 1993, Roth proposed that free radicals were not the cause of aging, but the result.  However, that theory has since been falsified. 

Let¡¦s look at why Roth posits this.

Unless you have the articles from Ageing (Milano), there is no information why Roth posits this.

There are two paramount reasons, biologically, that the human organism ages and dies. The first has to do with logical entropy within the cell. This logical entropy is similar to the entropy we see in a fire using up its fuel and dying out and coming to perfect equilibrium¡Xmaximum entropy.

On the ends of the chromosomes are little structures called telomeres that govern cellular division.

This is not part of thermodynamics, but the result of an inadequate amount of telomerase.  BTW, this is not part of the"entropy" theory, but a separate theory of aging first proposed by Leonard Hayflick in the 1960s.  It means that cells have a finite number of divisions.  It was thought, for a while, that telomerase controlled this.  There are 2 problems here:
1.  Stem cells have adequate telomerase and have unlimited cell divisions.
2. In many cell types, telomere length is not related to the number of cell divisions remaining.

These telomeres serve as biological clocks in that they grow shorter with each cellular division. Once the telomeres are used up (at around 50 divisions) the cell can no longer divide and dies (I¡¦m talking about the normal, healthy human cell. Not cancer cells that have gone nuts). So this would be increasing logical entropy in the form of FULL„³EMPTY. See why Dolly the clone aged very rapidly? The cells they cloned her from would have already depleted some or much of its telomeres.

There is so much wrong with this paragraph, Jeptha, that it's hard to know where to start. First, the premise that Dolly aged very rapidly is not supported by the data.  Normal sheep lifetimes are not known and Dolly didn't show abnormal degeneration at her death compared to other sheep housed in similar conditions. Also, if it was a stem cell that provided the nucleus, we have no idea what the telomere length was. Finally, the telomerase induced during development would have restored the telomeres anyway.

There is no logical connection between telomeres and entropy. 

The other form is a direct result of the food we eat and the manner that it is transformed into ATP/ADP the cell can use in the form of direct energy derived from the breaking of bonds as the phosphates dance back and forth.

But it is not heat rising in the cell that we are seeking to find our entropy in. This excess heat is simply emitted into the atmosphere raising the entropy of planet earth, then the solar system; and finally the universe.

This entropy is aging as a direct result of the above reaction. Many times when this reaction occurs, it goes haywire, emitting highly unstable charged oxygen particles called free radicals that you mention in a previous post.

Now you are getting into the free radical theory of aging. Why you don't call it by its proper name is confusing. Probably because you are trying to disguise that it is not a theory about entropy but one you are trying to misuse to make it about entropy.

The problem is that antioxidants usually cannot make it to the place where this reaction occurs, the mitochondria of the cell.

The damage from free radicals doesn't occur in the mitochondria anyway, so this is irrelevant.

Heres a good read on that:

http://www.lef.org/magazine/mag95/95jun3.htm

This is the title of the article: "Are Mutations In Mitochondrial DNA A Cause Of Aging In Humans?"

It was a theory popular 8 years ago.  What it states is that free radical reactions in the mitochondria inhibit the ability of the mitochondria to perform ox-phos.  Less energy available to the cell to do work.

Somewhere in all this, Jeptha, you seem to have lost your point.  Life itself is a local decrease in entropy.  The most that you are showing is that the ability to maintain this decrease in entropy declines during aging.  Cumulative damage to cells from free radicals eventually stops the chemical reactions needed to transform energy from food to energy available for work in the cells.  Thus, the cells can't maintain the homeostasis away from equilibrium (decreased entropy relative to surroundings) and die. At that time, of course, the entropy of the cells increases to that of the surroundings.

I can see here no violation of SLOT but rather the normal workings of SLOT.

Note that the article states that when the research was done (50s 60s, I believe) that this was slightly controversial. But today it is not! Some of the latest papers in show that aging is a result of this reaction and begins via damage of mitochondrial DNA. Can you now see why I¡¦ve postulated that the more food we eat, the quicker we will die??

No, because excess food goes into storage as either glycogen or fat and isn't converted in the mitochondria.  Ox-phos is regulated by negative feedback mechanisms to control the amount of ox-phos to produce the amount of ATP necessary.  If your hypothesis were correct, athletes using a lot of ox-phos, eating a lot would age faster than the a couch potato who is not eating.  I don't know of any study that does that but, in general, exercise retards aging.

In fact, the Merck Manual defines this destruction of tissue, cellular necrosis, as an entropic phenomenon:

Necrosis is different from what you are talking about.  You are talking about a diminution of activity in a live cell.  The Merk Manual is talking about a cell that actually dies.  As my discussion above shows, of course when a cell dies there is an increase in entropy.  Duh!


[lucaspa] Now, for the lurkers, Jeptha is using the "shell game" tactic of constantly shifting claims. He acknowledges that input of energy from the sun will decrease entropy by the chemical reactions in plants. What he then does is try to say that sunlight itself won't decrease entropy in humans. That's correct, but is irrelevant. No one has ever claimed that sunlight directly decreases entropy in humans.¡¨

JEP: Yes they have. Several of them have. Please re-read the posts.

No, they didn't. Instead, the claim has been that sunlight contributes energy to the planet, providing energy so that local systems -- life -- can decrease entropy.

Instead, humans and all other organisms use the chemicals of decreased entropy made from the energy of sunlight to couple the combustion of those chemicals to synthetic processes that decrease entropy in the organisms.¡¨

JEP: No. This is backward. Please see above. Again. I think you are confusing entropy with Gibb¡¦s Free Energy.

Your above has nothing to do with this.  Living cells are far away from homeostasis.  Breaking down sugar to CO2, H2O, ATP and waste energy harnesses some of the energy in ATP to do work.  A side effect of the reaction is the production of some free radicals of oxygen.

¨When looking at the total entropy of the solar system, it increases. Looking at the entropy only in living organisms, entropy decreases, but not by enough to be greater than the total entropy increase of the solar system.¡¨

JEP: This is not correct either. If you believe this to be true, then please show me how it happens as I just did you, above.

Jep, I did, but you didn't pay attention. Go back and look.  You haven't demonstrated increased entropy, just a decreased capacity to decrease entropy.  Do you understand the difference?

¨IOW, by the processes that Jeptha acknowledges to be true and accurate, Jeptha has shown that macroevolution doesn't violate SLOT.¡¨

You¡¦ve got a long row to hoe to get me there.

You've not even attempted to show that free radical production in mitochondria inhibits macroevolution.  You haven't even attempted to show a connection. 

 

[lucaspa]

Yesterday at 05:24 PM Jeptha said this in Post #153

You should read the article you quote. The article starts out saying that each individual has 4 mutations. It then states "On average, about 1.6 of them are bad enough that evolution and natural selection will eventually weed them out. "

1.6 is less than half of 4. Less than 50% doesn't justify a statement of "by and large most mutations are harmful ones".

JEP: You’ve either misunderstood me or the article; or perhaps I haven’t made myself clear. It is harmful mutations they are referring to. About four of them occur per generation,

Sorry, Jep, but the 4 mutations are total mutations. Not harmful ones. Go look at the article again.

but only 1.6 of these harmful mutations are weeded out by natural selection.

I see where you got confused. When they said "are bad enough that natural selection will weed them out" you assumed that the rest were also bad, but not that bad.

It was poor phraseology on their part.  The other mutations aren't necessarily "bad". 

The rest accumulate in the genome and will lead to extinction of the human race.

Only because we are no longer subject to natural selection. We are using our technology to prevent natural selection from working.

Thus, humans, because of their technology, are now a special species.  If the situation continues and there is a crash, civilization would fall due to the 90% dieoff and loss of necessary skills to maintain a technological civilization. But the species would survive because enough individuals would be around with healthy enough genomes to keep the population going while purifying selection again did its work.

”Now, the authors are also judging "good" and "bad" on their terms, not the environment's. Other, more rigorous studies have shown that the deleterious mutation rate is about 2.6 per thousand mutations.”

JEP: Sorry. I don’t believe this.

Too bad for you.  You don't get to choose whether you "believe" the data or not.

PD Keightley and A Caballero, Genomic mutation rates for lifetime reproductive output and lifespan in Caenorhabditis elegans.  Proc. Natl. Acad. Sci. USA 94: 3823-3827, 1997

This study documents the rate of deleterious mutations in the worm C. elegans.  Because they are hermaphroditic, the authors were able to separate the worms and run parallel populations descended from a single individual.  By maintaining independent sublines, the effect of selection could be minimized, and thus the deleterious mutations could be kept in the population.  Lethal mutations are still lethal, but the experimental design allows accumulation of deleterious mutations (as well as neutral mutations) and then the effect on lifespan and production of viable offspring, both of which are measurements of fitness.  The estimated deleterious mutation rate per haploid genome (the whole organism) was 0.0026, or 2.6 per thousand.  This is about 100 fold *less* than previously found for Drosophila.  All in all, deleterious mutation rates are very low, considering that total mutations are about 1 per genome (individual).

 

[lucaspa]

Today at 12:30 PM Frumious Bandersnatch said this in Post #154 

Either speciation can occur or it can't.  Speciation has been shown to occur so your claim is false.

All your ramblings about entropy , complexity,  energy and aging are just meaningless attempts to distract attention from the fact that you can't actually show that evolution violates the second law of thermodynamics.

The Frumious Bandersnatch

Good point.  I spent a lot of time trying to show people just how the shell game is working.  But yes, if you can't dazzle them with brilliance, try to blind them with bull feces.  And that is Jeptha's tactic.  Throw in some falsified hypotheses, a little argument from authority, and a lot of misinformation and voila! distraction!

 

[Jeptha]

“I did a PubMed search on Harman. He advocates the free radical theory of aging that I discussed in a previous post. He never mentions thermodynamics in his 31 papers available on PubMed.”

JEP: This doesn’t mean anything. Others, including some sites I have previously posted in this thread certainly equate the two. Maybe Harmon was not as savvy as some of his peers in the subject of thermo. Here: educate yourself on the thermodynamics of aging. It’s a long paper, but please at least read the abstract: “The findings of macrothermodynamics (supramolecular thermodynamics) of quasi-closed systems and the published data on the variation of the chemical composition of living organisms in ontogeny confirm the thermodynamic tendency of aging processes.”

http://www.endeav.org/evolut/text/ta1/

“(BTW, others in aging research have far more papers, your attempt to get Harman to be the "father of aging" is an appeal to authority, an invalid form of argument.)”

JEP: What does this have to do with the price of eggs in China as well?? I’m not appealing to authority. Harmon is a very old man and he was one of the first to research this. This is why some (not only me, I picked it up from others) call him the ‘father of aging.’ In fact, I believe he WAS the first: “Dr. Denham Harman, M.D., Ph.D., first proposed a theory of aging as the indiscriminate chemical reactivity of free radicals possibly leading to random biological damage. His idea has met with much experimental success, and is now considered a major theory of aging.”

http://pspinformation.com/nutrition/antioxidants/harman.shtml

”Not thermodynamics, but free radicals.”

JEP: I’m trying to ascertain where you are coming from. Did I not make it clear to you in previous posts that aging via destruction of organelles is disorder and an increase in entropy?? Even such mainstream publications such as the Merck Manual attribute cellular necrosis to increased entropy. Or is it that you are not aware that entropy is a measurement of the second law of thermodynamics?

“LOL! The article is on free-radicals and aging.”

JEP: Er…….Right. That was what we were talking about. Remember??

"It's not clear why reducing caloric intake should reduce the amount of free radicals produced in cells, although there are some candidate explanations. But George Roth, who heads the National Institutes of Aging study on calorically restricted monkeys, suspects that free radicals are part of the more general story of aging."

JEP: But it’s clear now that I walked you through the formula for ATP production, isn’t it? It must be as I see you aren’t going to refute it. Of course, if you don’t understand it, please tell me. I can go slower. BTW Lucaspa; haven’t we met before around the net? Are you the MD I think you are? Just curious.

“Unless you have the articles from Ageing (Milano), there is no information why Roth posits this.”

JEP: He posits this because he obviously understands what you did not until I walked you through it. Very simple. That was my point.

“This is not part of thermodynamics, but the result of an inadequate amount of telomerase.”

JEP: Not at all true. This happens to everyone and is a normal part of aging. See below.

“BTW, this is not part of the"entropy" theory, but a separate theory of aging first proposed by Leonard Hayflick in the 1960s. It means that cells have a finite number of divisions. It was thought, for a while, that telomerase controlled this. There are 2 problems here:
1. Stem cells have adequate telomerase and have unlimited cell divisions.
2. In many cell types, telomere length is not related to the number of cell divisions remaining.”

JEP: Really? Tell me. What is this entropy theory? I didn’t know there was one since entropy is just a measure of SLOT. Even the over simplistic publication called the Merck Manual disagrees with you on telomeres: “One biologic mechanism for Hayflick's limit is now understood. Telomeres are stretches of DNA at the end of chromosomes that serve as handles by which chromosomes are moved during the telophase of meiosis. Telomeres are irreversibly shortened each time a cell divides. When the telomeres become too short, the cell can no longer divide.”

http://www.merck.com/pubs/mm_geriatrics/sec1/ch1.htm

JEP: The addition of telemorase can inhibit this shortening but it is not the lack of it that causes it. This is a natural phenomenon of the aging process that happens to everyone. But you are correct in that stem cells are packed with this enzyme and are immune to this type of entropy. So are cancer cells, BTW.


“First, the premise that Dolly aged very rapidly is not supported by the data.”

Jep: Really? You better tell all the newspapers this because this was headline news for about a month: “LONDON, Feb. 14 — Dolly the cloned sheep was put to death Friday, after premature aging and disease marred her short existence and raised questions about the practicality of copying life.”

http://www.msnbc.com/news/872966.asp

And then we have: “Scientists also are watching the development of cloned animals with interest. If an older animal is cloned, will the clone have cells of a similar age and so age more quickly overall? Dolly the sheep seemed to confirm this theory when it was discovered that her telomeres were shorter than normal.”

http://www.dnafiles.org/about/pgm13/topic2c.html

“Normal sheep lifetimes are not known”

JEP: *chuckle* That’s a good one. I used to raise lambs in Colorado. Boy wouldn’t I be an incompetent shepherd if I didn’t even know how long sheep were supposed to live. Sheep live a natural life from 11 to 16 years at the max. But the average life of sheep is 12 years:

“SHEEP
Natural lifespan: 12 years.”

http://www.fortunecity.com/greenfield/shell/5/short.htm

JEP: And isn’t this interesting that Dolly was cloned from a six year old sheep and lived 6.5 years before they had to put her to sleep:
“That depends on whether you mean her birth age - six-and-a-half years - or her genetic age - twelve-and-a-half years. Dolly was born in 1997, but all the cells in her body originate from genetic material extracted from the udder of a six-year-old sheep.”

http://www.newscientist.com/hottopics/cloning/cloning_lifespanfaq.jsp

JEP: I’ll give you a friendly warning like I did the physicist. If you keep calling me on this stuff and quoting pseudo-science to support it, the dum kreationist is going to make the medical doctor look really silly. No disrespect intended, just being fair to you.

”There is no logical connection between telomeres and entropy.”

JEP: Sure there is. Full to empty is a classic example of logical entropy just as concentrated to diffused is.

”Now you are getting into the free radical theory of aging. Why you don't call it by its proper name is confusing.”

JEP: We can call it whatever you want to call it. Doesn’t bother me.


”The damage from free radicals doesn't occur in the mitochondria anyway, so this is irrelevant.”

JEP: Sheeze….Where do you get your material. You have me rolling. The mitochondria is the ONLY place in the cell where this reaction occurs: “Dr. Harman feels that getting antioxidants into mitochondria is critical because of the vast number of free radical reactions produced in these organelles, which literally explode with the kind of dynamic chain-crackling chemical activity that Harman believes is a major cause of aging.”

http://www.lef.org/magazine/mag95/95jun3.htm

”Somewhere in all this, Jeptha, you seem to have lost your point. Life itself is a local decrease in entropy.”

JEP: Please show me this mathematically using a standard formula of thermo how this is true. I just don't believe it.

“No, because excess food goes into storage as either glycogen or fat and isn't converted in the mitochondria. Ox-phos is regulated by negative feedback mechanisms to control the amount of ox-phos to produce the amount of ATP necessary. If your hypothesis were correct, athletes using a lot of ox-phos, eating a lot would age faster than the a couch potato who is not eating. I don't know of any study that does that but, in general, exercise retards aging.”
J
EP: This is true that energy is sometimes stored as fatty acids outside the mitochondria in Kreb’s cycle. In fact, I believe this is another form of rising entropy in that fatty acids kill people, clog arteries and cause all kinds of nasty diseases. I used to argue this as a form of increasing entropy. But I’ve since discovered that the research is not in to show whether these fatty acids are converted back into ATP or not. No one seems to know. We know they are used up in emergency situations, but to my knowledge no one has researched how they are used in everyday life.

”No, they didn't. Instead, the claim has been that sunlight contributes energy to the planet, providing energy so that local systems -- life -- can decrease entropy.”

JEP: You keep saying this. OK. I’ll bite. How does life decrease the entropy of the universe??

”Jep, I did, but you didn't pay attention. Go back and look. You haven't demonstrated increased entropy, just a decreased capacity to decrease entropy. Do you understand the difference?”

JEP: Why would I need to demonstrate this? Are you aware of any physicists that actively rail against the fact that the entropy of the universe is steadily increasing? Most posit that this is such stark reality that the universe will die a heat death and someday be so disorganized as to be nothing but a floating sea of random particles.

”You've not even attempted to show that free radical production in mitochondria inhibits macroevolution. You haven't even attempted to show a connection.”

JEP: That’s easy. There is no connection. We somehow got off on thermodynamical entropy in the human organism. This has only to do with the aging and death of an organism. But you challenged me on it, so here we are. These posits I’m making in this area are actually nothing new. Schrodinger made many of them in the forties and actually calculated this rising entropy in the human body using a re-hash of Ludwig Boltzmann’s old formula: -entropy = k log 1/D where k is Boltzmann’s contant dealing with heat and energy and D is the atomistic arrangement of the cell. Cool.

 

[lucaspa]

Yesterday at 10:28 PM Jeptha said this in Post #158

http://www.endeav.org/evolut/text/ta1/

I've read the paper.  Interesting, but nowhere in the paper does the author discuss delta S, or entropy.  All the discussions are on delta G, or free energy.  Therefore the statement in the abstract is not supported by the data in the paper itself.

Also, I'm surprised you are using this paper, since this paragraph directly contradicts your major thesis -- that macroevolution is contrary to thermodynamics.

"Let us stress once more that the principle of stability of chemical substances is a thermodynamic principle. It correlates with the principle of structural stabilization (Gladyshev, 1997) and states that the trend of a biological system in evolution (ontogeny and phytogeny) to the appearance of relatively more stable structures of higher hierarchies leads to the selection of relatively less stable structures of lower hierarchies. This evolutionary trend of biological systems seems to rejuvenate the lower hierarchic structures (preserves the optimal stability of these structures) and causes a practically unlimited development of the biological world."

In trying to "win" the small point, you have posted a paper that contradicts your main point.  Thank you for showing that macroevolution is not contrary to thermodynamics. 

"His idea has met with much experimental success, and is now considered a major theory of aging.”

And this contradicts your assertion that Harman doesn't understand thermodynamics and that his theory is about thermodynamics.

JEP: I’m trying to ascertain where you are coming from. Did I not make it clear to you in previous posts that aging via destruction of organelles is disorder and an increase in entropy?? Even such mainstream publications such as the Merck Manual attribute cellular necrosis to increased entropy.

First, increased entropy is a result of necrosis.  Perhaps the word "necrosis" confused you, but Merck is saying the same thing I am: when cells die there is an increase in entropy.  Necrosis is cell death. Prior to that point the cell is at lower entropy than the surroundings.  If it weren't, it wouldn't be alive.

JEP: Er…….Right. That was what we were talking about. Remember??

The discussion is whether the free radical theory is an increase in entropy of the organism.  It isn't.  It's about cellular damage caused by the production of free radicals during ox-phos.  The cell itself is still an area of lower entropy compared to the surroundings.  It is a local reduction in entropy. 

"It's not clear why reducing caloric intake should reduce the amount of free radicals produced in cells, although there are some candidate explanations. But George Roth, who heads the National Institutes of Aging study on calorically restricted monkeys, suspects that free radicals are part of the more general story of aging."

JEP: But it’s clear now that I walked you through the formula for ATP production, isn’t it?

I walked you through the production of ATP, remember?  Production of ATP means providing high energy bonds that can do work inside the cell -- reducing entropy in the process by taking more disordely small molecules and making macromolecules of reduced disorder.

Free radicals are a side effect of that reaction when electrons are transferred to oxygen but not to make H2O, instead O3 or H2O2. 


“This is not part of thermodynamics, but the result of an inadequate amount of telomerase.”

JEP: Not at all true. This happens to everyone and is a normal part of aging. See below.

“BTW, this is not part of the"entropy" theory, but a separate theory of aging first proposed by Leonard Hayflick in the 1960s. It means that cells have a finite number of divisions. It was thought, for a while, that telomerase controlled this. There are 2 problems here:
1. Stem cells have adequate telomerase and have unlimited cell divisions.
2. In many cell types, telomere length is not related to the number of cell divisions remaining.”

JEP: Really? Tell me. What is this entropy theory? I didn’t know there was one since entropy is just a measure of SLOT.

The "entropy theory" is the one you and Roth are proposing. Don't you remember your own position?  Here, let me refresh your memory from this post:
"Did I not make it clear to you in previous posts that aging via destruction of organelles is disorder and an increase in entropy?? "

The shortening of telomeres of DNA is not "destruction of organelles" and therefore not part of your theory. 

“One biologic mechanism for Hayflick's limit is now understood. Telomeres are stretches of DNA at the end of chromosomes that serve as handles by which chromosomes are moved during the telophase of meiosis. Telomeres are irreversibly shortened each time a cell divides. When the telomeres become too short, the cell can no longer divide.”

Again, this is not irreversibly shortened.  In the presence of the enzyme telomerase, the telomere length is maintained.  If you are going to be a self-proclaimed "semi-literate creationist", then you have to start reading all the data and not just that which agrees with your position.  Some papers you want to see are:
1:  Allsopp RC, Morin GB, DePinho R, Harley CB, Weissman IL.
Telomerase is required to slow telomere shortening and extend replicative
lifespan of HSC during serial transplantation.
Blood. 2003 Mar 27 [epub ahead of print]
PMID: 12663456 [PubMed - as supplied by publisher]

2:  Cherif H, Tarry JL, Ozanne SE, Hales CN.
Ageing and telomeres: a study into organ- and gender-specific telomere
shortening.
Nucleic Acids Res. 2003 Mar 1;31(5):1576-83.
PMID: 12595567 [PubMed - indexed for MEDLINE]

3:  Ramirez RD, Herbert BS, Vaughan MB, Zou Y, Gandia K, Morales CP, Wright WE,
Shay JW.
Bypass of telomere-dependent replicative senescence (M1) upon overexpression of
Cdk4 in normal human epithelial cells.
Oncogene. 2003 Jan 23;22(3):433-44.
PMID: 12545164 [PubMed - indexed for MEDLINE]

4:  Allsopp RC, Cheshier S, Weissman IL.
Telomerase activation and rejuvenation of telomere length in stimulated T cells
derived from serially transplanted hematopoietic stem cells.
J Exp Med. 2002 Dec 2;196(11):1427-33.


And these are only the recent ones.  From the abstract to the last paper:
"We now show that stimulation of T cells derived from serially transplanted HSC results in a telomerase-dependent elongation of telomere length to a size similar to that observed in T cells isolated directly from young mice.  ... Together, these results imply that one role for telomerase in T cells may be to renew or extend replicative potential via the rejuvenation of telomere length."

So, as much as you rely on the Merck Index, sometimes it is wrong.  This paper shows that telomere length is reversible.


JEP: The addition of telemorase can inhibit this shortening but it is not the lack of it that causes it.

Yes and no.  Telomeres are shortened because the DNA polymerases don't go to the end of the DNA strand. However, it is the job of telomerase to restore the telomere length to the DNA.  Only in cells lacking telomerase is the shortening seen.

“First, the premise that Dolly aged very rapidly is not supported by the data.”

Jep: Really? You better tell all the newspapers this because this was headline news for about a month: “LONDON, Feb. 14 — Dolly the cloned sheep was put to death Friday, after premature aging and disease marred her short existence and raised questions about the practicality of copying life.”

http://www.msnbc.com/news/872966.asp

It was in the scientific literature.  What you have demonstrated is that the papers got it wrong.  Not unknown in journalism, especially journalism on science.
"However, Ian Wilmut, who pioneered the research, said the early indications were that Dolly, cloned from a breast cell and named after the singer Dolly Parton, had contracted the disease from other animals in a shared pen.

"There is always a greater risk if you have animals inside that infections will spread, so we had been concerned about this," Professor Wilmut said."  http://www.theage.com.au/articles/2003/02/17/1045330539301.html

“Normal sheep lifetimes are not known”

JEP: *chuckle* That’s a good one. I used to raise lambs in Colorado. Boy wouldn’t I be an incompetent shepherd if I didn’t even know how long sheep were supposed to live. Sheep live a natural life from 11 to 16 years at the max.

You got this from the web.  My apologies for not including the phrase "in these living conditions", but lifetimes of sheep in pens is shorter, as the incidence of arthritis is higher because they are walking on concrete floors.

JEP: And isn’t this interesting that Dolly was cloned from a six year old sheep and lived 6.5 years before they had to put her to sleep:

Irrelevant, since she did not die of old age, but a lung infection.

JEP: I’ll give you a friendly warning like I did the physicist. If you keep calling me on this stuff and quoting pseudo-science to support it, the dum kreationist is going to make the medical doctor look really silly. No disrespect intended, just being fair to you.

  I'm not worried. 

”There is no logical connection between telomeres and entropy.”

JEP: Sure there is. Full to empty is a classic example of logical entropy just as concentrated to diffused is.

You haven't shown that shorter telomeres have less entropy than long ones.  Where are your calculations?

”The damage from free radicals doesn't occur in the mitochondria anyway, so this is irrelevant.”

JEP: Sheeze….Where do you get your material.

From the scientific literature.  Some of the damage does occur there, but a lot of it occurs to cell membranes since free radicals react with the double bonds of lipids there.

The mitochondria is the ONLY place in the cell where this reaction occurs:

ROFL!  You would have done better to state that mitochondria are one place where free radicals react.  Remember, part of the damage caused by free radicals is supposed to be to nuclear DNA. 

 “Dr. Harman feels that getting antioxidants into mitochondria is critical because of the vast number of free radical reactions produced in these organelles, which literally explode with the kind of dynamic chain-crackling chemical activity that Harman believes is a major cause of aging.”

As I said, one place. But you claimed "ONLY place". 

”Somewhere in all this, Jeptha, you seem to have lost your point. Life itself is a local decrease in entropy.”

Continued in next post.

 

[lucaspa]

Yesterday at 10:28 PM Jeptha said this in Post #158

JEP: Please show me this mathematically using a standard formula of thermo how this is true. I just don't believe it. Why not?  Is not DNA more ordered than individual nucleotides? Are not proteins more ordered than individual nucleic acids?  Isn't a cell more ordered than a pool of the same chemicals?

But, for calculations, see http://www.dkfz-heidelberg.de/tbi/people/koenig/documents/329.pdf
http://stingray.bio.cmu.edu/~web/bc/Lec/Lec08/lec08.PDF
http://class.fst.ohio-state.edu/FST822/lectures/Fold.htm


Now, the equation to calculate entropy is going to be Tdeta S = deltaH - deltaG

Therefore: deltaS = (deltaH - deltaG)/T

JEP: This is true that energy is sometimes stored as fatty acids outside the mitochondria in Kreb’s cycle. In fact, I believe this is another form of rising entropy in that fatty acids kill people, clog arteries and cause all kinds of nasty diseases. I used to argue this as a form of increasing entropy. But I’ve since discovered that the research is not in to show whether these fatty acids are converted back into ATP or not. No one seems to know.

Sometimes they are, sometimes they aren't. Depends on what food intake is.  If a person diets, then the fatty acids are metabolized for energy. 

We know they are used up in emergency situations, but to my knowledge no one has researched how they are used in everyday life.

See any biochemistry textbook.

Now, I did some PubMed research and found that it is not the caloric restriction that retards aging, but the reduction of methionine and cystine in the diet.  Diets with high calories but little methionine and cystine  increase lifespan just like low caloric diets.  The reason is still somewhat unknown but it seems that low methionine and cystine diets increase the levels of glutathione in organs. Glutathione is the major antioxidant in the body.  That data falsifies your hypothesis about caloric intake, entropy, and aging. 

1:  Zimmerman JA, Malloy V, Krajcik R, Orentreich N. Nutritional control of aging.Exp Gerontol. 2003 Jan;38(1-2):47-52.PMID: 12543260 [PubMed - in process]
2:  Knight JA. The biochemistry of aging.Adv Clin Chem. 2000;35:1-62. Review.PMID: 11040957 [PubMed - indexed for MEDLINE]
3:  Lass A, Sohal BH, Weindruch R, Forster MJ, Sohal RS. Caloric restriction prevents age-associated accrual of oxidative damage tomouse skeletal muscle mitochondria.Free Radic Biol Med. 1998 Dec;25(9):1089-97.PMID: 9870563 [PubMed - indexed for MEDLINE]
4:  Sohal RS, Ku HH, Agarwal S, Forster MJ, Lal H. Oxidative damage, mitochondrial oxidant generation and antioxidant defensesduring aging and in response to food restriction in the mouse.Mech Ageing Dev. 1994 May;74(1-2):121-33.PMID: 7934203 [PubMed - indexed for MEDLINE]
5:  Cadenas S, Rojas C, Perez-Campo R, Lopez-Torres M, Barja G. Caloric and carbohydrate restriction in the kidney: effects on free radicalmetabolism.Exp Gerontol. 1994 Jan-Feb;29(1):77-88.


”No, they didn't. Instead, the claim has been that sunlight contributes energy to the planet, providing energy so that local systems -- life -- can decrease entropy.”

JEP: You keep saying this. OK. I’ll bite. How does life decrease the entropy of the universe??

Nice try, but I didn't say that, did I?  The general increase in entropy in the universe can "fuel" the local decrease in entropy in life.  Please try to read what is written.

”Jep, I did, but you didn't pay attention. Go back and look. You haven't demonstrated increased entropy, just a decreased capacity to decrease entropy. Do you understand the difference?”

JEP: Why would I need to demonstrate this?

That is what you demonstrated.  What you think you "need" to demonstrate is irrelevant. What the research into aging shows is that the accumulation of free radical damage in the mitochondria interfere with the ability of the mitochondria to conduct ox-phos and produce ATP. Eventually, the theory is that the mitochondria doesn't produce enough energy to sustain the anabolic processes of the cell.

Are you aware of any physicists that actively rail against the fact that the entropy of the universe is steadily increasing? Most posit that this is such stark reality that the universe will die a heat death and someday be so disorganized as to be nothing but a floating sea of random particles.

And I'm not disagreeing with them.  So how do you think this has any relation to what I said?

”You've not even attempted to show that free radical production in mitochondria inhibits macroevolution. You haven't even attempted to show a connection.”

JEP: That’s easy. There is no connection. We somehow got off on thermodynamical entropy in the human organism. This has only to do with the aging and death of an organism. But you challenged me on it, so here we are. These posits I’m making in this area are actually nothing new.

Your formulation of them is very new. So are the implications you are drawing.