96 replies to this topic

[Johan]

The following might only apply to DNA mutations, and please correct me if I'm wrong, but if these 'misrepairs' don't lead to cancer (I'm sure some of them do, though), then they might not occur frequently enough to have a meaningful impact on aging. I mean, every cell probably has at least one 'faulty' gene due to misrepair, but for this to affect aging, it would have to affect a functionally important part of a gene that's actually used in a given cell (not all genes are) or another important component of a cell, and the same gene or component has to be damaged in almost every cell in that tissue, or at least the majority of cells, and that's not very likely, given the relatively low frequency of mutation compared to the number of genes and nucleotides in a given cell as well as the vast number of cells in any given tissue. The obvious exception to this would be cancer, though, since it only takes one cancerous cell to start a tumor. I think Aubrey writes a bit about this in the cancer/WILT chapter of Ending Aging.

Edited by Johan, 08 April 2009 - 10:47 PM.

[mpe]

If ageing is not at least partially programed whydo all men & women (with very few exceptions) age at nearly the same rate? Surely we cant all be exposed to the exact same damage at the same point in all our lives. If ageing were merely the result of damage wouldnt there be some 70 year olds with the bodies of 25 year olds?

[maestro949]

The following might only apply to DNA mutations, and please correct me if I'm wrong, but if these 'misrepairs' don't lead to cancer (I'm sure some of them do, though), then they might not occur frequently enough to have a meaningful impact on aging. I mean, every cell probably has at least one 'faulty' gene due to misrepair, but for this to affect aging, it would have to affect a functionally important part of a gene that's actually used in a given cell (not all genes are) or another important component of a cell, and the same gene or component has to be damaged in almost every cell in that tissue, or at least the majority of cells, and that's not very likely, given the relatively low frequency of mutation compared to the number of genes and nucleotides in a given cell as well as the vast number of cells in any given tissue. The obvious exception to this would be cancer, though, since it only takes one cancerous cell to start a tumor. I think Aubrey writes a bit about this in the cancer/WILT chapter of Ending Aging.

In regards to cancer, DNA mutations are indeed a red herring. Epigenetic drift is the real concern and may account for up to 90% of cancers. It may also account for much of the dysregulation that leads to the aging phenotype as well. There is still a decade's worth of research needed here but it may turn out to be the "programming" that is the easiest to hack in order to affect the rate of aging, faulty gene expression and/or reenable innate damage repair mechanisms.

[maestro949]

If ageing is not at least partially programed whydo all men & women (with very few exceptions) age at nearly the same rate? Surely we cant all be exposed to the exact same damage at the same point in all our lives. If ageing were merely the result of damage wouldnt there be some 70 year olds with the bodies of 25 year olds?

Complex machinery (computer equipment, etc) also has a similar failure rate but it's not because the engineers that designed them programmed in self destruct mechanisms. It's because any complex and iterative process is fighting the laws of thermodynamics and it's mean time between failure is dictated by the engineering effort put into accounting for potential failures. The same principles apply to us biological machines.

Evolution designs us to live long enough to reproduce + some statistically safe amount of time for a given environment. Poor designs (lack of adaptation) and changes in environment cause species to go extinct. We've managed to remove ourselves from our natural environment and are now finding the upper limits to our evolutionary designs as well as the weakest links in our genetic blueprints. This is why the human species is fitting nicely to a specific mortality curve and dying of fairly similar causes (cancer, heart disease, etc).

[VidX]

Yes. And reliabilty theory of ageing (http://en.wikipedia....g_and_longevity) makes a lot of sense. It's actually not just mechanisms (physical) but virtual "thing" like an OS of PC "acts" the same. 

 I'm very experienced user of PC (could call myself an IT specialist, but that's not my regular job, more of a hobby) and I noticed such a thing - no matter how "perfect" antivirus programs and "Registry repair" soft you'll install, the whole system will start to slow down after some time . I mean - I was using my PC without an antivirus for a long time and my experience has let me to avoid any dangerous viruses/infections, though system failed after reasonable time (non dangerous malware and similar stuff clogged it afterall), then I started using antiviruses, firewalls, other diagnostic tools, OS usually worked for a longer time, but still failed as I didn't refresh all the tools, actually I could have been able to resume it's work or even to wind up it to the former state, but reinstall allways seems a faster/easier option. 

 So human body coulb be similar - it's "arranged" from different parts of soft, different drivers are installed for different devices, various add-ons are used to prepare it for the job AND then it works perfectly for some time, may work for a very long time if user knows how to avoid unnecesarry dangers and repair existing ones, but the small errors/bugs will start to accumulate, and existing repair mechanisms won't be enough, you'll need to do a "Repair" form an install CD, or use some other more detailed way to restore your system to that optimal state (it's pretty possible/usual that you'll have to "rejuvenate" all the OS from the scratch with a "Stem CD"). 

Edited by Divine, 09 April 2009 - 11:02 PM.

[necroscope]

There's a special distinction between computer hardware/software and biology: whilst computer and other man-made technology is subject to the force of the 2nd law of thermodymamics (law of increased entropy) and results in inevitable failure, it appears that biological systems have developed a way to circumvent this. Consider that the cell lines that all lifeforms are composed of are in fact derived from the very beginnings of life on this planet and rather than succumbing to entropy, biological systems appear able to increase in complexity (RNA viruses > prokaryotes > multicellular organisms). Therefore, its not very useful to be reliant on metaphors of human technology when seeking to understand aging. 

The eminent researcher Hayflick also used the car analogy in the past so its a common falacy. 

[eternaltraveler]

second law of thermodymamics (law of increased entropy) and results in inevitable failure, it appears that biological systems have developed a way to circumvent this

the second law of thermodynamics says nothing about "inevitable failure", unless you are referring to the heat death of the universe. The second law of thermodynamics states that entropy increases in a closed system.

Earth is not a closed system, it is constantly receiving energy from the sun, and radiating away an equal amount in lower wavelengths and increased entropy. The sun does not provide earth with energy per se as the earth radiates away just as much energy as the sun gives it; the sun gives earth negative entropy which all the life and inanimate matter on earth use.

Life processes all increase entropy. That entropy just fortunately escapes into space. The entropy of the universe goes up for every biological reaction just like it does for every other chemical reaction.

Edited by eternaltraveler, 10 April 2009 - 02:01 AM.

[eternaltraveler]

biological systems don't fight entropy. They use entropy for fuel. (hint: so does everything else that uses fuel)

[DJS]

There's a special distinction between computer hardware/software and biology: whilst computer and other man-made technology is subject to the force of the 2nd law of thermodymamics (law of increased entropy) and results in inevitable failure, it appears that biological systems have developed a way to circumvent this. Consider that the cell lines that all lifeforms are composed of are in fact derived from the very beginnings of life on this planet and rather than succumbing to entropy, biological systems appear able to increase in complexity (RNA viruses > prokaryotes > multicellular organisms). Therefore, its not very useful to be reliant on metaphors of human technology when seeking to understand aging. 

Actually, the inappropriate analogy is the one you're making between Life and individual biological systems (organisms). Mark Hamalainen states it much more eloquently than I could:

Thermodynamics and Information in Aging

In order for life to stabilize information in a viable form it needs a method of entropy export. This is provided by replication coupled with natural selection. Random mutations to a germ-line’s genetic information are constantly occurring and, of those which affect function, most are deleterious. However, if the information is continually copied at sufficiently high levels, it is always possible to maintain a viable subset. This process works most efficiently when single copies of genetic information are passed between generations. Each extra copy would increase the probability of the new organism carrying a deleterious mutation, decreasing the fractional size of the viable subset. Also, single copies can be scrutinized completely by natural selection, whereas in the case
of multiple copies, some mutations would be silent unless every copy carried them and could accumulate rapidly.

The somatic body is a continually replicating organism that passes every copy of its genetic information from one instant to another. From this perspective, it is obvious why natural selection or some analogous internal selection would be difficult. Each copy of genetic information within us continually undergoes changes independent of other copies. Our bodies can try to destroy or silence deleterious mutations by internal selection, but there are two obstacles to this method: selection criteria and positive selection. In natural selection, only a single copy of information is passed from an organism to the new generation and the selection criteria is life or death. Whether the organism is viable and able to reproduce, or not, determines the survival of that copy. In this way, natural selection is able to scrutinize the entire content of a copy of information that seeded an organism. Internal selection cannot use these criteria. Whether a cell lives or dies while in the somatic body does not depend on the functionality of its entire genetic content. Therefore, internal selection must try to approximate natural selection’s abilities by other means. There are only two ways to accomplish this: either a copy can perform selection on itself (intracellular selection), or it can be scrutinized through comparison to another copy (intercellular selection). Intracellular selection is
performed by built-in mechanisms that detect deleterious changes to a cell’s biochemistry and trigger death (apoptosis) or growth arrest (cellular senescence). This system eventually fails; since these mechanisms are encoded by the DNA they are also vulnerable to incapacitated by mutations. Intercellular selection is performed by surface recognition (adaptive immunity for example), and upon detection of an abnormal biochemical state, results in either attacking (by phagocytosis for example) or signaling to the intracellular machinery of the abnormal cell to destroy itself. These systems are also subject to incapacitation by mutation, and cannot work indefinitely. In addition, intra/intercellular selection is limited by the ingenuity of the selection criteria. It is not feasible to select for every possible deleterious mutation (indeed this problem emerges in the context of stem cell culturing), and this highlights the second obstacle to internal selection: it has the potential
to become deleterious. Mutant copies of information that increase their replication rate and difficulty of being selected against will be positively selected for. This problem is most obviously
manifested in cancer, where treatments are designed to try to kill the cancer based on differences (such as growth rate) detected between the cancer and healthy tissue. Such treatments are ultimately flawed for the same reasons as intra/intercellular selection. Hence, natural selection acts only on generations. It does not stabilize informational deterioration within the somatic body, and no internal selection process can fully supplement it. From an evolutionary perspective, maintenance of the germ-line is most important. The somatic body is just an elaborate shell designed to protect it and be periodically discarded.

Edited by DJS, 10 April 2009 - 04:26 AM.

[DJS]

biological systems don't fight entropy. They use entropy for fuel. (hint: so does everything else that uses fuel)

If you believe this, then you're obligated to subscribe to the programmed theory of aging.

Usually I think your positions are well thought out, but in this case I think maybe you have some things confused. To be reductionist about it, biological systems are essentially information systems. Information is maintained on a physical substrate. Everything physical (iow, the entire universe) undergoes entropy. Ergo, information also undergoes entropy, ergo, information systems undergo entropy, ergo, biological systems undergo entropy.

[DJS]

biological systems appear able to increase in complexity (RNA viruses > prokaryotes > multicellular organisms).

Perhaps a better way of putting this is that evolution by natural selection is able to produce biological systems of increasing complexity.

Complexity theory is an incredibly interesting subject... a bunch of thoughts are floating in my head right now which I'll just spew out because I feel too lazy to merge them into a coherent line of thought.

A sound refutation of Gould's drunkard's walk theory of complexity by Robert Wright:

To explain what he means by "random," Gould uses the metaphor of "the drunkard's walk." A drunk is heading down a sidewalk that runs east-west. Skirting the sidewalk's south side is a brick wall, and on the north side is a curb and a street. Will the drunk eventually veer off the curb, into the street? Probably. Does this mean he has a "northerly directional tendency"? No. He's just as likely to veer south as north. But when he veers south the wall bounces him back to the north. He is taking "a random walk" that just seems to have a directional tendency.

If you get enough drunks and give them enough time, one of them may eventually get all the way to the other side of the street. That's us: the lucky species that, through millions of years of random motion, happened to get to the far north, the land of great complexity. But we didn't get there because north is an inherently valuable place to be. If it weren't for the brick wall—that is, the fact that no species can have less than zero complexity—there would be just as many drunks south of the sidewalk as north of it, and the randomness of all their paths would be obvious. Gould writes, "The vaunted progress of life is really random motion away from simple beginnings, not directed impetus toward inherently advantageous complexity."

What Gould neglects is a number of nonrandom factors that fall under the rubric of "positive feedback." The bombardier beetle is a good example. Since there was a time when beetles didn't exist, there must have been a time when no animals were specially adapted to kill and eat them. Then beetles came along, and then various animals did acquire, by natural selection, the means to kill and eat them. This growth in behavioral complexity spurred a response: the beetle's binary weapon. Thus does complexity breed complexity—positive feedback.

One might expect that, given enough time, beetle predators would up the ante, developing some clever way to neutralize the beetle's noxious spray. In fact, they have. Skunks and one species of mouse, the biologists James Gould (no relation) and William Keeton have written, "evolved specialized innate behavior patterns that cause the spray to be discharged harmlessly, and they can then eat the beetles." Evolutionary biologists call this form of positive feedback an "arms race." Richard Dawkins and John Tyler Bonner, among others, have noted that arms races favor the evolution of complexity. Yet Gould's two books on the evolution of complexity don't even mention the phenomenon.

Dennett on copying fidelity

One of the best ways of ensuring copying fidelity over many replications is the "majority rule" strategy that is the basis for the uncannily reliable behavior of computers. It was the great mathematician John von Neumann who saw a way of applying this trick in the real world of engineering, so that Alan Turing's imaginary computing machine could become a reality, permitting us to manufacture highly reliable computers out of unavoidably unreliable parts. Practically perfect transmission of trillions of bits is routinely executed even by the cheapest computers these days, thanks to "von Neumann multiplexing", but this trick has been invented and reinvented over the centuries in many variations. In the days before raid communication and GPS satellites, navigators used to take not one or two but three chronometers aboard their ships on long voyages. If you have just one chronometer and it starts running slow or fast, you'll never know it is in error. If you bring two and they eventually disagree, you won't know whether one is running slow or the other is running fast. If you bring three, you can be quite sure that the odd one out is the one in which the error is accumulating, since otherwise the two that are still in agreement would have to be going bad in exactly the same way, an unlikely coincidence under most circumstances.

[DJS]

The following might only apply to DNA mutations, and please correct me if I'm wrong, but if these 'misrepairs' don't lead to cancer (I'm sure some of them do, though), then they might not occur frequently enough to have a meaningful impact on aging. I mean, every cell probably has at least one 'faulty' gene due to misrepair, but for this to affect aging, it would have to affect a functionally important part of a gene that's actually used in a given cell (not all genes are) or another important component of a cell, and the same gene or component has to be damaged in almost every cell in that tissue, or at least the majority of cells, and that's not very likely, given the relatively low frequency of mutation compared to the number of genes and nucleotides in a given cell as well as the vast number of cells in any given tissue. The obvious exception to this would be cancer, though, since it only takes one cancerous cell to start a tumor. I think Aubrey writes a bit about this in the cancer/WILT chapter of Ending Aging.

In regards to cancer, DNA mutations are indeed a red herring. Epigenetic drift is the real concern and may account for up to 90% of cancers. It may also account for much of the dysregulation that leads to the aging phenotype as well. There is still a decade's worth of research needed here but it may turn out to be the "programming" that is the easiest to hack in order to affect the rate of aging, faulty gene expression and/or reenable innate damage repair mechanisms.

If I recall, this was part of Epstep's SENS challenge argument. I sure hope you're wrong (and PPCD is right) regarding a direct causal link between epigenetic drift and aging because it really is difficult to invision (here in 2009) how we would go about repairing that kind of damage. It would be very bad news for all of us.

[necroscope]

biological systems don't fight entropy. They use entropy for fuel. (hint: so does everything else that uses fuel)

I said nothing about 'fight'. I said circumvent. Additionally, I applied the definition of entropy in the context of the breakdown of a mechanical system, i.e. the transition of a highly ordered state towards disorder. Extending this notion to biological systems it is evident that they harbor the ability to reduce entropy in contrast to the mechanical systems which they have been compared with such as cars and computers. I hope that makes it clearer for you.

[necroscope]

There's a special distinction between computer hardware/software and biology: whilst computer and other man-made technology is subject to the force of the 2nd law of thermodymamics (law of increased entropy) and results in inevitable failure, it appears that biological systems have developed a way to circumvent this. Consider that the cell lines that all lifeforms are composed of are in fact derived from the very beginnings of life on this planet and rather than succumbing to entropy, biological systems appear able to increase in complexity (RNA viruses > prokaryotes > multicellular organisms). Therefore, its not very useful to be reliant on metaphors of human technology when seeking to understand aging.

Actually, the inappropriate analogy is the one you're making between Life and individual biological systems (organisms). Mark Hamalainen states it much more eloquently than I could:

On the contrary, the author states in the first sentence (frankly I don't see the relevance of the copy that follows): "In order for life to stabilize information in a viable form it needs a method of entropy export.", which is precisely my point, i.e. biological systems circumvent entropy and mechanical systems (which continue to be used analogically despite their inappropriateness) don't.

[necroscope]

biological systems don't fight entropy. They use entropy for fuel. (hint: so does everything else that uses fuel)

If you believe this, then you're obligated to subscribe to the programmed theory of aging.

Usually I think your positions are well thought out, but in this case I think maybe you have some things confused. To be reductionist about it, biological systems are essentially information systems. Information is maintained on a physical substrate. Everything physical (iow, the entire universe) undergoes entropy. Ergo, information also undergoes entropy, ergo, information systems undergo entropy, ergo, biological systems undergo entropy.

Actually, fuel is used to reduce entropy. As a refrigerator uses fuel to reduce entropy in the items that are stored within it whilst increasing entropy in its environment, biological systems reduce endogenic entropy by various biochemical transductive processes whilst increasing exogenous entropy.

Lehninger (the name should be familiar to biochemistry students) states:

"living organisms preserve their internal order by taking from their surroundings free energy in the form of nutrients or sunlight, and returning to their surroundings an equal amount of energy as heat and entropy."

If sunlight is considered a consequence of entropy, i.e. the entropy process of a star, then it follows that entropy, in fact serves as fuel for reducing entropy in biological systems and that biological systems are uniquely placed entropy transducers, which means eternaltraveler is on the right track. But cars and computers, once again, are not.

[DJS]

On the contrary, the author states in the first sentence (frankly I don't see the relevance of the copy that follows): "In order for life to stabilize information in a viable form it needs a method of entropy export.", which is precisely my point, i.e. biological systems circumvent entropy and mechanical systems (which continue to be used analogically despite their inappropriateness) don't.

It (the quoted text) is relevant because it presents a major distinction between how individual organisms and the biosphere deal with entropy - an organism can only offer an approximation of the in toto external selection which evolution provides to populations. This goes back to my original point that your statement about the increasing complexity of life and a directionality to evolution was not germane to the conversation. However, upon looking at my original post I will acknowledge that my choice of wording was off in one respect, as I didn't mean to imply that I totally disagreed with your basic point that biological systems circumvent entropy. Perhaps rather than 'circumvent' I would use the term 'reduce'.

[DJS]

biological systems are essentially information systems. Information is maintained on a physical substrate. Everything physical (iow, the entire universe) undergoes entropy. Ergo, information also undergoes entropy, ergo, information systems undergo entropy, ergo, biological systems undergo entropy.

Actually, fuel is used to reduce entropy. As a refrigerator uses fuel to reduce entropy in the items that are stored within it whilst increasing entropy in its environment, biological systems reduce endogenic entropy by various biochemical transductive processes whilst increasing exogenous entropy.

I understand that there can be localized reductions in entropy, but what I'm arguing is that this phenomenon is produced by information systems, and that these information systems are themselves subject to entropy.

Edited by Michael, 15 April 2009 - 11:28 AM.

[maestro949]

In regards to cancer, DNA mutations are indeed a red herring. Epigenetic drift is the real concern and may account for up to 90% of cancers. It may also account for much of the dysregulation that leads to the aging phenotype as well. There is still a decade's worth of research needed here but it may turn out to be the "programming" that is the easiest to hack in order to affect the rate of aging, faulty gene expression and/or reenable innate damage repair mechanisms.

If I recall, this was part of Epstep's SENS challenge argument. I sure hope you're wrong (and PPCD is right) regarding a direct causal link between epigenetic drift...

Research is showing quite a bit of crosstalk between aging and epigenetic pathways. Sirtuins are one example but epigenetic links are also being found in the progerias, alzheimer's, and several other aging diseases. Here's a good "summary" read on this...

Epigenetics and aging: the targets and the marks - Mario F. Fraga and Manel Esteller 2007

... and aging because it really is difficult to invision (here in 2009) how we would go about repairing that kind of damage. It would be very bad news for all of us.

I would see it as rather good news, at least for those that can manage to eek out another 4-5 decades of life and for future generations. The fact that cancer is turning its guns towards epigenetics means significant funding being poured into this research area which may also significantly benefit aging therapeutics. Epigenetic drugs targeting histone and methylation patterns may be designed as cancer preventatives but could also have the side affect of significantly slowing the aging process as well due to their pleiotropic nature.

[maestro949]

biological systems circumvent entropy and mechanical systems (which continue to be used analogically despite their inappropriateness) don't.

You need to successfully argue that there is a distinction between biological systems and mechanical systems. Smaller, faster and more complex are mere differences rather than distinctions. From a classification perspective, a biological system is a type of mechanical system thus is subject to the same laws of physics as the rest of the systems in the universe.

[aikikai]

Researchers suggest that misrepair is a significant cause of aging. Just wondering if this is a bit of semantics. There seems to be a fuzzy line between damage and "misrepair". It also sounds a bit like Vijg's genetic drift theory, after all, doesn't misrepair result in a slightly different DNA coding.

Still, if misrepair is a significant cause of aging, then how do we fix it? The SENS approach of getting rid of malfunctioning cells?

Getting rid of of malfunctioning cells requires that new fresh (non-damaged) cells are produced or placed into the body, as misrepair eventually will affect every cell in the body.

[VidX]

There's a special distinction between computer hardware/software and biology: whilst computer and other man-made technology is subject to the force of the 2nd law of thermodymamics (law of increased entropy) and results in inevitable failure, it appears that biological systems have developed a way to circumvent this. Consider that the cell lines that all lifeforms are composed of are in fact derived from the very beginnings of life on this planet and rather than succumbing to entropy, biological systems appear able to increase in complexity (RNA viruses > prokaryotes > multicellular organisms). Therefore, its not very useful to be reliant on metaphors of human technology when seeking to understand aging. 

The eminent researcher Hayflick also used the car analogy in the past so its a common falacy. 

Well life generally goes to extropy when whole universe does a vice versa, that's interesting feature of life, though it "goes", but doesn't sustain it for indefinite time, immortality would seem like a loggical "end product" of being able to "fight" entropy for as long as you want. And as somebody mentioned - mechanic system isn't really different from biological system as they both are "mechanic" in fundamental level.

[eternaltraveler]

biological systems don't fight entropy. They use entropy for fuel. (hint: so does everything else that uses fuel)

If you believe this, then you're obligated to subscribe to the programmed theory of aging.

err.... doesn't follow. I'm not referring to inevitable increased entropy of a biological system (biological systems are locals of decreased entropy). I am referring to increased entropy of the universe as a result of biological activity, which is obviously the case. Biological systems locally turn randomly arranged CO2 in the air into complex information containing macromolecules, and larger biological structure.

Usually I think your positions are well thought out, but in this case I think maybe you have some things confused. To be reductionist about it, biological systems are essentially information systems. Information is maintained on a physical substrate. Everything physical (iow, the entire universe) undergoes entropy. Ergo, information also undergoes entropy, ergo, information systems undergo entropy, ergo, biological systems undergo entropy.

wrong.

The entropy of the universe always increases. Any local part of the universe (say, you, or the earth in general) can undergo decreased entropy as long as the total entropy of the universe increases. If all systems always increased in entropy there would be no such thing as crystal formation, biological function, or pottery.

Edited by eternaltraveler, 10 April 2009 - 05:38 PM.

[eternaltraveler]

Extending this notion to biological systems it is evident that they harbor the ability to reduce entropy in contrast to the mechanical systems which they have been compared with such as cars and computers. I hope that makes it clearer for you.

it was perfectly clear what you were saying before. It's simply incorrect.

No system exists that can reduce total entropy; none. Nor do biological systems circumvent entropy. They move it from one place to another, yes. But entropy is absolutely vital to their function (driving action potentials, glucose getting where it needs to go, and every other biological reaction).

Yes, biological systems can move entropy out of themselves, though imperfectly. Car engines use entropy as fuel just as human cells do (this is very evident with human cells that rely on gradients of things like sodium and potassium, the slight equilibration of which drives a wide range of cellular functions, entirely entropy driven; these gradients themselves set up at a cost of even more entropy in the forum of inefficiencies in the sodium and potassium atpases, radiated away as heat) . Energy is neither created or destroyed, it simply changes form. Accompanying each one of these form changes is an increase in entropy of the system (car + universe). i.e. Energy is not used up, entropy is increased with every reaction (entropy rich energy makes bad fuel, entropy poor energy makes good fuel). This entropy change is really what drives your car. Some extraordinarily tiny portion of this entropy increase ends up damaging the physical system of the car (ie increasing the entropy of the physical system of the car), and you're right. Cars don't tend to have self repair mechanisms, they rely instead on extrinsic repair systems (mechanics). This

Edited by eternaltraveler, 10 April 2009 - 05:23 PM.

[DJS]

Usually I think your positions are well thought out, but in this case I think maybe you have some things confused. To be reductionist about it, biological systems are essentially information systems. Information is maintained on a physical substrate. Everything physical (iow, the entire universe) undergoes entropy. Ergo, information also undergoes entropy, ergo, information systems undergo entropy, ergo, biological systems undergo entropy.

wrong.

The entropy of the universe always increases. Any local part of the universe (say, you, or the earth in general) can undergo decreased entropy as long as the total entropy of the universe increases. If all systems always increased in entropy there would be no such thing as crystal formation, biological function, or pottery.

Since when did you become more blunt than me?

Wouldn't making explicit the fact that entropy must be removed or "exported" from a biological system just be stating the blatantly obvious? Isn't this something we all learned in high school science? Doesn't the very fact that we exist make these sorts of clarifying digressions pedantic?

But let's just continue being pedantic. I want to go back to your statement, "biological systems don't fight entropy. They use entropy for fuel. (hint: so does everything else that uses fuel)". I'd point out once more that you're confusing your terminology. Biological systems don't use entropy for fuel, they use Free Energy.

Where I think you're still not getting me is my point concerning informational entropy. Organisms are heirarchically structured information systems. Informational entropy is never 'useful', but it can be selected against (eliminated from the system) when it happens in secondary information structures. Hence the reason evolution has allowed RNA polymerase to lack the proofreading capabilities which DNA polymerase has -small quantities of defective mRNAs or misfolded proteins have only a trivial effect and are easily identified and recycled. Allowing the same error rate for DNA replication would be catastrophic. There are all sorts of clever mechanisms designed by evolution to deal with insult to genetic and epigenetic (primary information) structures. Yet even a miniscule rate of error in the primary structure will gradually accumulate, eventually resulting in system failure. Simply put, there is no way for individual organisms to remove, on their own, entropy which accumulates in their primary information structure. On a theoretical level this is not at all controversial (except with some fringe thinkers who will not be named here), only the practical effect this theoretical reality has on our biology in a 'normal' human life span is hottly contested.

Edited by DJS, 11 April 2009 - 02:18 AM.

[trumann]

Extending this notion to biological systems it is evident that they harbor the ability to reduce entropy in contrast to the mechanical systems which they have been compared with such as cars and computers. I hope that makes it clearer for you.

it was perfectly clear what you were saying before. It's simply incorrect.

No system exists that can reduce total entropy; none. Nor do biological systems circumvent entropy. They move it from one place to another, yes. But entropy is absolutely vital to their function (driving action potentials, glucose getting where it needs to go, and every other biological reaction).

Yes, biological systems can move entropy out of themselves, though imperfectly. Car engines use entropy as fuel just as human cells do (this is very evident with human cells that rely on gradients of things like sodium and potassium, the slight equilibration of which drives a wide range of cellular functions, entirely entropy driven; these gradients themselves set up at a cost of even more entropy in the forum of inefficiencies in the sodium and potassium atpases, radiated away as heat) . Energy is neither created or destroyed, it simply changes form. Accompanying each one of these form changes is an increase in entropy of the system (car + universe). i.e. Energy is not used up, entropy is increased with every reaction (entropy rich energy makes bad fuel, entropy poor energy makes good fuel). This entropy change is really what drives your car. Some extraordinarily tiny portion of this entropy increase ends up damaging the physical system of the car (ie increasing the entropy of the physical system of the car), and you're right. Cars don't tend to have self repair mechanisms, they rely instead on extrinsic repair systems (mechanics). This

The claim was never made that total entropy can ever be reduced - only circumvented (one is assuming sufficient familiarity with the fundamentals of the 2nd law to be aware of the difference between open and closed systems in respect to entropy reduction). The term circumvented in this case was used to aid in making the distinction between man-made mechanical systems, which as yet (maestro949) do not share the same level of entropy reduction/circumvention that biological systems do.

As eternaltraveler pointed out above the difference between cars and biological systems (and the fallacy of the Hayflick argument) is that whilst they both break down (due to entropy) over time, biological systems can self repair.

However, the critical message buried in this difference is why, given that biological systems are capable of self-repair, do they allow damage to occur that contributes to aging?

[trumann]

Simply put, there is no way for individual organisms to remove, on their own, entropy which accumulates in their primary information structure. On a theoretical level this is not at all controversial (except with some fringe thinkers who will not be named here), only the practical effect this theoretical reality has on our biology in a 'normal' human life span is hottly contested.

But they do (remove entropy in their primary information structure). Not only does the information retain its integrity - because if it did not life would have ceased long ago as it vanished into randomness - but the information is given sufficient plasticity (a small degree of entropy is permitted) with directionality (selection) to enable organisms to adapt, and if necessary, increase in complexity over time.

Before getting too excited about the mention of a small degree of entropy permitted, which may lead you to conclude that biological systems cannot (rather than do not) remove damage, think on the diversity of repair mechanisms that exist. A case in point is the polyextremophile microbe deinococcus radiodurans which harbors extraordinary repair abilities to protect its primary information structure (genome).

In other words, there is no paucity of repair ability that may evolve, but there is strategic application.

[struct]

Simply put, there is no way for individual organisms to remove, on their own, entropy which accumulates in their primary information structure. On a theoretical level this is not at all controversial (except with some fringe thinkers who will not be named here), only the practical effect this theoretical reality has on our biology in a 'normal' human life span is hottly contested.

But they do (remove entropy in their primary information structure). Not only does the information retain its integrity - because if it did not life would have ceased long ago as it vanished into randomness - but the information is given sufficient plasticity (a small degree of entropy is permitted) with directionality (selection) to enable organisms to adapt, and if necessary, increase in complexity over time.

.. No, they don't (or at least it has not been shown yet since it's hard to put individual(s) in isolation from external forces.) Trumann you probably overlooked the clause 'on their own' (i.e. in isolation, no external perturbations).

[VidX]

 

However, the critical message buried in this difference is why, given that biological systems are capable of self-repair, do they allow damage to occur that contributes to aging?

Well..PC OS software is capable to repair itself too, but still fails after some time. That means - repair mechanisms aren't perfect and needs to be developed more, or other solutions (like in Linux) must be adapted to avoid complete failure of a whole system.

[trumann]

Simply put, there is no way for individual organisms to remove, on their own, entropy which accumulates in their primary information structure. On a theoretical level this is not at all controversial (except with some fringe thinkers who will not be named here), only the practical effect this theoretical reality has on our biology in a 'normal' human life span is hottly contested.

But they do (remove entropy in their primary information structure). Not only does the information retain its integrity - because if it did not life would have ceased long ago as it vanished into randomness - but the information is given sufficient plasticity (a small degree of entropy is permitted) with directionality (selection) to enable organisms to adapt, and if necessary, increase in complexity over time.

.. No, they don't (or at least it has not been shown yet since it's hard to put individual(s) in isolation from external forces.) Trumann you probably overlooked the clause 'on their own' (i.e. in isolation, no external perturbations).

Without immersing ourselves too deeply into the role of entropy in biological systems, if we can agree that all other things being equal, that there exists a rate of breakdown in any system, both human-made mechanical and biological, then can we agree that biological systems are able to deal more effectively with the forces of breakdown?

[trumann]

However, the critical message buried in this difference is why, given that biological systems are capable of self-repair, do they allow damage to occur that contributes to aging?

Well..PC OS software is capable to repair itself too, but still fails after some time. That means - repair mechanisms aren't perfect and needs to be developed more, or other solutions (like in Linux) must be adapted to avoid complete failure of a whole system.

It's very interesting to consider the sort of programs one could employ to safeguard the integrity of PC software. Perhaps have the software residing in three copies and have a daemon that is constantly comparing the three? (if one is not in agreement then delete and recopy it).

Biologically there are numerous methods and strategies that have evolved to perform such error checking and maintenance.