bob b, Re: 'Increasing Genetic Information'

[Yorzhik]

According this misinterpretation of the SLOT, machines and animals don't exist because they violate the SLOT. Geesh. Hint: organisms use energy from the sun to maintain their reproductive mechanisms (i.e., DNA).



See above. According to this misinterpretation of the SLOT, animals and machines don't exist. But I assure you they do. And they do by using the energy of the sun to maintain their reproductive systems. Those not good at this fall by the way side. It's called evolution.



We have such "machines." They're called organisms and they are really good at using the energy from the sun to maintain their DNA.

Finish high school and then come back. I've already written enough that you should be passed the argument you've presented here.

 

[noguru]

So when Miller/Urey created amino acids they were in a closed system and we can apply the SLoT. That's great, we can keep the discussion in that context.

Just as a side note, can we apply the SLoT to anything that spontaneously goes from high energy to low energy. Right?


Yes, I'm aware of those ideas. I see problems with both information and also with energy for evolution. If you want to stick with one, then we can stick with the energy problem.


Yes, they are complicated systems of machines that control the energy that is ultimately available from the sun. The problem is that without the control of the energy (without the machines), uncontrolled energy (like that which comes from the sun) will destroy information carrying media, and then the information will be lost forever (2 steps - one for energy, and another for information).

Chlorophyll

A green pigment, present in algae and higher plants, that absorbs light energy and thus plays a vital role in photosynthesis. Except in Cyanophyta (blue-green algae), chlorophyll is confined to chloroplasts. There are several types of chlorophyll, but all contain magnesium and iron. Some plants (e.g., brown algae, red algae, copper beech trees) contain additional pigments that mask the green of their chlorophyll.

Chlorophyll as a Photoreceptor

Chlorophyll is the molecule that traps this 'most elusive of all powers' - and is called a photoreceptor. It is found in the chloroplasts of green plants, and is what makes green plants, green. The basic structure of a chlorophyll molecule is a porphyrin ring, co-ordinated to a central atom. This is very similar in structure to the heme group found in hemoglobin, except that in heme the central atom is iron, whereas in chlorophyll it is magnesium.

We have constructed a phylogenic tree for green plants by comparing 5S rRNA sequences. The tree suggests that the emergence of most of the uni- and multicellular green algae such as Chlamydomonas, Spirogyra, Ulva, and Chlorella occurred in the early stage of green plant evolution. The branching point of Nitella is a little earlier than that of land plants and much later than that of the above green algae, supporting the view that Nitella-like green algae may be the direct precursor to land plants. The Bryophyta and the Pteridophyta separated from each other after emergence of the Spermatophyta. The result is consistent with the view that the Bryophyta evolved from ferns by degeneration. In the Pteridophyta, Psilotum (whisk fern) separated first, and a little later Lycopodium (club moss) separated from the ancestor common to Equisetum (horsetail) and Dryopteris (fern). This order is in accordance with the classical view. During the Spermatophyta evolution, the gymnosperms (Cycas, Ginkgo, and Metasequoia have been studied here) and the angiosperms (flowering plants) separated, and this was followed by the separation of Metasequoia and Cycas (cycad)/Ginkgo (maidenhair tree) on one branch and various flowering plants on the other.

So Yorzhik, do you consider chlorophyll do be a machine or a mechanism?

Does the molecular makeup of chlorophyll require supernatural intervention?

Are you familiar with anaaerobic life forms?

Are you familiar with prokaryotic and eukaryotic life forms?

Are you failiar with the precursor to these?

Precursor

 

[Jukia]

Yorzhik and a few others have been pounding this "mutations lead to reduced information" and somehow it all violates the Second Law. Am I right in suspecting that this is just the latest creationist attempt us appear to know some science and interpreting it in way that is absurd? They seem soo intelligent throwing around information theory but it just does not seem to apply to the situations they want it to. I must admit I am over my head in the info theory area but the argument seems to do little to actually damage the major thrust of evolutionary theory.

 

[noguru]

Yorzhik and a few others have been pounding this "mutations lead to reduced information" and somehow it all violates the Second Law. Am I right in suspecting that this is just the latest creationist attempt us appear to know some science and interpreting it in way that is absurd? They seem soo intelligent throwing around information theory but it just does not seem to apply to the situations they want it to. I must admit I am over my head in the info theory area but the argument seems to do little to actually damage the major thrust of evolutionary theory.

Yes, there argument conflates several distinct ideas into a muddied model of biology. First they confuse abiogenesis with macroevolution.Then they confuse simple mechanisms that are found in the biological world with a kind of irreducibly complex machine that must be attributed to intelligent design. They use biological life as it currently exists as this example of a machine that is irreducibly complex. They fail to recognize that current biological systems are made of many smaller components that can be viewed as mechanisms of metabolism and/or chemical reactions. They fail to realize that throughout the history of life on this planet these mechanisms have been used interchangeably within the entire machine of a biological system.

All of the components of complex biological machinery have been around since very early on relative to the history of life. Some of the aspects of biology that facilitate the current conditions are cell specialization and the synthesis of different functions into a larger functioning system. These concepts are often, and quite tellingly, omitted by advocates of ID.

 

[ThePhy]

In response to the mention of an improved biological message, Yorzhik asked:

How would we measure "improved"? By a measure Shannon would use?

As I alluded to a few posts ago, I am unclear how you tie Shannon’s work to the efficiency of biological functioning. If you can specify an unambiguous way of doing that, I will gladly consider it.

My allusion to “improved’ is just what most people would call an improvement in the operation of the organism. Better survival and procreation odds.

If one adds to a message, then there must be additional processing to understand it. If one replaces a message, then the cost is the loss of the original message. One way or another, there is a cost.

I’m not sure that adding to a message always entails additional processing, but in a normative case, that is probably true. But for evolution, again if that gives a survival advantage, the additional cost is worth it.

As to the loss of a message being a cost - for evolution, the cost that is relevant is how much chance will an organism have of procreating. Sure, the efficiencies of individual biological processes in the organism may vary as changes occur, but the sum total of those changes as manifested in the organism’s survival advantage is the measure that is important to evolution.

 

[ThePhy]

So when Miller/Urey created amino acids they were in a closed system and we can apply the SLoT. That's great, we can keep the discussion in that context.

No, “closed” as applied to the SloT means no matter is allowed to enter or leave the system, and no energy is allowed to enter or leave the system. The electrical discharge the chemicals were subjected to was a very strong localized injection of energy into the system. Conditions for applying SLoT violated.

Just as a side note, can we apply the SLoT to anything that spontaneously goes from high energy to low energy. Right?

As far as we know, you can apply the SLoT to any process in the universe, - IF – IF – IF - the conditions under which the SLoT is defined are met.

Yes, they are complicated systems of machines that control the energy that is ultimately available from the sun. The problem is that without the control of the energy (without the machines), uncontrolled energy (like that which comes from the sun) will destroy information carrying media, and then the information will be lost forever (2 steps - one for energy, and another for information).

If someone is given an injection of a small amount of a highly lethal nerve agent, comparing their (now dead) body to the way it was just prior to the injection, the details of their body structure has only been slightly changed. But that change was sufficient to stop the correct functioning of a crucial piece of the biological machine that is their body. The energy from the sun, the environment, and so on will soon cause the body to decay into a “disorganized” mass, whereas shortly before that machine-body was taking in food and extracting energy from part of it and using that to create new highly organized tissues, repair injuries, and so on. Our bodies are capable of absorbing sunlight (“uncontrolled energy”) (as least in moderation) without damage. For some organisms, such as Iguanas, that uncontrolled sunlight provides the heat to elevate their bodies to the temperatures needed for digestion. When they die, that same sunlight causes decay. Body-machine uses energy to make baby body-machines, then body-machine gets old or injured and dies, and loses it’s ability to control the use of the energy around it.

 

[Greenrage]

Finish high school and then come back. I've already written enough that you should be passed the argument you've presented here.

Translation of this creation-ese: you can't rebut what I say, so you're reduced to diversion and personal invective. That's the way with creationist.

Back to the subject: do you deny that living organisms maintain their DNA using energy that ultimately derives from the sun?

Let us know.

 

[Greenrage]

I don't think so. Ultraviolet breaks down plastic. I imagine it breaks down other things too. Is this what you might think I'm referring to?

Plasma breaks down all organic material.

However, perched safely 93M miles away in the form of the sun, it provides the energy for growing plants here on earth.

Are you honestly arguing that chlorophyl doesn't function through the sun's energy? Is that the level of absurdity creationists are reduced to?

 

[Yorzhik]

In response to the mention of an improved biological message, Yorzhik asked: As I alluded to a few posts ago, I am unclear how you tie Shannon’s work to the efficiency of biological functioning. If you can specify an unambiguous way of doing that, I will gladly consider it.

I'm merely saying that as the information on a DNA is transmitted to do things, it can be measured. If there is a mutation, then when that section is transmitted again, it can be measured again.

My allusion to “improved’ is just what most people would call an improvement in the operation of the organism. Better survival and procreation odds.

And so would you argue that Sickle Cell Anemia comes from an increase in information?

...

I’m not sure that adding to a message always entails additional processing, but in a normative case, that is probably true. But for evolution, again if that gives a survival advantage, the additional cost is worth it.

I agree that if additional or replacement information leads to a survival advantage, then the cost is worth it. Another way to say it would be that the value of benefit would be greater than the cost. Can mutations provide this?

As to the loss of a message being a cost - for evolution, the cost that is relevant is how much chance will an organism have of procreating. Sure, the efficiencies of individual biological processes in the organism may vary as changes occur, but the sum total of those changes as manifested in the organism’s survival advantage is the measure that is important to evolution.

Of course. But the devil is in the details. The chances of getting a less efficient message are vast (assuming a change has taken place). And the chances of getting clearer messages are small (and they are the two ends of the same ratio). And the chances of getting a worse ratio increase each time the message is transmitted. So "vary" is not quite accurate unless you are willing to concede that varying means "to get continually worse" (perhaps not in every case, but overall).

 

[Yorzhik]

No, “closed” as applied to the SloT means no matter is allowed to enter or leave the system, and no energy is allowed to enter or leave the system. The electrical discharge the chemicals were subjected to was a very strong localized injection of energy into the system. Conditions for applying SLoT violated.

As far as we know, you can apply the SLoT to any process in the universe, - IF – IF – IF - the conditions under which the SLoT is defined are met.

Then what are we dealing with? If the reactions in the Miller/Urey experiment are not operating under the SLoT, then what do we call it when the energy in the experiment always flows from high energy to low energy?

If someone is given an injection of a small amount of a highly lethal nerve agent, comparing their (now dead) body to the way it was just prior to the injection, the details of their body structure has only been slightly changed. But that change was sufficient to stop the correct functioning of a crucial piece of the biological machine that is their body. The energy from the sun, the environment, and so on will soon cause the body to decay into a “disorganized” mass, whereas shortly before that machine-body was taking in food and extracting energy from part of it and using that to create new highly organized tissues, repair injuries, and so on. Our bodies are capable of absorbing sunlight (“uncontrolled energy”) (as least in moderation) without damage. For some organisms, such as Iguanas, that uncontrolled sunlight provides the heat to elevate their bodies to the temperatures needed for digestion. When they die, that same sunlight causes decay. Body-machine uses energy to make baby body-machines, then body-machine gets old or injured and dies, and loses it’s ability to control the use of the energy around it.

All I'm saying is that you cannot get information carrying media to be maintained without the use of machines. And your quote here supports that. What was your point?

 

[ThePhy]

Then what are we dealing with? If the reactions in the Miller/Urey experiment are not operating under the SLoT, then what do we call it when the energy in the experiment always flows from high energy to low energy?

I don’t know of any special name for it – maybe “water always flows downhill”.

But if you examined my answer on Miller’s experiment not conforming with the requirements for SLoT, ask yourself this. What if we repeat the Miller experiment, except the spark comes from a battery that is totally enclosed within the apparatus. No input of external energy or mass. Now we have a SLoT system. Would the chemicals still form into amino acids?

All I'm saying is that you cannot get information carrying media to be maintained without the use of machines. And your quote here supports that. What was your point?

On the surface I agree that machines need to be involved in maintaining information integrity. That’s what biological systems are – machines, part of whose function is maintaining the integrity of the DNA, and when presented with an improvement in DNA, keeping it.

 

[ThePhy]

And so would you argue that Sickle Cell Anemia comes from an increase in information?

Don’t know much about the details of Sickle Cell anemia. As to it coming from an increase in information, I am still waiting for you or someone to tell me how to measure information in biological systems. Sans that, I cannot answer your question.

I agree that if additional or replacement information leads to a survival advantage, then the cost is worth it. Another way to say it would be that the value of benefit would be greater than the cost. Can mutations provide this?

Ask the rabbit living on the edge of a snow field, whose family has had uniformly brown fur. This rabbit got zonked with a cosmic ray, and now has white fur. Runs in the snow in plain view of the hungry fox, who can’t see him. No biological down side, just a pigment change. Did that mutation have a benefit greater than the cost?

Of course. But the devil is in the details. The chances of getting a less efficient message are vast (assuming a change has taken place). And the chances of getting clearer messages are small (and they are the two ends of the same ratio). And the chances of getting a worse ratio increase each time the message is transmitted. So "vary" is not quite accurate unless you are willing to concede that varying means "to get continually worse" (perhaps not in every case, but overall).

Not true. Just because the chances of getting clearer messages are much smaller than the chances of degraded messages does not mean the degraded ones will come to predominate. In the more traditional terminology, we are just talking about good mutations versus bad ones. Bad and good mutations are not selected for equally by natural selection. If we start with the premise that most members of a species are very close copies of their parents, then the survivability of the species is nearly static. When one member gets a bad mutation, it dies without reproducing, or if it has kids, they have poor reproductive odds. Ultimately, the bad mutation is eliminated from the population, and the average member of the species is still the norm. When a good mutation comes, that animal has slightly higher reproductive success, as do its kids, and their kids, until they come to dominate the population. What was the norm before is now the less fit.

 

[Greenrage]

I On the surface I agree that machines need to be involved in maintaining information integrity. That’s what biological systems are – machines, part of whose function is maintaining the integrity of the DNA, and when presented with an improvement in DNA, keeping it.

This is virtually a paraphrase of evolutionary theory. Beneficial mutations in DNA are maintained and reproduced and become more prominent in the gene pool. Determental mutations fall out of the gene pool. Do this for a long period of time and you have the diversity of life on this planet. It isn't magic and it doesn't violate the SLoT. It's what DNA and the organisms that contain DNA (i.e. all life as we know it) do.

 

[Greenrage]

Of course. But the devil is in the details. The chances of getting a less efficient message are vast (assuming a change has taken place). And the chances of getting clearer messages are small (and they are the two ends of the same ratio). And the chances of getting a worse ratio increase each time the message is transmitted. So "vary" is not quite accurate unless you are willing to concede that varying means "to get continually worse" (perhaps not in every case, but overall).

Since DNA is contained in organisms that express phenotypes, and since organisms maintain and reproduce their DNA, this claim is simply contrary to the facts.

1. DNA mutation is observable.

2. The rate of DNA mutation is measurable.

3. The expression of DNA mutation as phenotype is observable.

4. The reproduction of beneficial traits through natural selection is observable.

That's evolution. Again, your claims, however much you're invested in them, are simply contrary to the observed facts.

 

[Yorzhik]

I don’t know of any special name for it – maybe “water always flows downhill”.

"Water always flows downhill" isn't covered by the Second Law?

But if you examined my answer on Miller’s experiment not conforming with the requirements for SLoT, ask yourself this. What if we repeat the Miller experiment, except the spark comes from a battery that is totally enclosed within the apparatus. No input of external energy or mass. Now we have a SLoT system. Would the chemicals still form into amino acids?

Yes. Which proves my point that the SLoT works the same under any condition. We just need to know how much energy is coming from where.

On the surface I agree that machines need to be involved in maintaining information integrity. That’s what biological systems are – machines, part of whose function is maintaining the integrity of the DNA, and when presented with an improvement in DNA, keeping it.

Again, the devil is in the details. The machines won't save an improvement to the DNA unless they have the programming and the ability for it. The chances of not having one or the other or both increase as time (read: amount of change) increases.

Don’t know much about the details of Sickle Cell anemia. As to it coming from an increase in information, I am still waiting for you or someone to tell me how to measure information in biological systems. Sans that, I cannot answer your question.

I thought Shannon measured information. Let's stick with that for now.

Ask the rabbit living on the edge of a snow field, whose family has had uniformly brown fur. This rabbit got zonked with a comic ray, and now has white fur. Runs in the snow in plain view of the hungry fox, who can’t see him. No biological down side, just a pigment change. Did that mutation have a benefit greater than the cost?

Are you sure that wouldn't be due to sexual recombination? Is there a way we can tell?

Of course. But the devil is in the details. The chances of getting a less efficient message are vast (assuming a change has taken place). And the chances of getting clearer messages are small (and they are the two ends of the same ratio). And the chances of getting a worse ratio increase each time the message is transmitted. So "vary" is not quite accurate unless you are willing to concede that varying means "to get continually worse" (perhaps not in every case, but overall).

Not true. Just because the chances of getting clearer messages are much smaller than the chances of degraded messages does not mean the degraded ones will come to predominate. In the more traditional terminology, we are just talking about good mutations versus bad ones. Bad and good mutations are not selected for equally by natural selection. If we start with the premise that most members of a species are very close copies of their parents, then the survivability of the species is nearly static. When one member gets a bad mutation, it dies without reproducing, or if it has kids, they have poor reproductive odds. Ultimately, the bad mutation is eliminated from the population, and the average member of the species is still the norm. When a good mutation comes, that animal has slightly higher reproductive success, as do its kids, and their kids, until they come to dominate the population. What was the norm before is now the less fit.

So you are saying that you go with the probabilities here. If a slight advantage is presented, then the tendency will be for that advantage to become fixed in the population. Of course there are things like bad luck and thresholds that might stop an advantage at any point - but the point is that the probabilities favor the advantage overall. Is that correct?

 

[ThePhy]

From ThePhy (previously):

But if you examined my answer on Miller’s experiment not conforming with the requirements for SLoT, ask yourself this. What if we repeat the Miller experiment, except the spark comes from a battery that is totally enclosed within the apparatus. No input of external energy or mass. Now we have a SLoT system. Would the chemicals still form into amino acids?

Yorzhik’s response:

Yes. Which proves my point that the SLoT works the same under any condition.

Too broad a statement. As was shown a couple posts ago, the way Miller had his original apparatus set up the SLoT was not applicable, because energy flowed in from outside the system. Once again, the SLoT only applies when its preconditions are satisfied.

We just need to know how much energy is coming from where.

Not necessarily. In the “batteries inside the system” versions of Miller I postulated, I can make predictions based on the SLoT with no understanding at all about how it is wired internally or even what the batteries are used for.

From ThePhy (previously):

On the surface I agree that machines need to be involved in maintaining information integrity. That’s what biological systems are – machines, part of whose function is maintaining the integrity of the DNA, and when presented with an improvement in DNA, keeping it.

Yorzhik’s response:

Again, the devil is in the details. The machines won't save an improvement to the DNA unless they have the programming and the ability for it.

Invoking the word “programming” evokes images of computer programs, which can be misleading when talking about biological entities. But yes, I agree that beneficial changes will not be kept unless they are compatible with what is already there.

The chances of not having one or the other or both increase as time (read: amount of change) increases.

Why? I don’t see why this follows.

Yorzhik (on information and sickle cell anemia):

I thought Shannon measured information. Let's stick with that for now.

I want to be very sure that if we are talking Shannon’s information, then any conclusions that are drawn do not imply the corresponding conclusions about thermodynamics and entropy. Arguments about energy flows from the sun and closed systems are not what Shannon was discussing.

As I said, I am not a sickle anemia expert, so you tell me what Shannon’s view would be of increase in information as related to sickle cell anemia.

From ThePhy (previously):

Ask the rabbit living on the edge of a snow field, whose family has had uniformly brown fur. This rabbit got zonked with a comic ray, and now has white fur. Runs in the snow in plain view of the hungry fox, who can’t see him. No biological down side, just a pigment change. Did that mutation have a benefit greater than the cost?

Yorzhik’s response:

Are you sure that wouldn't be due to sexual recombination? Is there a way we can tell?

Irrelevant, unless you are willing to go on record as saying that there are no cases where a mutation would not confer a distinct survival advantage. On a bacterial level, strains have isolated where there was no genetic variation left in the strain to select from. Yet when presented with a situation where they had to change or die, a small number survived and were found to have done so by what can only be called a beneficial (life-saving) mutation.

From ThePhy (previously):

Not true. Just because the chances of getting clearer messages are much smaller than the chances of degraded messages does not mean the degraded ones will come to predominate. In the more traditional terminology, we are just talking about good mutations versus bad ones. Bad and good mutations are not selected for equally by natural selection. If we start with the premise that most members of a species are very close copies of their parents, then the survivability of the species is nearly static. When one member gets a bad mutation, it dies without reproducing, or if it has kids, they have poor reproductive odds. Ultimately, the bad mutation is eliminated from the population, and the average member of the species is still the norm. When a good mutation comes, that animal has slightly higher reproductive success, as do its kids, and their kids, until they come to dominate the population. What was the norm before is now the less fit.

Yorzhik’s response:

So you are saying that you go with the probabilities here. If a slight advantage is presented, then the tendency will be for that advantage to become fixed in the population. Of course there are things like bad luck and thresholds that might stop an advantage at any point - but the point is that the probabilities favor the advantage overall. Is that correct?

Remember that even though detrimental mutations substantially outnumber the beneficial ones, the average member of the species has neither. It is not as though an animal is born with 98 bad mutations and one good one. An occasional animal will have a bad mutation. Far less often one will come out on the plus side. But these are the ones that natural selection acts on. The bad ones loose out, the good ones multiply.

As to probabilities, there is an element of that. An animal is born with a good mutation, but breaks its leg and gets infection and dies as an infant. Mutation terminated. As to thresholds that block further progression, occasionally there may be. But biology is capable of modifications in myriads of directions, and blocking one does not block all. Better hearing, better eyesight, protective coloration, wings, pheromones, speed, agility, claws, immune system, echo-location, smell, strength, scales, intelligence, neck length, manual dexterity, and on and on. Lots of ways for every species to experience beneficial changes.

 

[Yorzhik]

Too broad a statement. As was shown a couple posts ago, the way Miller had his original apparatus set up the SLoT was not applicable, because energy flowed in from outside the system. Once again, the SLoT only applies when its preconditions are satisfied.

It's okay. I would have always expected that the tendency for things to go from high energy to low energy spontaneously would have been covered by the Second Law of Thermodynamics. It's only what I've been taught all my life, but then again, I didn't study thermodynamics directly in college. And all I would be interested in is a way to reference "all things tend to go from high energy to low energy if given the chance". If that can be established, then the strict definition of the Second Law of Thermodynamics doesn't matter.

So can we call this tendency for things to go from high energy to low energy spontaneously a particular name? Something shorter than "water flows downhill". How about "Slotty"? It's arbitrary, but overlaps a bit with a reference to the Second Law. Or perhaps you have a better name? I'm surprised that since 99.99999 (or more) of the situations where the Second Law is referenced they are not truly open. And with that in mind, you'd almost wonder why science doesn't have a simple way to reference this phenomenon of "water runs downhill".

We just need to know how much energy is coming from where.

Not necessarily. In the “batteries inside the system” versions of Miller I postulated, I can make predictions based on the SLoT with no understanding at all about how it is wired internally or even what the batteries are used for.

Eh, no. I think we are talking past each other a bit here. I'm only saying that if the energy comes from a battery, or if the energy comes from a power supply, we can still make predictions about the energy flow. You seem to be hung up on the definition of the SLoT, which I hope I cleared up in my immediately previous quote.

Invoking the word “programming” evokes images of computer programs, which can be misleading when talking about biological entities. But yes, I agree that beneficial changes will not be kept unless they are compatible with what is already there.

Invoking "programming" isn't too misleading. The point is only that getting a beneficial change to stick is harder than just actually, as it were, figuring out what a beneficial change would be and adding it to the DNA without consideration of all the changes required or all the other interrelated systems involved.

Why? I don’t see why this follows.

Because the chances of breaking the program and/or machinery that maintains the information media also increases over time. In other words, the chances of losing the programming or machinery that would accommodate a positive change is at risk just as the rest of the system is.

I want to be very sure that if we are talking Shannon’s information, then any conclusions that are drawn do not imply the corresponding conclusions about thermodynamics and entropy. Arguments about energy flows from the sun and closed systems are not what Shannon was discussing.

Of course.

As I said, I am not a sickle anemia expert, so you tell me what Shannon’s view would be of increase in information as related to sickle cell anemia.

I'm pretty sure Shannon would be ruthless about insisting that information decreased. The mutation would be seen as a hole poked in the message/noise of what a red blood cell is.

Irrelevant, unless you are willing to go on record as saying that there are no cases where a mutation would not confer a distinct survival advantage. On a bacterial level, strains have isolated where there was no genetic variation left in the strain to select from. Yet when presented with a situation where they had to change or die, a small number survived and were found to have done so by what can only be called a beneficial (life-saving) mutation.

There is no overall trend that mutations can confer general survival advantages. For example; let's look at the survival of a player at a craps table in Las Vegas. They may win certain rolls of the dice, but as time increases, their chances of having those rolls overcome the odds are less and less to the point of being impossible. Thus, it is almost certain that if the bacteria that you cite here were placed back in a normal environment, they would be less apt to survive. I guess you could say that's another prediction that creationists make.

Not true. Just because the chances of getting clearer messages are much smaller than the chances of degraded messages does not mean the degraded ones will come to predominate.

No; that's exactly what it means. If the tendency is in one direction, then as the sample increases (read: increased mutations over time) it becomes more sure in that direction. That is as sure as "all energy will go from high energy to low energy spontaneously if given the chance."

ThePhy continues:

In the more traditional terminology, we are just talking about good mutations versus bad ones. Bad and good mutations are not selected for equally by natural selection. If we start with the premise that most members of a species are very close copies of their parents, then the survivability of the species is nearly static. When one member gets a bad mutation, it dies without reproducing, or if it has kids, they have poor reproductive odds. Ultimately, the bad mutation is eliminated from the population, and the average member of the species is still the norm. When a good mutation comes, that animal has slightly higher reproductive success, as do its kids, and their kids, until they come to dominate the population. What was the norm before is now the less fit.

If it only worked that way. Unfortunately, good mutations are very rare. So rare, in fact, that there will be a number of neutral or bad mutations before a good one can possibly come along. How do I know this? Because not only will a good mutation have to be changed in whatever point it did change, but it will have to also come with changes (or wait for changes) to other systems that are dependent on that other single change. The odds are against the idea that a pure strain will survive generation through generation, stacking good mutation upon good mutation in their DNA. In fact, mutational load is a serious topic in genetics.

Remember that even though detrimental mutations substantially outnumber the beneficial ones, the average member of the species has neither. It is not as though an animal is born with 98 bad mutations and one good one. An occasional animal will have a bad mutation. Far less often one will come out on the plus side. But these are the ones that natural selection acts on. The bad ones loose out, the good ones multiply.

No, it is as though an animal will be born with 98 bad mutations and one good one (I'll make the bold prediction that it would be a much worse ratio). The average member of the species will have mutational load that only gets worse as time goes by. Your foundation is wrong and thus your conclusion that "the bad ones lose out, the good ones multiply" is wrong.

As to probabilities, there is an element of that. An animal is born with a good mutation, but breaks its leg and gets infection and dies as an infant. Mutation terminated. As to thresholds that block further progression, occasionally there may be. But biology is capable of modifications in myriads of directions, and blocking one does not block all. Better hearing, better eyesight, protective coloration, wings, pheromones, speed, agility, claws, immune system, echo-location, smell, strength, scales, intelligence, neck length, manual dexterity, and on and on. Lots of ways for every species to experience beneficial changes.

So I take that as a "yes", you go with the probabilities. Do you always go with the probabilities, or just in this case?

I'd say it's more like this; your white bunny might win the roll of the dice today, but he has to keep rolling, and the odds will get him if enough time goes by. But the question is begged... how did that bunny roll so many good rolls to get there in the first place? Or is that your proof? - "the bunny exists, therefore evolution is true"

But it's even worse. Your bunny might be lucky enough to get white fur from just a single point mutation, but most advantages are going to require many mutations to many interconnected systems.

And it get's worse; sometimes those systems have to be changed at the same time or the part of the system that did change will be a detriment, not a help to the organism.

 

[Johnny]

Because not only will a good mutation have to be changed in whatever point it did change, but it will have to also come with changes (or wait for changes) to other systems that are dependent on that other single change.

First, it is suspected (and has been observed) that proteins often evolve from frame-shift mutations of internally repetitious sequences. Second, many proteins have multpile copies on the genome. Third, many proteins have different isoforms which function identically or almost identically.

Here's the bottom line: People can make whatever claims about how unlikely it is for a beneficial mutation to happen or for a system to evolve, but it can be demonstrated in a laboratory setting that novel protein and novel protein interactions do evolve. It's like someone arguing over the statistical improbability of cars working ignoring the 500 cars that pass his window daily. Seriously, examples of protein evolution is so well studied and documented that it takes an exceptionally important example to even be published in a big name journal (science, nature, journal of evolutionary biology) these days. You'd have 10,000 unimpressed and unsurpised biologists asking why it is significant.

 

[noguru]

First, it is suspected (and has been observed) that proteins often evolve from frame-shift mutations of internally repetitious sequences. Second, many proteins have multpile copies on the genome. Third, many proteins have different isoforms which function identically or almost identically.

Here's the bottom line: People can make whatever claims about how unlikely it is for a beneficial mutation to happen or for a system to evolve, but it can be demonstrated in a laboratory setting that novel protein and novel protein interactions do evolve. It's like someone arguing over the statistical improbability of cars working ignoring the 500 cars that pass his window daily. Seriously, examples of protein evolution is so well studied and documented that it takes an exceptionally important example to even be published in a big name journal (science, nature, journal of evolutionary biology) these days. You'd have 10,000 unimpressed and unsurpised biologists asking why it is significant.

It is quite obvious that Yorzhik has very little expertise in this area. His rants are full of ignorance and misconceptions. One would think that if Yorzhik was so well versed in genetics that he might be leading the field in research for that area.

 

[Yorzhik]

First, it is suspected (and has been observed) that proteins often evolve from frame-shift mutations of internally repetitious sequences. Second, many proteins have multpile copies on the genome. Third, many proteins have different isoforms which function identically or almost identically.

As to your first thing. Whether a single mutation causes a cascade of changes or not does not give you the required new system. In fact, if you have a cascade of changes you need more control to insure that the changes made don't remove a required function, and you also need more positive changes to account for a larger dynamic system.

It's like the difference between chipping out a brick in a house and saying you've got a positive change (better air flow?), but to really make it work you need to send a wrecking ball through.

As to your second and third statements, you may be on to something. Can you tell me why mutiple copies and mutiple identical (or nearly identical functions) has any relevance?

Here's the bottom line: People can make whatever claims about how unlikely it is for a beneficial mutation to happen or for a system to evolve, but it can be demonstrated in a laboratory setting that novel protein and novel protein interactions do evolve.

So what... novel proteins and novel protein interaction is only a way of digging your grave. I've never denied it.

Johnny continues:

It's like someone arguing over the statistical improbability of cars working ignoring the 500 cars that pass his window daily. Seriously, examples of protein evolution is so well studied and documented that it takes an exceptionally important example to even be published in a big name journal (science, nature, journal of evolutionary biology) these days. You'd have 10,000 unimpressed and unsurpised biologists asking why it is significant.

Ah, yes, great argument: "obviously evolution is true; we're here!"