Punctuated Equilibria theories

[bumab]

Uhhh... we were not talking about ambiogenisis.

 

1. The fossil record shows rapid speciation events following large scale extinctions.

2. Traditionally, this is ascribed to niche availability.

3. Niche availability is a nice, logical thought, but fails to answer all the questions

- Species are built to AVOID mutations (spellchecking during transcription, for example). Why the rapid speciation after an extinction event, and why can't we trigger that in a lab?

- Mutations are often "against the odds," so why are so many beneficial ones conserved, when new protiens introduced into creatures induce an autoimmune response? How do they recognize their own new mutations? Etc...

 

Let's stay on topic.

[Biochemist]

Thus, a new, regulated metabolic pathway arising via a chain of beneficial mutations.

Possible, but unlikely. And I suspect you are aware that this example is broadly refuted.

 

The mutant enzyme also metabolizes arabitol in this case, at least more that the original enzyme did. Ergo, the enzyme decreases efficacy on ribulose (the actual target) and increases on xylitose and arabinose. All it did was lose specificity. These are three very similar sugars, and all it shows it that a damaged enzyme still works. This is not a beneficial mutation. It is a mutation with minimal damage.

[ldsoftwaresteve]

Paultrr:

Something I mentioned in another thread about we really do not fully understand all the conditions present when life first evolved comes into play here. What would be considered suffiecient conditions for X at epoch t1 is not suffiecient conditions at epoch t2. The early universe had less elements required to produce life as we know it than it did a few billion years later, so to speak. Our local area itself while ripe for development of planets, etc a few billion years ago is not now ripe for planetary development now. Yet, other regions out there are ripe at the present which also raises the issue of both time and place coming into play when we look at the origins of life.

I don't have the knowledge in this area that you folks do but I think this statement is key. Why? Don't laugh, it's just a gut feeling.

I assume that most, if not all, actions are the result of some system trying to achieve an equilibrium within context. What is it about life that is a result of this contextual pressure? What you pointed out Paultrr is a context.

The end result (coming at it from my strange point of view) is that 'higher' forms of life are more aware - even to the point of being able to enhance their own awareness.

Perhaps the difference with the contexts (epochs) is what is there to be aware of.

We are trying to understand what the driving force behind the changes is. Well, to me at least, existence generates little awareness engines in the form of different kinds of life which are aware of different kinds of things. Why? How does awareness stabilize existence?

[bumab]

.....all it did was lose specificity. These are three very similar sugars, and all it shows it that a damaged enzyme still works. This is not a beneficial mutation. It is a mutation with minimal damage.

 

While I agree it's not a "novel" new ability, or a new enzyme, I disagree about the implications. This could be considered a beneficial mutation, especially if types of sugars available changed, and the generalists won out.

[paultrr]

Uhhh... we were not talking about ambiogenisis.

 

Why the rapid speciation after an extinction event, and why can't we trigger that in a lab?

 

Two things:

 

One the subject no matter how far into the past one pushes it still has implications for all the rest since one cannot have mutating life without first having life.

 

Two, I would suggest that the above I mentioned just prior to you're last post enters into all this. Untill we know the exact conditions for any given point any lab experiments we wish to conduct are rather guessing in the dark, so to speak. However, there is also the issue of time. Sudden apperances of life filling gaps is not actually taking place on scales we can reproduce at present in the labs unless someone wants to start an experiment and let a couple of generations or more monitor it. I doub't anyone could talk the financial powers that be into that one today. Its simply not a realistic objection to the general idea given the actual time spans involved in earth's historical case to try and mimick such in a normal lab setting. Here again, we are rather stuck with using indirect evidence instead of direct evidence.

[paultrr]

While I agree it's not a "novel" new ability, or a new enzyme, I disagree about the implications. This could be considered a beneficial mutation, especially if types of sugars available changed, and the generalists won out.

 

I agree it is an example of beneficial mutation even if we are not talking say a new species at this point. I might also add that as Telemad pointed out Creationist tend not to argue any more about mutational changes even leading to new species. Its what they term "Kinds" that they tend to argue over. One thing I have noticed in some of the ID arguments is a lack of up to date data. Its rather like the data the older creationist camp tended to think represented the majority view of evolutionists unless one stays up to date.

[paultrr]

Paultrr: I don't have the knowledge in this area that you folks do but I think this statement is key. Why? Don't laugh, it's just a gut feeling.

I assume that most, if not all, actions are the result of some system trying to achieve an equilibrium within context. What is it about life that is a result of this contextual pressure? What you pointed out Paultrr is a context.

The end result (coming at it from my strange point of view) is that 'higher' forms of life are more aware - even to the point of being able to enhance their own awareness.

Perhaps the difference with the contexts (epochs) is what is there to be aware of.

We are trying to understand what the driving force behind the changes is. Well, to me at least, existence generates little awareness engines in the form of different kinds of life which are aware of different kinds of things. Why? How does awareness stabilize existence?

 

Good point. Yet it's also a point that tends towards metaphysics which one trys to avoid in pure science as much as possible. However, I suspect that awareness of at least the environment has impact on all this. Even primitive cells respond to changes in their environment via chemical stimulus, etc. That in turns runs us right back to having to know specific factors of the envirnoment at any given epoch in history to fully understand why things happened the way they do. Let's face facts, early earth when life first evolved was not the same earth we sit on today when it comes to that environment. Before we can actually even attempt to duplicate things from then we do need to know a lot more about those times.

[Biochemist]

While I agree it's not a "novel" new ability, or a new enzyme, I disagree about the implications. This could be considered a beneficial mutation, especially if types of sugars available changed, and the generalists won out.

I read the link that Telemad posted, and discovered that "beneficial mutation" is apparently a reserved phrase. The argument that others have made separates "beneficial mutation" from increased information in the gene. This specific example is just a moderate loss of information content that results in an increased ability to survive in one environment (with a decremented ability to survive in the original).

 

I don't think this makes any case for liklihood of serial mutation driving speciation, since each mutation makes incremental decrements in specificity of substrate. All this does is extrapolate to moralitiy of the mutant line, not speciation.

[Biochemist]

I might also add that as Telemad pointed out Creationist tend not to argue any more about mutational changes even leading to new species. Its what they term "Kinds" that they tend to argue over....

I really wish that we would defend and refute arguments presented here, rather than refute unrelated arguments proposed elsewhere. To my knowledge, there are no "creationisists" in this discussion, although there are some in this forum.

[Biochemist]

Paultrr-

 

You have started a new discussion on abiogenesis that is tangential to thie thread. I suggest you start a new thread on that topic.

[bumab]

I read the link that Telemad posted, and discovered that "beneficial mutation" is apparently a reserved phrase. The argument that others have made separates "beneficial mutation" from increased information in the gene. This specific example is just a moderate loss of information content that results in an increased ability to survive in one environment (with a decremented ability to survive in the original).

 

"Beneficial" and "detrimental" can only be understood in terms of context. Thus a loss of information, or a gain of information, can be either based on the situation. If this mutation (a reduction in coding or an increase) caused and increased survival rate in the offspring, it's a beneficial mutation.

[Biochemist]

If this mutation (a reduction in coding or an increase) caused and increased survival rate in the offspring, it's a beneficial mutation.

Absolutely true. I just accidentally stepped into the wrong discussion by using a reserved phrase.

 

The position I am trying to defend is that mutation does not drive speciation (at least, not much). Gene damage probably can occasionally act as a benefit. But serial damage is not likely to create a large enough change to launch a species.

[TeleMad]

bumab: Species are built to AVOID mutations (spellchecking during transcription, for example).

 

Species are "built" to OPTIMIZE mutations, not avoid them. Both too many and too few mutations can be detrimental to a species.

 

bumab: Why the rapid speciation after an extinction event...

 

Tow reasons are the opening up of new niches and the reduction in selective pressures due to decreased competition.

 

bumab: ... and why can't we trigger that in a lab?

 

We can trigger rapid speciation in the lab. I gave an example involving plants.

 

We can also see organisms adapting to new niches in the lab: look at the example I posted last night about a chain of beneficial mutations leading to a new regulated metabolic pathway. The "eat xylitol" niche was vacant and and bacteria evolved the ability to metabolize it efficiently.

 

One reason we can't do these experiments with humans (or other organism that have similar generation times) is simply time. If an experiment involves 10,000 generations of bacteria, that could come to only about 7 months (many bacteria have generation times of 20 to 30 minutes). For a human the same number of generations would take about 150,000 years (considering a generation time of 15 years). That's not feasible. Heck, evolutionary theory is only about 150 years old, nowhere near 150,000.

 

bumab: Mutations are often "against the odds," so why are so many beneficial ones conserved, ...

 

Uhm, because they are beneficial.

 

bumab: ... when new protiens introduced into creatures induce an autoimmune response?

 

I am not aware of the goats engineered to produce spider silk having autoimmune responses, especially not any that killed them.

 

bumab: How do they recognize their own new mutations?

 

I don't know that they do.

 

Foreign proteins are not automatically rejected by the cells; in fact, we know this because we can insert protein-coding genes into many organisms and they will happily produce that protein.

 

The main determinant of whether or not a synthesized protein is given the thumbs up or thumbs down may be related to folding. In euks, the RER (rough endoplasmic reticulum) has proteins that check for unfolded proteins, and prevent them from entering the Golgi apparatus; in fact, the unfolded proteins (if they can't be folded properly by a chaperone) are taking backwards and ejected from the RER. So in general if a protein is folded - whether it's a self protein or a foreign protein - it's allowed to continue into the Goldi; if a protein - self or foreign - is not folded, it's rejected.

 

Note that the protein synthesizing machinery itself has no idea what it is making (i.e., foreign or self proteins). That's why viruses can function: they inject their genetic material into the host cell and the host cell blindly goes about synthesizing proteins from it.

[Biochemist]

Species are "built" to OPTIMIZE mutations, not avoid them. Both too many and too few mutations can be detrimental to a species.

Pure conjecture, but a nice idea.

We can trigger rapid speciation in the lab. I gave an example involving plants.

But you might have noticed that the topic of the thread is PE, and this is a discussion about animals. The plant examples (as have been noted at least twice in this thread) are not applicable to animals due to significant variances in the handling of foreign proteins.

We can also see organisms adapting to new niches in the lab: look at the example I posted last night about a chain of beneficial mutations leading to a new regulated metabolic pathway. The "eat xylitol" niche was vacant and and bacteria evolved the ability to metabolize it efficiently.

...And this one is directly refuted above. It is nice that a damaged enzyme still works at all, but this is hardly an example of a trend toward speciation.

[TeleMad]

Possible, but unlikely. And I suspect you are aware that this example is broadly refuted.

 

No, I recognize that YOU are broadly refuted.

 

Biochemist: The mutant enzyme also metabolizes arabitol in this case, at least more that the original enzyme did. Ergo, the enzyme decreases efficacy on ribulose (the actual target) and increases on xylitose and arabinose. All it did was lose specificity.

 

Nothing but Creationist spin.

 

The 'mutant' enzyme INCREASED its efficiency in processing xylitol. Thats an improvement in function - those were beneficial mutations.

 

And at the end, some bacteria could efficiently metabolize BOTH xylitol AND the original sugar: that's a gain of a new function and a new source of food - those were beneficial mutations.

 

Biochemist: These are three very similar sugars, and all it shows it that a damaged enzyme still works.

 

What it shows is that you are wrong.

 

Your statements, unlike a real scientist's, about the high specificity of enzymes would lead the lay person to wrongly conclude that enzymes can function on only one substrate. In this experiment a single enzyme catalyzed reactions for 2 different sugars, and you are stating that it can actually use yet a third as a substrate. And this isn't some freakish enzyme with some freakish ability to work on more than one substrate: many enzymes can catalyze reactions for multiple, similar substrates.

 

And what the experiment shows is that mutations can produce a more efficient enzyme. (Here, we're not even talking about the mutations that lead to the gene being expressed continuously, and the bacteria's ability to utilize xylitol therefore being increased 20 fold: a beneficial mutation to be sure). Mutations in the enzymes structure improved it's ability to catalyze the conversion of xylitol.

 

There were clearly beneficial mutations. You and the other Creationists can bury your heads in the sand all you want, that doesn't change the facts.

[Biochemist]

Note that the protein synthesizing machinery itself has no idea what it is making (i.e., foreign or self proteins). That's why viruses can function: they inject their genetic material into the host cell and the host cell blindly goes about synthesizing proteins from it.

This is another example of pure conjecture.

 

The fact that some proteins slip through unrecognized does not mean that most do, even if folded. There are only about 300,000 proteins in a human cell. If there were a large number of non-functional proteins being transcribed, the vast majority of proteins in the cell would be nonfuncitional. This is clearly not the case. There is certainly much more going on in recognition of "self" vs "non-self" than whether a protein is folded appropriately.

[TeleMad]

Biochemist: I read the link that Telemad posted, and discovered that "beneficial mutation" is apparently a reserved phrase.

 

"Beneficial mutation" means a mutation that is beneficial: gee, how hard is that to recognize! If you are using it different way, perhaps its because you are a Creationist.

 

Biochemist: The argument that others have made separates "beneficial mutation" from increased information in the gene.

 

There was CLEARLY an increase in genetic information in the genome. Where there was originally only one gene, whose product could not effienciently catalyze xylitol, there ended up being two different genes, whose products could efficiently catalyze reactions of two different substrates, and with the two genes being regulated individually. New copy of a gene, new function, new regulation.

 

And there was also an increase of information in the 'mutated' gene. It originally could not efficiently catalyze the converstion of xylitol, but after some mutations, it could.

 

Biochemist: This specific example is just a moderate loss of information content

 

More Creationist spin. You're wrong ... dead wrong. There was an INCREASE in genetic information content.

 

Biochemist: ... an increased ability to survive in one environment (with a decremented ability to survive in the original).

 

Nope. After the duplication, there were two different genes. One mutated and thereby its product became more efficient at using xylitol as a subtrate. The original gene did not undergo these same mutations, and its product could continue to efficiently use the original sugar as a substrate.

 

Biochemist: I don't think this makes any case for liklihood of serial mutation driving speciation, since each mutation makes incremental decrements in specificity of substrate.

 

Yet more Creationist warped logic.

 

The mutations led to an INCREASE in the specificity of one of the enzymes for xylitol.