Wholly Natrualistic Alternative To Neo-Darwinism?

[Dancing David]

1969
...

... 19666

Wow , so research paper fail, citations are more than three years old outside of literature review.

More straw and appeal to old authority

"F"

 

[Dinwar]

Say you have some animal (or whatever fits the following description) that hasn't changed phenotype in forever -- as far as we can tell from fossil evidence. I'm assuming there is something like this or close to it.

Living fossils, they're called. In general they change a little, but the changes are relatively minor--for example, crocs are still recognizable as the same critters from the Mesozoic (ignoring the fact that the clade was once MUCH more diverse). They're living fossils, with very few changes. Compare that with dinosaurs, which went from the Tyrant Lizard King to a sparrow.

So what I'm trying to get at is a living thing that is immune to selection at the population/whole organism level because of molecular stability.

Doesn't need to be so weird. Natural selection frequently operates as a stabilizing force--until something changes, many organisms are at a local fitness high, and almost any change will decrease their fitness (please note the caveats; I'm not a Creationist, just explaining Punctuated Equilibrium). As Gould said, stasis is data.

Of course, that' all from a morphology perspective--biochemically even crocs have altered dramatically (changes in oxygen levels, changes in ozone levels, changes in diet, it all has an affect on the biochemistry).

 

[Patrick1000]

Semantics Slight Of Hand, First A Dinosaur, Then A Bird, No Problem

I think Patrick's argument is worthwhile because it illustrates a misunderstanding well. The root mistake, as I see it, is that evolution is used to mean any change at all and the only path from there to here. But we know it isn't so.

For instance, you can figure out the age of a star by looking at things like its mass and the ratio of hydrogen and helium -- there's a clock-like mechanism there that has nothing to do with evolution. We sometimes use the word, but not in the biology or Darwinian sense. So we know that things do change with time, even when selection is not happening.

This same process occurs in living things. Mutations come along. The difference between the non-evolutionary change and the evolutionary change is whether or not the change is fixed by survival. A beneficial change that increases survivability will tend to stay and a negative change will tend to disappear.

But what about a neutral change? These aren't acted upon by selection, so they pretty much follow the star analogy and accumulate over time.

But the picture is made more complex because at each step, a mutation may fall into one of the three categories (or partially into more than one). And, there are mechanisms for DNA repair that kick in as well.

You get a sequence like this: drift --> negative --> drift -->more drift --> positive --> drift that extends over a long time. Those organisms that reach a negative spot on the chain get set aside, the positive remain, and everything experiences some drift when that is neutral.

I expect this is too shallow an explanation for the experts, but I'm still hoping Patrick can fit it into his worldview. In a sense, he is right, drift isn't really classic evolution, unless or until selection acts to preserve or delete it. Is that a new "mechanism"? Not really, it's an assumption underlying evolution itself. If you count any sort of change over time as evolution, you get evolving stars, mountain ranges and so on.

SEMANTICS SLIGHT OF HAND, FIRST A DINOSAUR, THEN A BIRD, NO PROBLEM?

I FOR ONE DON'T BUY IT!

The themes of your post here marplots are far from shallow, plenty good enough for so called "experts", downright eloquent you are my good friend, if I may be so forthright in my telling you so.

The "root mistake" as you refer to it marplots is indeed that "evolution" has come to mean, for some anyway, any change at all. THE TERM HAS AN ELASTICITY THAT IT SHOULD NOT BE PERMITTED TO HAVE, certainly not without oodles of qualifiers anyway. I'll use the penicillin resistance example again to make my point. It is very much your point as well marplots, the term
"evolution" 's inappropriate elasticity in day to day "scientific" parlance.

In mainstream "science speak", penicillin sensitive bacteria become penicillin resistant upon prolonged exposure to the antibiotic, and this change in the bacteria's complement of information, and the accompanying phenotypic expression of that change(penicillin resistance), is referred to as "evolution" in a Darwinian sense.

No argument from me there. In this example, we have a case of "evolution" as understood by way of its "fully modern synthesis". I say this as here we are dealing with a case in which armed with 21st century sophistication, we recognize that the underlying mechanism for this evolutionary change is one having to do with the bacteria's acquiring the ability to resist penicillin by way of its DNA "mutating", mutating such that the bacteria's DD-transpeptidase enzyme(s) now coded for are penicillin unfriendly and no longer permit the antibiotic to bind. This is full on neo-Darwinism(Darwin plus Mendel) understood in the light of our knowing that it is DNA which is the medium carrying the message, and knowing as well how it is that the DNA carries the message, and in some general sense at least, knowing moreover how it is that the message, the information, might be changed through the process of mutation. (Bacteria have many ways of becoming penicillin resistant, from the transpeptidase enzyme losing its penicillin binding site through mutation, to the bacteria making enzymes that lyse/cleave the antibiotic, and so on.)

So in the bacterial resistance case, we have a population with variation, or at least the potential to become a population characterized by variation penicillin sensitivity/resistance wise through the process of mutation/DNA sequence change, and we have an environmental pressure, the presence of penicillin, which indeed selects for those bacteria that are equipped to deal with the pressure. And so, in the presence of the penicillin, the bacterial population changes, becomes one in which the variation with the transpeptidase enzyme/the penicillin binding protein(s) becomes predominant, selected for. If this penicillin resistant trait wasn't in the population to begin with, but occurred by way of a "spontaneous mutation" after the introduction of the antibiotic to the environment, we can say that the bacteria has really "evolved", a great example of natural selection. Again, no argument from me there.

But this penicillin resistant bug, as cool as it is, is not an airplane, nor is it a rocket ship. It is a hot air balloon. I can take it up and fly it around the Sonoma wine country here in California, but if I try to go to New York City in this thing, more likely than not, I simply ain't gonna make it. And if I try to take this bad boy into earth orbit, or fly it to the moon, well I'm gonna' die for sure. The balloon simply does not have the requisite sophistication, technical capabilities.

A group of bacterial proteins that become altered, and in so doing no longer bind penicillin and thereby confer penicillin resistance, is a hot air balloon, a cool little novelty item for floating about. Biologically/informationally, a bird's heart/lung is a jillion times as complicated as are the penicillin binding proteins responsible for penicillin sensitivity/resistance. A bird's heart/lung is a rocket ship.
Just because I can see that you are able to build a hot air balloon with the equipment you have in your garage, it far from necessarily follows that with the same equipment, you will be able to build a space ship.

Here is where the evolutionary biologist's semantics slight of hand trick comes into play. Just because one has demonstrated "evolution" with a small "e", doesn't mean you can ride this thing to the moon and make the claim that you've got a rocket ship. If you say to me " but Patrick, "evolution" is "Evolution" is "EVOLUTION" ". I will say that the penicillin resistance case is evolution with a small "e", and I grant it, by all means. Indeed it is fascinating, insanely cool. But my friend, it is most decidedly not EVOLUTION with a BIG "E". And I for one will not let anyone tell me that because bacteria become resistant to penicillin when exposed to the antibiotic, "evolution" with a small "e", the penicillin resistance as hot air balloon case, that this provides proof that a reptile heart/lung was transformed by virtue of the same process to an avian/bird heart/lung, EVOLUTION with a huge "E", the bird cardiopulmonary system as rocket ship case.

This type of thing goes on all the time with "evolution". "Evolutionary biologists" demonstrate the truth of a limited claim, and then bogusly parlay that into some huge claim. In my example above, bacterial penicillin sensitivity/resistance understanding proves we understand how it was dinosaurs became birds. Apples and oranges my friends? Worse than that! Hot air balloons and rocket ships it is no less.

This is what I like to call "semantics slight of hand", "evolution" elasticity par excellence. As scientists here, critical thinkers, the genuinely curious, we all vow to one another, we all pledge to one another, not to buy into such gobbledygook. This way, when we hit on something real, meaningful, beautiful, then we know we have something, something true.

Darwin's idea is not only wickedly imaginative, insanely creative, but it is an idea which provides us also with some LIMITED truth with regard to our understanding of biological systems, how they change over time. Darwin's idea is one which gives us even perhaps a hint, a LIMITED inkling, as to what biologic systems fundamentally ARE. But it is an idea with as best any honest biologist can tell, LIMITED applications, the hot air balloon analogy again.

No one is saying you'll have to go to church if you acknowledge the truth of the matter, that we simply do not know the details with regard to the origins of living things, the genesis of biological systems, their development over time. I don't go to church. I am not a "creationist", whatever that may or may not mean. AND by the way, of course there is absolutely nothing wrong with creationism. 76 % of American adults self identify with Christianity, say they are believers. That is 175,000,000 people here in my country. As such, most of the people I will encounter today, both at work and at play, will be de facto intelligent design advocates, have to be. This is what Christianity is. Fine by me.


Darwin's answers may be around the corner. People, scientists, should continue to look. On the other hand, it is important to acknowledge, I believe so anyway, that though we should enthusiastically proceed in life always trying our best to learn more, we are limited ourselves. General Relativity, Einstein's theory of gravity, is utterly incompatible with quantum mechanics. Both simply cannot be correct. Will someone ever figure out how to reconcile the domestic difficulties of the world's great physicists? Perhaps, but perhaps not. There may be things simply beyond the ken of our understanding, whether those things prove to be ultimately grounded in "God", or grounded in the nature of a Godless world too complex for our pea brains to handle.

One thing we can handle however is being precise, clear, accurate with our use of words/language. When it comes to "evolution" we have a lot of tightening up to do.

 

[Dinwar]

The "root mistake" as you refer to it marplots is indeed that "evolution" has come to mean, for some anyway, any change at all. THE

Actually, this is backwards. Darwin only used the term once in his book, because AT THAT TIME it meant any change--that's why we have concepts like "stellar evolution". Over time, evolution came colloquially to mean BIOLOGICAL evolution, and then to changes in DNA (it's expanding again, based on work with RNA).

e term
"evolution" 's inappropriate elasticity in day to day "scientific" parlance.

Considering you've yet to show any understanding of modern scientific thought, I somehow doubt you're qualified to speak on how any term is used in scientific parlance.

No one is saying you'll have to go to church if you acknowledge the truth of the matter, that we simply do not know the details with regard to the origins of living things, the genesis of biological systems, their development over time. I

You've been called out for equivocating between evolution and abiogenesis before--obviously you're not interested in using terms precisely. And as for development through time, the only game in town is evolution. You can say that you don't like the fact that the term encompasses directional, stabilizing, and neutral selection, but frankly your opinion doesn't matter. The term DOES encompass all of those in biology. Live with it, or convince biologists to change their usage of the term (which requires you to gain some expertise in the field, as opposed to name-dropping and discussing a few isolated situations).

 

[Jack by the hedge]

Patrick's argument appears to be that explaining a single evolutionary step does not mean that a series of such steps explains its walking a long way. Or rather, in his analogy, just because a balloon can fly does not mean it can travel to the moon.

Well, there is a fundamental reason why a balloon cannot do that. It can only rise through the atmosphere. I don't believe Patrick has yet explained why he thinks that part of his analogy is appropriate to describe evolution. What aspect of evolution by natural selection is the equivalent barrier to a balloon ascending into thinner and thinner atmosphere?

Where is the limit, and what is its cause?

 

[AdMan]

I don't believe Patrick has yet explained why he thinks that part of his analogy is appropriate to describe evolution. What aspect of evolution by natural selection is the equivalent barrier to a balloon ascending into thinner and thinner atmosphere?

Where is the limit, and what is its cause?

He can't answer this. As has been pointed out a bunch of times, he is just arguing from incredulity.

 

[Dinwar]

Where is the limit, and what is its cause?

I'm waiting for him to say "Microevolution can happen but macroevolution is impossible". He's getting most of his interpretations of evolutionary theory from the Discovery Institute and the like (directly or indirectly, I'm not sure), and that's one of the favorite lines of that crowd.

 

[Dinwar]

bacterial penicillin sensitivity/resistance understanding proves we understand how it was dinosaurs became birds. Apples and oranges my friends? Worse than that! Hot air balloons and rocket ships it is no less.

I've already explained this to you. First, birds ARE dinosaurs, for the same reason that you're a member of your grandfather's family. Second, we know the specific genes that were affected to turn a distinctly non-avian dinosaur into Avis. Jack Horner is currently playing with emu embryos to illustrate that transition via DNA. To say that we don't understand how dinosaurs became birds is to illustrate your complete ignorance of the fields of evolution and of paleontology--to the point where I can only conclude you haven't even gone so far as to flip on the Discovery Channel. Meaning you've actually done less to understand this than your idol, the man on the street.

 

[Wowbagger]

Here is where the evolutionary biologist's semantics slight of hand trick comes into play. Just because one has demonstrated "evolution" with a small "e", doesn't mean you can ride this thing to the moon and make the claim that you've got a rocket ship.

In this case, it is NOT mere sematics.

Lots of "little e" evolutions, over time, can emerge as a "Big E" Evolution.

There are several examples found in the real world, deduced through fossil records and DNA evidence, etc.

We can also simulate the process in computer systems: We can see how "balloons can sail to the moon", so to speak. We know it is possible, assuming "going to the moon" is a significant selection pressure for "balloons".

General Relativity, Einstein's theory of gravity, is utterly incompatible with quantum mechanics. Both simply cannot be correct.

But, they are! We know they are both correct, experimentally. Their predictions agree with each other everywhere, except perhaps in a black hole.

But, even then, the differences can be resolved with a unified theory. String Theory is one such idea: It might not be correct, itself. But, it still demonstrates something very important: It is possible for both to remain correct!

Saying "Both simply cannot be correct." is not accurate. Yes, they both CAN be correct. We have some ideas how to do that, even if we don't know which one is the most accurate, yet.

 

[Lowpro]

<snip>

Meaning you've actually done less to understand this than your idol, the man on the street.

I laughed out loud in class reading this

 

[marplots]

Patrick has a good point. If that were the whole story, it would be a solid challenge. But it is not.

First of all, the bacterial example came after the general ideas were already in place. It is more properly a demonstration of what we expected should be going on and as it turned out, it was going on. It's an example of the explanatory power of an existing theory.

Second, the scale is misapplied. Small bacteria with very short cycles of reproduction are not the same as large animals with much longer cycles on a set time or volume scale. What should be more important is the number of generations and the amount of change needed to show up in fossils.

So, for instance, if it takes a thousand generations and a 0.2% change in bacterial DNA (made that number up for illustration purposes) to alter one enzyme or transport protein (gifting resistance to an antibiotic), then you would translate this into a thousand generations of the larger animal for the same kind of small change -- "small" because one enzyme may not make much difference at all in what we see preserved. So at the least, one should take this into consideration. The result is a great stretching out of time, even though the "step" as measured by DNA sequence change is the same.

But this is still too crude. Why? Because bacteria have some handy mechanisms to get genes we don't see in higher taxa. So it may be much quicker with bacteria than other animals.

If I remember right, time has always been something worth discussing in evolutionary theory and may still be actively disputed -- I don't know.

If anti-biotic resistance had to uphold the majority of the evidence for evolution, Patrick's criticism would have more heft. But it doesn't. It is used as one arrow in the quiver, and it is sometimes overused when trying to get a point across, but it certainly isn't the primary driver of why we think evolution is the right answer. Small, accumulated change is certainly a main pillar, but the evidence comes from all over the planet. Darwin noticed just such small variation in separate populations of mostly identical, living birds and found the same kind of movement we see in fossils, dogs, bacteria and elsewhere.

The individual mechanisms can be challenged, but the broad picture remains the same -- serial accumulation of change under the influence of selection pressures.

And as an aside, I think Dinwar explained that I was wrong to assume that minimal or no phenotypic change is evidence of "no evolution" but rather an example of evolution acting to hold a state more stable than the norm. I think I understand that concept much better than when I posted my objections.

 

[Dinwar]

If I remember right, time has always been something worth discussing in evolutionary theory and may still be actively disputed -- I don't know.

It certainly is. There's definitely interest in calibrating the paleontological record with molecular clocks, with some interesting results. There's also continued discussion of the tempo of evolution--is it gradual or punctuated, and is that general or species-specific?

Gould and Eldritch estimated that it took a few thousand generations for speciation to occur--not that speciation occurd every few thousand generations, but rather that once it got going that's how long it would take.

But this is still too crude. Why? Because bacteria have some handy mechanisms to get genes we don't see in higher taxa. So it may be much quicker with bacteria than other animals.

Yeah....if you really want to criticize our view of evolution, this is where you should do it. Horizontal gene transfer between bacteria is really the best example of evolution occuring by some means other than those typically discussed in evolutionary biology. In fact, the whole concept of species breaks down with bacteria (in one famous experiment, the concept of "alive" was shown to break down thanks to horizontal gene transfer!). The foundation of the tree of life isn't a nice neat stick, like most cladograms show--it's a chaotic tumbleweed, the branches of which we do not and perhaps CANNOT know. I can see some justification in objecting to calling horizontal gene transfer evolution, or associating it with Darwinian concepts--it's a whole different game, and should probably be treated as such, though Darwinian fitness certainly would still necessarily play some role.

 

[AdMan]

SEMANTICS SLIGHT OF HAND, FIRST A DINOSAUR, THEN A BIRD, NO PROBLEM?

<snip>

One thing we can handle however is being precise, clear, accurate with our use of words/language.

For the next time, Patrick--it's sleight of hand.

 

[sphenisc]

Where it says "some figures in the study of evolution". The use of "some" implies that most figures in the study of evolution do not use the term this way, at least that is how I read that statement.

How do you interpret the phrase "However, such usage has been described by some as incorrect"?

 

[Dinwar]

How do you interpret the phrase "However, such usage has been described by some as incorrect"?

I'd interpret that as "Someone asked two scientists their opinion on some issue".

 

[abaddon]

SEMANTICS SLIGHT OF HAND, FIRST A DINOSAUR, THEN A BIRD, NO PROBLEM?

Seconded, it is "sleight".

I FOR ONE DON'T BUY IT!

I don't much care what you buy.

The themes of your post here marplots are far from shallow, plenty good enough for so called "experts", downright eloquent you are my good friend, if I may be so forthright in my telling you so.

Yet you reject the experts in favour of your own opinion.

The "root mistake" as you refer to it marplots is indeed that "evolution" has come to mean, for some anyway, any change at all. THE TERM HAS AN ELASTICITY THAT IT SHOULD NOT BE PERMITTED TO HAVE, certainly not without oodles of qualifiers anyway. I'll use the penicillin resistance example again to make my point. It is very much your point as well marplots, the term
"evolution" 's inappropriate elasticity in day to day "scientific" parlance.

Why should flexibility not be allowed? You use it all the time.

<snip>Again, no argument from me there.

Yet, you are arguing for three or four tedious paragraphs.

But this penicillin resistant bug, as cool as it is, is not an airplane, nor is it a rocket ship. It is a hot air balloon.

Three more things you do not understand as witnessed in other threads. Don't make me quote.

I can take it up and fly it around the Sonoma wine country here in California,

Aren't you in China?

but if I try to go to New York City in this thing, more likely than not, I simply ain't gonna make it.

Unless you have the right sort of balloon.

And if I try to take this bad boy into earth orbit, or fly it to the moon, well I'm gonna' die for sure. The balloon simply does not have the requisite sophistication, technical capabilities.

Oh dear, now you are getting strange. Take a balloon into orbit? Or to the moon?
Are you serious?

<snip>you will be able to build a space ship.

Ah we return to your previous obsession.

Here is where the evolutionary biologist's semantics slight of hand trick comes into play.

Once again, it's "sleight".

Just because one has demonstrated "evolution" with a small "e", doesn't mean you can ride this thing to the moon and make the claim that you've got a rocket ship. If you say to me " but Patrick, "evolution" is "Evolution" is "EVOLUTION" ". I will say that the penicillin resistance case is evolution with a small "e", and I grant it, by all means. Indeed it is fascinating, insanely cool. But my friend, it is most decidedly not EVOLUTION with a BIG "E". And I for one will not let anyone tell me that because bacteria become resistant to penicillin when exposed to the antibiotic, "evolution" with a small "e", the penicillin resistance as hot air balloon case, that this provides proof that a reptile heart/lung was transformed by virtue of the same process to an avian/bird heart/lung, EVOLUTION with a huge "E", the bird cardiopulmonary system as rocket ship case.

This type of thing goes on all the time with "evolution". "Evolutionary biologists" demonstrate the truth of a limited claim, and then bogusly parlay that into some huge claim. In my example above, bacterial penicillin sensitivity/resistance understanding proves we understand how it was dinosaurs became birds. Apples and oranges my friends? Worse than that! Hot air balloons and rocket ships it is no less.

This is what I like to call "semantics slight of hand", "evolution" elasticity par excellence. As scientists here, critical thinkers, the genuinely curious, we all vow to one another, we all pledge to one another, not to buy into such gobbledygook. This way, when we hit on something real, meaningful, beautiful, then we know we have something, something true.

Why are you conflating evolutionary science with rocket science?

Darwin's idea is not only wickedly imaginative, insanely creative,

Ah, now I see where you intend to go.

<snip religiousity>

Oh boy, closet creationism.

 

[Lowpro]

No I'm telling you, he's parroting Michael Denton to the freakin' letter.

 

[sphenisc]

I'd interpret that as "Someone asked two scientists their opinion on some issue".

That's just about compatible with Hoke's usage... but only if they're both smaller than each other...

 

[Dinwar]

And I for one will not let anyone tell me that because bacteria become resistant to penicillin when exposed to the antibiotic, "evolution" with a small "e", the penicillin resistance as hot air balloon case, that this provides proof that a reptile heart/lung was transformed by virtue of the same process to an avian/bird heart/lung, EVOLUTION with a huge "E", the bird cardiopulmonary system as rocket ship case.

I just noticed this--it's an example of a typical Creationist tactic. They pick two living organisms, and say "There's no way this current organism can evolve into this other current organism! Evolution is wrong!!!!!" The thing is, though, that that's not what happened. No modern reptile evolved into a modern bird. Birds have reptilian ancestors, but they were as different from modern reptiles as the mammals of that time are different from modern mammals. We know, from fossil evidence, that the reptiles the birds evolved from had very unique cardiopulmonary systems--including a four-chambered heart (that caused something of a stir a few years back). And when you consider that the dinosaur in question was the end result of a hundred million years or so of evolution since its ancestors diverged from the line that gives us modern lizards, the question of "How did that system evolve?" becomes relatively easy to answer: it evolved slowly, over more time than a human mind can fully grasp.

If you want to talk evolution, you have to look at ancestors. Which means, you have to look at fossils if they're available. You can't simply pick two modern animals and say "Show me how this evolved into that", because only Creationists have ever said that this evolved into that.

This type of thing goes on all the time with "evolution". "Evolutionary biologists" demonstrate the truth of a limited claim, and then bogusly parlay that into some huge claim.

Well, once you've written a few million pages about the small claims, the big ones sort of jump out at you. I mean, are you even aware of the plethera of literature on the subject? Buy Valentine's "On the Origin of the Phyla" to see a glimps--a VERY brief one--of what's known. Look through "The Dinosauria" to see a glimps--again, a VERY brief one--of what we know about that single taxa. And there are hundreds of books like that.

We have the evidence. The fact that you don't know it proves nothing.

 

[Reality Check]

I just noticed this--it's an example of a typical Creationist tactic. They pick two living organisms, and say "There's no way this current organism can evolve into this other current organism! Evolution is wrong!!!!!"

It is also a typical ID tactic. PZ Meyers calls this the cousin problem:
How not to examine the evolution of proteins

The cousin problem. You should have picked up on the key problem from my short description above: they picked two extant proteins and then asked how they could have evolved from each other. Imagine if I picked one of my many cousins — say, the tall, red-headed Mormon fellow from Oregon, or the slender fan of horses in California — and started enumerating our many differences and declared that I couldn't possibly have evolved from either of them. You would rightly stop me and suggest that maybe my problem is that I didn't evolve from my cousins — that maybe the smarter approach would be to look at our respective parents, and the grandparents we have in common, and trace the lines of descent.