DNA Says Evolution Unfolds According to a Plan

[Edtharan]

I don't see the relevance of convergent evolution. What is it that you have determined in foresight, rather than in hindsight, by noticing that birds and bats (and bees?) have wings and fly? They all also absorb oxygen through respiration, so what?

It shows that there are general solutions to challenges faced in survival. This is important.

 

No two organisms, even of the same species, are phenotypically identical any one regard. Therefore, we can always discern some difference or other in a given "trait" across individuals. Therefore, by your definition, any feature of an organism is a "trait." And, so, by defining everything, you've defined nothing.

Yes, any feature is a trait. But, what is important is that such traits can then be examined to see if they provide an advantage, disadvantage (or neither) and how they develop. It is by looking at what is measureable and defineing what is meant in certain contexts that the word "trait" becomes important. Basically, yes, it is jargon and means very little to those who don't know the jagon, but it is still a very important word.

 

Take, for example, the jargon (from my own skill set): "Case".

 

Now, most people will have some sense of what this word means. But, in the context of programming, it has a very specific meaning, and, more so, in the context of a specific programming language it will havea slightly different meaning than in another programming language.

 

In the everyday language, this word can mean: a specific example or even a box like object to hold things. But, in the context of the programming language of C++, it means: a branching statement that examines multiple options and chooses which first means the criteria.

 

As you can see, that seems like a very different definition of the word "Case" than common language would suggest and is pretty meaningless to anyone who doesn't know the subject of programming. Such as it is with any jargon. Thus the use of the word "Trait" in biology, might seem to be meaningless, but it has a very specific useage and it also depends on the context and knowledge of the subject before it makes sense.

 

The purpose of the word "Trait" is to allow biologists to know what each other is talking about. If one biologists uses the trait of eye colour, then the other biologists know that they are talking about no only the colour of the eye, but the genes that define eye colour and the developmental pathways and chemical reactions needed to produce it. So as you can see, the word "Trait" is actually very important as it allows scientists to better understand what each other is talking about, however, to someone who is not a biologists, and does not understand why they need a word for that particular use, then it does seem like a meaningless word

 

Wait a minute. Let me indulge a privilege that you Darwinian evolutionists seem to take for granted. Let me make up a story.

 

First off, whether eye color, or any other "trait", conveys any significant advantage or disadvantage depends, as you folks like to insist, on the environment. That includes the social environment. I imagine that if blue eyes ever pop up in a jungle village in equatorial Africa, the person is considered an oddball, or worse, and probably sexually selected against. Hence, eye color can bestow a disadvantage.

 

For any difference in "traits" among organisms or species that you care to cite, I'll make up a story about how the difference came to be in terms of "advantage" and "disadvantage." That's all Darwinian evolutionists do anyway. We can all make up stories.

And this is exactly why the word needs to exist. By allowing biologists to understand that they are discussing something the organism has and that there is a variation between the organisms and it is this variation that is the topic of the discussion.

 

So by identifying that it is the trait of eye colour rather than the trait of social bigorty that caused the disadvantage they have made it clear to the other what is being discussed.

 

Remember, the word "Trait" does not convey anyhting about advantage or disadvantage (or if it is neutral). So by pointing out that a trait can be advantagious or disadvantagious is meaningless. It is like pointing out that a particual car can come in Red or White colours. It makes no difference to the make and model of the car.

 

Yes, but you can keep making finer distinctions all the way down to indiscernability. If creature A produces X amount of vitamin C in time Y, then that's a "trait". If creature B produces half as much in the same time, then that's also a "trait". If creature C produces half that much in infancy and production tapers off in adulthood, at a given rate, that's also a "trait". And on and on. What if it tapers off at a variable rate? We can make all the distinctions you want, and they're all "traits". So no matter what genes get passed on, you can point to a "trait" that accounts for the "advantage" that produced the genetic outcome, thereby explaining nothing.

Bu the fact is, you can still make a distinction between them or you would say that they were identical. The fact that there is a "measurable difference" between them means that it can not be indecernable.

 

In each of the above examples you gave, there are definitly differences so this means that they are not indecernable as you argued (thus you contradict yourself). Not only that, each of these examples would have different developmental pathways and DNA structures governeing their behaviours. In that respect, looking at them as different Traits is exactly what is they correct thing to do.

 

Not only that, you had to use the term "Trait" to describe these differences. can't you see, you are having to use the term "Trait" just to construct your argument that the word trait is unnecesary. In otherwords, before you can even begin to argue against it, you have had to accept that it is true. It is therefore logically impossible for you to argue your point because if you prove argument is true, then you have just falseified your own argument.

 

I won't make it happen again, but you can see how your concept of "trait" evaporates from its own incoherence.

Only if you use the general terms in place of the specific term, but then that applies to any technical term (and almost any word too). Have a read of this: http://en.wikipedia.org/wiki/Equivocation

 

Or, are you using words in inappropriate ways? Find better words. Central to my argument is the claim that the language of Darwinian evolution is riddled with mumbo-jumbo, empty concepts that evaporate under examination.

 

If you're not being understood, then maybe you're expressing yourself poorly.

Ok, have a go at this example:

 

What is the meaning of this word: Live

 

Well for one it can actually be 2 different words. Live as in to Live, or Live as in a live wire. It is only through the context that the word is in can you give a definite menaing for that word. Also, each of those words has several meanings, so even if you were to know the pronunciation of the word (and so know what the word was), there is still a lot that is needed that can only be got from the context that the word is found in.

 

And this is why you are having a problem with the word "Trait" as the meaning of the word in the context of biology is different to the meaning of the word in general speech. You keep confusing the two and thus you end up with something that seems to be meaningless.

 

Oh, I get it. Improvements ceased once the bacteria arrived. After all, nobody can claim greater reproductive success than those little buggers. They really know how to do it! Whew!

 

But then, no other kinds of creatures should exist, because superior reproductive success determines every evolutionary outcome. Or is that not what you said?

Ok, here you begin you mistake that you repeat for the rest of your post.

 

First of all: "Reproductive Success" is not the same as "Number of Offspring".

 

I said that it wasn't in my first post, but you seem to have either missed it or "conveniently" left it out.

 

Reproductive success is about whoes offspring survive to breed. Yes, this can be done with large numbers, or it can be done by having a few offspring but you assist them in surviving to breed (and many other strategies too).

 

It is your mistake to assume that it is only about the number of offspring you have.

 

Wow. You're really good at telling stories.

SO it is alright for you to use hypothetical examples and thought experiments, but not for anyone else.

 

As you posted above: "Let me make up a story." This is being obviously hypocritical don;t you think.

 

Do ecological niches exist independently of the organisms that fill them? Or are they defined by their occupants? Is average temperature sufficient to define a niche? Temperature and water salinity? Temperature, salinity, and the density of predators? "Niche" is, if not an essential, at least a supporting concept in evolution theory, but it amounts to a conceptual blur. Nobody can say what the necessary and sufficient conditions are to define a "niche." (more at http://starlarvae.bl...-undefined.html )

A Niche is something that an organism can exploit to avoid competing with other organisms. There are many variations of environmental factors, and one of them is the organisms in it. So a nech can be created by organims, or it can exist indipendent of the organisms. However, if an organisms can't exploit it then it doesn't get defined as such.

 

And I just know you are going to try and say that it makes it a meaningless defintion, but then this would be your mistake. The reason is that it does create a distinction between two (or more) situations: That an organism can/does exploit a particular variation, or that it can't/doesn't exploit it.

 

No, we don't know beforehand what the outcome will be. Recall the law of unintended consequences. The genetic modification you suggest might make the crop more susceptible to other kinds of threats, such as fungi or bacteria. It might make the crop sterile. It might make it unpalatable and so unmarketable. It might have all kinds of unintended consequences.

Sure, there are many complexities, but we can know that the change would solve a proble the organism faced and that without other complications that might occur it will have an advantage.

 

So what, there a degree of uncertanty in the change, it might cause an unforseen complecation. But remember this is a "might" and it is not a certanty. It might have some other effect that give the organism a massive and unforseen advantage too, but that would not have fit with what you want to believe would it so you didn't let that enter as a possiblilty. ALso, it might not have any other effect at all and work exactly as anticipated.

 

See, there are other options you are ignoreing here. But, the important thing is that the problem that existed (thus had a certainty) is solved.

 

Humans have only just begun to understand the complexities of genetics and ecologies. So yes, due to our imperfect knowledge we will have unforseen complications. But not all of the change we make will have unforseen complications, and as we learn of these unforseen complications they will no longer be unforseen.

 

You won't know if you've "improved" the crop until you see what sprouts and what fruit is yields. That's why lands are set aside for "experimental" crops -- to see what actually happens. If you were right, there'd be no need for such testing.

If we had full knowledge of genetics, biological chemistry and ecology, then we wouldn't need to make these experiments, however, as humans have only just begun to learn how all these work, we do need to perform experiments.

 

Part of the problem is to do with interactions.

 

Are you familiar with: The traveling salesman problem (see this if you aren't: http://en.wikipedia.org/wiki/Travelling_salesman_problem )

 

This problem has to do with combinations too. With the traveling saleman problem the number of ways he can travel between the cities is dependent on the combinations of cities. With just 3 cities there are just 6 different ways to combine the cities into a path for the salesman to travel.

 

However, this increase massivly as the number of cities increases. With 4 cities there are 24 posible paths (that is just with 1 more city). With 10 cities there are 3,628,800 possible paths. With 20 cities there are 2,432,902,008,176,640,000 paths.

 

Now, in the Human genome there are around 23,000 protine coding genes. Of course there are not as many combinations between these are there would be if they were cities in the travelling saleman problem, but we don't know what combinations there are until we examine them, so we have to proceed as if it were equivelent to the traveling saleman problem untill we learn differently.

 

Now, lets look at the time to solve these kinds of problems: If, with the traveling salesman problem, we could check 1 every second (very slow I know), for 10 cities, it would take around 42 days to solve. For 20 cities it would take around 77,146,816,596 years. That is longer than the universe has been around!

 

Think of the time it would take for 23,000 cities.

 

The experiments we do allow us to take shortcuts, they allow us to make a change without knowing the full consiquences of the change, and then seeing what it consiquences it has. It allows us to prune out many potential combinations and thus dramatically reducing the number of things we have to considder when makeing future changes.

[starlarvae]

Yes, any feature is a trait. But, what is important is that such traits can then be examined to see if they provide an advantage, disadvantage (or neither) and how they develop. It is by looking at what is measureable and defineing what is meant in certain contexts that the word "trait" becomes important. Basically, yes, it is jargon and means very little to those who don't know the jagon, but it is still a very important word.

If you think I'm misconstruing what evolutionary biologists intend when the use words like "trait", "niche" "adaptation", "advantage" etc., then give me operational definitions for those terms.

[starlarvae]

Again exactly what is predicted by the theory of evolution. New things don't just magically appear out of thin air; descent with modification requires the ancestors to have similar bits to the descendants. Does that make the genes "anticipatory"? No, the genes have to have a function in the organism in question. And the comparison to an embryo and adult is a false comparison, since the organism uses its genes none of those genes are anticipatory.

The results keep coming in. take a look at this from U of Chicago:

 

Genetic switch for limbs and digits found in ancient fish --- http://www.uchospita...10711-limb.html

[Cap'n Refsmmat]

How does that article support your hypothesis, exactly?

[pantheory]

starlarvae,

 

Something funny is afoot in the biological sciences. Labs peering into DNA are seeing things that nobody expected. And because the received view of evolution failed to predict these findings, and because it has little room to incorporate them, a crisis is brewing for the theory. Something more than selecting random variants is going on in evolution.

There are lots of well know variations to evolution other than natural selection. But the model of natural selection is so well documented by evidence that you could bet your life, my life, and your family's life against a six pack that the theory is valid and still be certain that you have taken advantage of some misguided young-Earth creationist. In the next 50 years plus or minus, this theory will move into the "proven" category like the Earth is round theory. Most other present mainstream theories will not last that long and will certainly be replaced in total, in my opinion, so I believe you are totally concerned with the wrong theoretical target.

 

The evidence for natural selection is overwhelming and is the primary facet of evolution as a whole which has a number of known variations unrelated to natural selection but still totally consistent with the over-all evolution model. "Seeing things that nobody expected" is not a valid criticism since alternative explanations are almost never available to the public, press, or mainstream theorists at any level since it can only be found in alternative journals which nobody reads. Almost everything that can be imagined can be found there.

 

• Addressing your concerns one by one.

1. Junk DNA. It has been very well known for at least 30 years that most DNA of all organisms are inactive and seem to serve no purpose.

 

2. Conservation of DNA. It has also long been know, for at least 30 years, that epigenetics is a major player in evolution and that genes alone are only a part of the game. Epigenetics not only determines which genes are turned on or off but that junk DNA determines how the genome is folded which determines which genes are turned on or off. With epigenetics much less gene variation is required between organisms.

 

3. Genetic switches. Although regulatory genes are not junk, whether they are turned on or off for a particular gene sequence. is related to DNA folding and consequently junk DNA.

 

4. Anticipatory genes: Are nothing special. They are genes that control DNA sequences that are more readily influenced by internal environmental factors such as hormonal and other protein produced internal chemistry. This is an active part of research today concerning which genes might be influenced by organic chemistry and drugs.

None of this knowledge challenges the present day theory of evolution in any way nor challenges the original natural selection model. Most of these factors have long been known to be different avenues of evolution other than only natural selection.

Edited July 28, 2011 by pantheory

[starlarvae]

How does that article support your hypothesis, exactly?

A developmental model of evolution, which I advocate, predicts that genes necessary for descendant phenotypes will be present already in ancestors, hence the relevance of the article. According to a developmental model, innovation among phenotypes need not depend solely, or even very much, on new or mutated genes. Epigenetic innovation is sufficient to produce phenotypic diversity, as we see in cell differentiation during the development of complex organisms. Evolutionary theorists increasingly are borrowing developmental mechanisms to explain how evolution proceeds in the light of new genomic, epigenetic, and related discoveries. I say, let's stop pussyfooting around and just recognize evolution as a developmental -- ontogenetic -- process.

[Cap'n Refsmmat]

A developmental model of evolution, which I advocate, predicts that genes necessary for descendant phenotypes will be present already in ancestors, hence the relevance of the article. According to a developmental model, innovation among phenotypes need not depend solely, or even very much, on new or mutated genes.

Which part of the article supports this hypothesis?

[pantheory]

A developmental model of evolution, which I advocate, predicts that genes necessary for descendant phenotypes will be present already in ancestors, hence the relevance of the article. According to a developmental model, innovation among phenotypes need not depend solely, or even very much, on new or mutated genes. Epigenetic innovation is sufficient to produce phenotypic diversity, as we see in cell differentiation during the development of complex organisms. Evolutionary theorists increasingly are borrowing developmental mechanisms to explain how evolution proceeds in the light of new genomic, epigenetic, and related discoveries. I say, let's stop pussyfooting around and just recognize evolution as a developmental -- ontogenetic -- process.

It would seem that the active genes which determine species were originally acquired by mutation. Much of the inactive genes were also acquired by mutation. Of course there are other factors involved, some of which have been discussed. The largest secondary player briefly discussed was epigenetics.

 

There are at least two other known players than mutation that assist in genetic flow and species determination. The first one involves "epi-genetic speciation," also having other names, and the second agent is called "cross genetic flow," also having other names to it. These two are not exactly in competition with natural selection but certainly play some part in genetic flow and speciation in general but ultimately involve natural selection to continue the existence and/or "improvements" of new species. I will briefly explain the details of each:

 

Both of these processes are a type of instant speciation. There are several other known and possible agents for speciation (more speculative) that I won't discuss.

 

First concerning epi-genetic speciation: It involves external agents like radiation, many types of chemicals, whether natural or organic via food, ingested, inhaled, puncture wounds, etc., or internal errant excretion processes. All organisms have two systems concerning there genetic character. One is called its gene structure each of which contains long stands of DNA. And secondly their epi-genetic system, which determines which DNA strands of particular genes are active and which are not (turned on or off). For all organisms most DNA strands concerning potentially active strands, are inactive (turned off). Through epigenetic changes through the mentioned processes, conceivably a new species could be created by a single individual, usually a female (in plants or animals) when sex is involved. Some of the same processes can also create DNA mutations leading to evolutionary changes by random processes which are then tested by natural selection. Some of the known epigenetic changes can be cause by radiation, by eating a foreign food/ material for instance, or random processes. The ovum DNA might be changed by foreign or aberrant internal agents in rare cases. In such cases, if a change in the genes themselves (long stands of DNA where there is a change in turning DNA on or off) occur by chance, some offspring may not be able to breed with the main stock and may only be able to bread with their brothers and sisters which have the same epi-genetic characteristics. This epi-genetic change(s) may also cause an individual to look different so that in one generation speciation has occurred. It is theory in that it has never been observed in nature but it is fact in that such epigenetic changes have occurred in the lab, primarily through radiation. Some epigenetic speciation is also thought to involve Lemarckism which relates to lifetime changes within an individual which can possibly effect its offspring in rare instances.

 

The other agent of speciation is called cross genetic flow, which also concerns a one-step process of speciation. In its most common form it involves viruses or bacteria getting into the DNA of animals (or plants) from their blood stream into their ovaries of testes. Accordingly before an animal is born and during the time of their development. If an genetic invasion happens during this formative time then the ovaries or testes will have genetic variations that can be greatly replicated in the animals reproductive organs. The animals themselves most often will be normal physically to others of their species but offspring may only be fertile concerning mating with some of its brothers or sisters respectively and may not be able to reproduce with the parent stock of animals. Again in one generation a new species might be created in this way with greatly different characteristics. The new species does not have to be better adapted, it only needs to be able to eat and reproduce with its own kind and then it will survive as a new species. All of these occurrences are rare in nature but we are aware of both viral and bacterial stands of DNA in our own genetics concerning all humans. These DNA strands do not have to be active but they change the folding of our DNA which determines which DNA sequences in our genome are turned on and off -- so without at least some of them, we would not be the same.

 

The same processes described above for animals also apply to plants. There are a great many things about evolution that we still do not know or understand but you can believe that natural selection will probably never be replaced as the dominant player concerning gene development, speciation, and evolution in general.

Edited July 28, 2011 by pantheory

[starlarvae]

starlarvae,

There are lots of well know variations to evolution other than natural selection.

Please elaborate. I am interested in alternative modes of evolution.

But the model of natural selection is so well documented by evidence that you could bet your life, my life, and your family's life against a six pack that the theory is valid and still be certain that you have taken advantage of some misguided young-Earth creationist.

Natural selection cannot be documented. Descent with modification can be documented. The modalities of modification are what's in dispute. There are many conceptual problems with the theory of natural selection. Jerry Fodor's recent book, What Darwin Got Wrong, is a good place to start.

 

"Seeing things that nobody expected" is not a valid criticism since alternative explanations are almost never available to the public, press, or mainstream theorists at any level since it can only be found in alternative journals which nobody reads. Almost everything that can be imagined can be found there.

Thanks for that incoherent word salad. "Surprises" are a valid criticism of a scientific theory, because surprises reflect predictive failures, and theories are supposed to be good at making predictions.

 

• Addressing your concerns one by one.

1. Junk DNA. It has been very well known for at least 30 years that most DNA of all organisms are inactive and seem to serve no purpose.

When this was discovered, it came as a surprise.

 

2. Conservation of DNA. It has also long been know, for at least 30 years, that epigenetics is a major player in evolution and that genes alone are only a part of the game. Epigenetics not only determines which genes are turned on or off but that junk DNA determines how the genome is folded which determines which genes are turned on or off. With epigenetics much less gene variation is required between organisms.

You're making my point. In the ways you cite, evolution looks like development.

 

3. Genetic switches. Although regulatory genes are not junk, whether they are turned on or off for a particular gene sequence. is related to DNA folding and consequently junk DNA.

See #2.

 

4. Anticipatory genes: Are nothing special. They are genes that control DNA sequences that are more readily influenced by internal environmental factors such as hormonal and other protein produced internal chemistry. This is an active part of research today concerning which genes might be influenced by organic chemistry and drugs.

My reference to anticipatory genes was in the context of evolution (controversial) not development (noncontroversial).

None of this knowledge challenges the present day theory of evolution in any way nor challenges the original natural selection model. Most of these factors have long been known to be different avenues of evolution other than only natural selection.

See Evolution, the Extended Synthesis for additional "different avenues."

[pantheory]

Please elaborate. I am interested in alternative modes of evolution. Natural selection cannot be documented. Descent with modification can be documented. The modalities of modification are what's in dispute. There are many conceptual problems with the theory of natural selection. Jerry Fodor's recent book, What Darwin Got Wrong, is a good place to start.

I discussed two well-known alternatives to natural selection. There are a number of other hypothesis that you can find by Googling "alternatives to natural selection." Most of these hypothesis that you can find are not considered mainstream, and many seem speculative at best, in my opinion.

 

Thanks for that incoherent word salad. "Surprises" are a valid criticism of a scientific theory, because surprises reflect predictive failures, and theories are supposed to be good at making predictions.

I agree with your statement starting with the word "Surprises." But otherwise if you cannot understand what I am saying then ask questions. Using sarcasm is simply rude and convinces nobody.

Edited July 29, 2011 by pantheory

[starlarvae]

Which part of the article supports this hypothesis?

The part about fish having genes for legs.

[Cap'n Refsmmat]

The part about fish having genes for legs.

Ah. You misread it, then. That's why I asked. Some quotes:

 

Genetic switches control the timing and location of gene activity. When a particular switch taken from fish DNA is placed into mouse embryos, the segment can activate genes in the developing limb region of embryos, University of Chicago researchers report in Proceedings of the National Academy of Sciences.

"The genetic switches that drive the expression of genes in the digits of mice are not only present in fish, but the fish sequence can actually activate the expression in mice," said Igor Schneider, PhD, postdoctoral researcher in the Department of Organismal Biology and Anatomy at the University of Chicago and lead author on the paper.

http://www.uchospitals.edu/news/2011/20110711-limb.html

 

These quotes refer to genetic "switches," which do not code for limbs or limb features but control the expression of other genes that do. The research does not say that fish have the genes to code for legs; it says that fish genes which regulate fin-making genes can also regulate leg-making genes in mice. So the genetic switch for fins was reused for limbs.

 

Fish do not have genes for legs. Mice do, and if you give them a genetic switch from a fish, it can turn on their leg genes.

[starlarvae]

Ah. You misread it, then. That's why I asked. Some quotes:

 

http://www.uchospita...10711-limb.html

 

These quotes refer to genetic "switches," which do not code for limbs or limb features but control the expression of other genes that do. The research does not say that fish have the genes to code for legs; it says that fish genes which regulate fin-making genes can also regulate leg-making genes in mice. So the genetic switch for fins was reused for limbs.

 

Fish do not have genes for legs. Mice do, and if you give them a genetic switch from a fish, it can turn on their leg genes.

 

So, it's not just DNA that is conserved during evolution, but the epigenetic regulatory mechanisms are too.

 

That would seem to compound the difficulty for Darwinian evolution theory. Evo-devo claims to account for phenotypic variety across species far exceeding genotypic variety by saying that the differences lie in the regulatory mechanisms. But it turns out, according to this research, that even the regulatory mechanisms are conserved.

 

Or at least receptivity to the mechanisms is conserved. The test would be whether the switches that activate limb and digit development in mice could be transplanted into the fish and activate, or regulate, fin development.

 

Increasingly it looks like most of evolutionary history was already pre-programmed into the early species and just took time to unfold, like tissues that differentiate from a zygote during development.

[Cap'n Refsmmat]

In this case, the epigenetic regulatory mechanisms were not "pre-programmed" to account for future development: they were programmed to account for current features (fins), and when new features developed (limbs) they didn't bother changing, since they didn't have to. How does this support they hypothesis that features such as limbs were pre-programmed? The development of limbs required the mutation of many other genes.

 

Suppose I put a natural gas line into my house to feed my water heater, and it has a cutoff valve on the outside of the house. Years later, I put in a gas-powered stove, a hot tub, a natural-gas-powered car, and a toy flamethrower on the back patio, all connected through the external cutoff valve. Was the cutoff valve developed in anticipation of the future devices, or was it merely reused by them because it was convenient?

[starlarvae]

In this case, the epigenetic regulatory mechanisms were not "pre-programmed" to account for future development: they were programmed to account for current features (fins), and when new features developed (limbs) they didn't bother changing, since they didn't have to. How does this support they hypothesis that features such as limbs were pre-programmed? The development of limbs required the mutation of many other genes.

So, the many genetic mutations needed to go from fins to limbs happened to occur in a manner that preserved genetic compatibility with the pre-existing regulatory mechanisms. That would seem to impose quite a constraint on the possible genetic changes. They would all have had to remain backward-compatible with the legacy system of regulatory mechanisms. Neat trick for natural selection to pull off.

 

Is there anything conceivable at the genetic, epigenetic, or cellular level that might be discovered that would falsify natural selection? I can't think of anything. No matter what is discovered, we can say that natural selection explains why it is the way it is. The theory is not falsifiable.

 

Suppose I put a natural gas line into my house to feed my water heater, and it has a cutoff valve on the outside of the house. Years later, I put in a gas-powered stove, a hot tub, a natural-gas-powered car, and a toy flamethrower on the back patio, all connected through the external cutoff valve. Was the cutoff valve developed in anticipation of the future devices, or was it merely reused by them because it was convenient?

Did the standard fixture on your cutoff valve, which fits all the various gas appliances, come to have its traits by a process of natural selection? I think it's a dubious proposition to look at human technologies and assume that natural selection can do whatever we can do, or works in any similar manner.

[Cap'n Refsmmat]

So, the many genetic mutations needed to go from fins to limbs happened to occur in a manner that preserved genetic compatibility with the pre-existing regulatory mechanisms. That would seem to impose quite a constraint on the possible genetic changes. They would all have had to remain backward-compatible with the legacy system of regulatory mechanisms. Neat trick for natural selection to pull off.

Well, yes; anything not compatible with the existing regulatory mechanism would never work, and hence would be selected against. Just like anything not compatible with, say, the existing circulatory and respiratory systems would never work.

 

Is there anything conceivable at the genetic, epigenetic, or cellular level that might be discovered that would falsify natural selection? I can't think of anything. No matter what is discovered, we can say that natural selection explains why it is the way it is. The theory is not falsifiable.

Do you refer to natural selection, the theory of universal common descent, or the theory of evolution as a whole (encompassing multiple kinds of selection pressure)?

 

Falsifying natural selection is easy: demonstrate that organisms do not change characteristics because of their environmental fitness. But I presume you meant falsifying the notion that existing common traits previously evolved due to natural selection -- i.e. "you can't falsify the hypothesis that wings evolved through natural selection." But that can be done: you could find evidence showing that another mechanism caused the wings to evolve, such as alien intervention; you could show that the change happened more quickly than selection pressures can account for; you could show that the proportion of the population with the trait over time grew faster than could be explained by ordinary inheritance; you could find precambrian rabbits; you could find that the trait appeared spontaneously from one generation to the next; you could find that the trait did not change for millions of years despite extreme selection pressures; and so on.

[starlarvae]

Well, yes; anything not compatible with the existing regulatory mechanism would never work, and hence would be selected against. Just like anything not compatible with, say, the existing circulatory and respiratory systems would never work.

Right. So the question is whether natural selection can account for the varieties of phenotypes, given that endogenous factors tightly constrain phenotypic variation. And the constraints keep getting tighter, as research continues to discover new constraints. Natural selection is left with little to select from.

 

Do you refer to natural selection, the theory of universal common descent, or the theory of evolution as a whole (encompassing multiple kinds of selection pressure)?

Natural selection. I have no problem with evolutionary descent with modification. The question, again, is how much modification can be credited to natural selection. A diminishing amount, it seems.

 

Falsifying natural selection is easy: demonstrate that organisms do not change characteristics because of their environmental fitness.

How would the theory of natural selection inform you as to whether any given change was due to environmental fitness or some other cause?

 

But I presume you meant falsifying the notion that existing common traits previously evolved due to natural selection -- i.e. "you can't falsify the hypothesis that wings evolved through natural selection." But that can be done: you could find evidence showing that another mechanism caused the wings to evolve, such as alien intervention;

I don't know how you would show that another mechanism was the cause. What would be an example of such evidence? If we found a wingless creature with webbed feet and a duck-like bill that layed eggs but was covered with fur, had a beaver-like tail and sported poison barbs it might be tempting to invoke aliens, but we assume instead that some crazy combination of selection pressures produced the platypus.

you could show that the change happened more quickly than selection pressures can account for;

I didn't know there was a time limit. What is it?

you could show that the proportion of the population with the trait over time grew faster than could be explained by ordinary inheritance;

What's the time limit on ordinary inheritance?

you could find precambrian rabbits;

I know about those rabbits. Their discovery would pretty much hose the whole thing. I'm only interested in debunking Nat Sel as the primary mode of modification during evolutionary descent. The established sequence in which novel forms appear I accept.

you could find that the trait appeared spontaneously from one generation to the next;

I don't think that would do it. If by coincidence a lineage got a toe cut off at a given age, the missing-toe trait would appear spontaneously from generation to generation, but that wouldn't tell us anything about selection.

you could find that the trait did not change for millions of years despite extreme selection pressures; and so on.

I don't know that amoebas or similar unicellular creatures have changed much over millions of years. How can we demonstrate whether their phenotypes persist because of, or despite, selection pressures?

[Cap'n Refsmmat]

How would the theory of natural selection inform you as to whether any given change was due to environmental fitness or some other cause?

 

I don't know how you would show that another mechanism was the cause. What would be an example of such evidence? If we found a wingless creature with webbed feet and a duck-like bill that layed eggs but was covered with fur, had a beaver-like tail and sported poison barbs it might be tempting to invoke aliens, but we assume instead that some crazy combination of selection pressures produced the platypus.

You could compare the modification to know facts about the environment and other species. If the fossil record shows that an animal developed thick, heavy fur, and various techniques (tree rings, ice cores) show that global temperatures rose rapidly around the same time, you start thinking about other possible mechanisms.

 

I didn't know there was a time limit. What is it?

What's the time limit on ordinary inheritance?

With inheritance and selection you have to consider that a trait is introduced by mutation in only one animal, and grows more prevalent as that animal's descendants outcompete other animals. A trait that appears within an entire population faster than enough generations can be bred cannot have occurred by natural selection.

 

I don't think that would do it. If by coincidence a lineage got a toe cut off at a given age, the missing-toe trait would appear spontaneously from generation to generation, but that wouldn't tell us anything about selection.

Certainly it would. It would tell us that selection is not what's causing the toe to be cut off.

 

I don't know that amoebas or similar unicellular creatures have changed much over millions of years. How can we demonstrate whether their phenotypes persist because of, or despite, selection pressures?

By examining the environments they've lived in, and how similar organisms in those environments have changed.

[starlarvae]

You could compare the modification to know facts about the environment and other species. If the fossil record shows that an animal developed thick, heavy fur, and various techniques (tree rings, ice cores) show that global temperatures rose rapidly around the same time, you start thinking about other possible mechanisms.

You'd have to show that local, not global, temps rose. But even that would prove nothing. Maybe the creature discovered a food source that promoted hair growth. And its descendants also exploited the find. Maybe a viral infection triggered the hair, and by HGT the trait persisted. Nothing to do with selection. You can always make up stories involving adaptive selection and stories not involving adaptive selection to explain a trait. Maybe the creatures were selected for longer snouts and snout length was genetically coextensive with hair length, so the lengthening hair was a side effect of the lengthening snout. We can make up stories all day.

 

With inheritance and selection you have to consider that a trait is introduced by mutation in only one animal, and grows more prevalent as that animal's descendants outcompete other animals. A trait that appears within an entire population faster than enough generations can be bred cannot have occurred by natural selection.

A viral infection could hit many individuals in a local population at the same time, producing some phenotypic expression across the population within a single generation. AND via HGT, get passed on to offspring. Such an occurrence would have no bearing on the theory of natural selection.

 

Certainly it would. It would tell us that selection is not what's causing the toe to be cut off.

Right. But you said such an exception would falsify the theory. Are you saying that the toe example falsifies the theory of natural selection? I hope not.

 

By examining the environments they've lived in, and how similar organisms in those environments have changed.

We can correlate traits and environments endlessly. If that's what the theory of natural selection comes down to, then it's not worth bothering with. As Jerry Fodor observed, to say that phenotypes are adapted to their environments is merely to say that there are such phenotypes.

[Cap'n Refsmmat]

You questioned how much modification can be credited to natural selection. My examples do not have to falsify the theory of natural selection entirely -- merely show it is possible to determine if natural selection applies in certain cases. There's not much point falsifying the hypothesis "natural selection occurs" because we've seen it occur. The question is a matter of scale.

[pantheory]

starlarvae,

 

.....Is there anything conceivable at the genetic, epigenetic, or cellular level that might be discovered that would falsify natural selection? I can't think of anything. No matter what is discovered, we can say that natural selection explains why it is the way it is. The theory is not falsifiable.

There is probably more evidence to support natural selection than any other theory in all of science today so it is probably the most certain theory. Since we know of other mechanisms that can produce speciation, like epigenetics for one, the only question left might be, is natural selection the prime cause of speciation? The evidence is very great that it is but if someday, somehow, they might prove that epigenetics was the prime cause of speciation, it could never discount the major role that natural selection plays in determining evolution. The only way that I can think of concerning "disproving" the theory of natural selection, would be to provide irrefutably evidence that there is a more important cause for speciation. One could never discredit natural selection as a major player in speciation since there is too much evidence to support it, in my opinion.

/

Edited August 10, 2011 by pantheory

[finiter]

What is particularly striking about these findings ..... evolutionary process look an awful lot like a developmental process, like a stage, or stages, in the life cycle of a developing organism.

Is this your original idea, or is it that you represent a school of thought? I also subscribe to that idea. In my opinion, it is the expansion of the universe (more than anything else) that maintains life. The expansion itself is programmed to end at a finite time and then the universe contracts back to the original state because the universe is built up of particles having energy as quality (it is just my proposal). If it is so, the half way of expansion (say, a period of 100 million years at the midway) will be the time when intelligent beings having consciousness will appear in the universe. From the primitive life to consciousness, the evolution is a programmed one. To be more basic, consciousness is programmed in matter.

[starlarvae]

You questioned how much modification can be credited to natural selection. My examples do not have to falsify the theory of natural selection entirely -- merely show it is possible to determine if natural selection applies in certain cases. There's not much point falsifying the hypothesis "natural selection occurs" because we've seen it occur. The question is a matter of scale.

Right. And the debate now, coming out of the "Extended Synthesis" and Jerry Fodor's critique, among others, is whether natural selection deserves its status as the primary shaper of phenotypes. I'm looking forward to the de-throning of natural selection.

 

Is this your original idea, or is it that you represent a school of thought? I also subscribe to that idea. In my opinion, it is the expansion of the universe (more than anything else) that maintains life. The expansion itself is programmed to end at a finite time and then the universe contracts back to the original state because the universe is built up of particles having energy as quality (it is just my proposal). If it is so, the half way of expansion (say, a period of 100 million years at the midway) will be the time when intelligent beings having consciousness will appear in the universe. From the primitive life to consciousness, the evolution is a programmed one. To be more basic, consciousness is programmed in matter.

I make my basic case at www.starlarvae.org. The Phylogeny and Ontogeny pages are a little dated - I'm working the edits offline.

 

starlarvae,

 

There is probably more evidence to support natural selection than any other theory in all of science today so it is probably the most certain theory. Since we know of other mechanisms that can produce speciation, like epigenetics for one, the only question left might be, is natural selection the prime cause of speciation? The evidence is very great that it is but if someday, somehow, they might prove that epigenetics was the prime cause of speciation, it could never discount the major role that natural selection plays in determining evolution. The only way that I can think of concerning "disproving" the theory of natural selection, would be to provide irrefutably evidence that there is a more important cause for speciation. One could never discredit natural selection as a major player in speciation since there is too much evidence to support it, in my opinion.

/

 

What if I said that when cells differentiate during development, from a unicellular zygote to the many tissue types of a complex organism, their form and functions are shaped by natural selection -- that as the zygote divides into two, four, eight cells, and so on, slight variations occur and natural selection takes over to determine the forms of the cells that make up the adult of the given species. The types of cells that result -- muscle, nerve, skin, etc., -- emerge over time because they turn out to be the most fit, in the given environment, compared to other possibilities.

 

How would you falsify this hypothesis?

[pantheory]

starlarvae,

 

What if I said that when cells differentiate during development, from a unicellular zygote to the many tissue types of a complex organism, their form and functions are shaped by natural selection -- that as the zygote divides into two, four, eight cells, and so on, slight variations occur and natural selection takes over to determine the forms of the cells that make up the adult of the given species. The types of cells that result -- muscle, nerve, skin, etc., -- emerge over time because they turn out to be the most fit, in the given environment, compared to other possibilities.

 

How would you falsify this hypothesis?

This supposition can easily be disproved. Take a few dozen fertilized eggs "in-vitro." As the zygote divides, all cells except the outermost can still become any cells of the body since they are pluripotent stem cells. The outer-most cells can only form the placenta. It you separate the cells from each other and from their surrounding chemistry, they will not differentiate into any particular cell type, which has been proven based upon their surrounding environment, chemistry, electrical, etc. and linkage of agglomeration. If the process is unimpeded, a sequence of events concerning development of progressive cell types can be predicted for all normal fetuses. Such a process would be unrelated to natural selection (survival of the fittest) to the extent that those zygotes that are genetically unfit will not survive. The natural environment in utero is controlled by the mother. Natural selection could involve which fetus might survive, but not what kind of cells will develop. This would only occur in the rare instances of mutations.

/

Edited August 13, 2011 by pantheory

[starlarvae]

starlarvae,

 

This supposition can easily be disproved. Take a few dozen fertilized eggs "in-vitro." As the zygote divides, all cells except the outermost can still become any cells of the body since they are pluripotent stem cells. The outer-most cells can only form the placenta. It you separate the cells from each other and from their surrounding chemistry, they will not differentiate into any particular cell type, which has been proven based upon their surrounding environment, chemistry, electrical, etc. and linkage of agglomeration. If the process is unimpeded, a sequence of events concerning development of progressive cell types can be predicted for all normal fetuses.

How does this predictability falsify my "hypothesis" that cellular differentiation is due to natural selection? Whatever environment the embryos develop in selects the surviving cell types according to fitness. Whether those types can be predicted is irrelevant. You know the story about the moths that were selected for dark pigment when air pollution made the surfaces of their environment darker? That evolutionary response might have been predictable, but predictability doesn't mean that natural selection is not at work.

 

Such a process would be unrelated to natural selection (survival of the fittest) to the extent that those zygotes that are genetically unfit will not survive. The natural environment in utero is controlled by the mother.

It doesn't matter who or what "controls" the environment. The intrauterine environment selects which cell variants survive as the cells differentiate. Call it descent with modification, or adaptive radiation, or whatever evolutionary term you care to use.

 

Remember, I'm defending a straw man, here. My point is to make the case that you can explain descent with modification equally well by invoking natural selection or life cycle. Neither one is falsifiable in either context : development or evolution.

 

Natural selection could involve which fetus might survive, but not what kind of cells will develop. This would only occur in the rare instances of mutations.

Edited August 15, 2011 by starlarvae