DNA Says Evolution Unfolds According to a Plan

[CharonY]

That's easy to say in hindsight. But I suspect that if someone asserted the presence of significant amounts of noncoding DNA BEFORE it was discovered, the mainstream evolutionists would have dismissed the idea. "Why would there be noncoding DNA? It would just get in the way. And besides, where would it come from? "

 

IF it is "what physiologically is expected" why did no one expect it? If you have a reference to someone predicting the discovery of large amounts of noncoding DNA, I'd like to see it.

 

Dude, you are still operating under the wrong assumption what junk DNA is. It was very well known that gene expression is dependent on stimuli and is necessary for cell differentiation. Just following logic, how the heck are cells supposed to differentiate when there are no expression differences. Also, gene expression analyses have been done for ages. This would be quite futile if there were no differences to be expected, no?

 

Also non-coding DNA with regulatory functions are VERY well known. How, do you think, is transcription regulated (textbooks may help you here). A surprise were the detection of functional sRNAs (they were simply not known as class and have not been detected).

Seriously, read a basic genetics textbook and then we can discuss some more. I see little value in discussing erroneous assumptions.

Edited December 23, 2010 by CharonY

[Sisyphus]

Putting aside the issue of whether junk DNA was a "surprise" and assuming it was, what significance is attached to that? Whence comes this requirement that all practical consequences of a theory be deduced before they are observed?

[swansont]

Right. I know that the theory itself has evolved. All I'm humbly proposing is yet another modification.

 

Can't you test this? Say, by checking to see if an organism does or does not have a gene which helps it survive under some new condition? And if it lacks that gene, that the gene shows up in some later generation?

[Ringer]

I did mean what I say, but when I say that I don't try to say that a single statement is the whole of the theory. It's an obvious oversimplification that is used as to avoid being long winded, I suppose I assumed that was understood so allow me to restate. the idea of natural selection is that natural variation among populations will allow certain alleles that are better suited to an environment to reproduce better than those that are not as well suited. These alleles can be anything from size, color, metabolism, etc. Natural selection is not mutually exclusive to other explanations of evolution, such as HGT, nor does it disallow random variation without consequence such as genetic drift. Again this is a somewhat oversimplification but i assume you know what I mean.

 

The reason it looks like a development process is because we are looking at it after the fact, and that it IS a developmental process. But that does not mean that genes are were already there waiting to be used since the beginning of life. And if these genes were in fact present before they were needed, as what I think you are saying, then how do you explain the reason for them to be there except that they had prior knowledge that the environment will change. What purpose did they serve, and if they served none; why would they be there if they were not aware that something could change.

 

Also, if genes needed for future populations were already present in ancestral populations wouldn't it be reasonable to assume that all DNA sequences should be almost entirely the same. Why would genes only code for certain changes and not others?

[starlarvae]

Dude, you are still operating under the wrong assumption what junk DNA is. It was very well known that gene expression is dependent on stimuli and is necessary for cell differentiation. Just following logic, how the heck are cells supposed to differentiate when there are no expression differences. Also, gene expression analyses have been done for ages. This would be quite futile if there were no differences to be expected, no?

 

Also non-coding DNA with regulatory functions are VERY well known. How, do you think, is transcription regulated (textbooks may help you here). A surprise were the detection of functional sRNAs (they were simply not known as class and have not been detected).

Seriously, read a basic genetics textbook and then we can discuss some more. I see little value in discussing erroneous assumptions.

 

I don't have an issue with any of this. It doesn't pertain to the points I'm making.

 

Putting aside the issue of whether junk DNA was a "surprise" and assuming it was, what significance is attached to that? Whence comes this requirement that all practical consequences of a theory be deduced before they are observed?

 

OK. What's the cutoff? What percent of "practical consequences" of a theory should be deduced before they are observed? I thought that scientific theories were supposed to predict. At some point the mountain of surprises suggests that the theory might need to be modified.

 

I did mean what I say, but when I say that I don't try to say that a single statement is the whole of the theory. It's an obvious oversimplification that is used as to avoid being long winded, I suppose I assumed that was understood so allow me to restate. the idea of natural selection is that natural variation among populations will allow certain alleles that are better suited to an environment to reproduce better than those that are not as well suited. These alleles can be anything from size, color, metabolism, etc. Natural selection is not mutually exclusive to other explanations of evolution, such as HGT, nor does it disallow random variation without consequence such as genetic drift. Again this is a somewhat oversimplification but i assume you know what I mean.

Yes I know this, though I think the "better suited " idea is needless. Some alleles proliferate through generations more than others. We can call them "suited," "lucky," "fated," or whatever.

 

The reason it looks like a development process is because we are looking at it after the fact, and that it IS a developmental process.

It is ??!! Then you agree with me. That's my point, the evidence suggests that evolution is a developmental process.

 

 

But that does not mean that genes are were already there waiting to be used since the beginning of life. And if these genes were in fact present before they were needed, as what I think you are saying, then how do you explain the reason for them to be there except that they had prior knowledge that the environment will change. What purpose did they serve, and if they served none; why would they be there if they were not aware that something could change.

Why are liver, kidney, skin, etc., genes present already in the zygote? Because they will be needed by those descendant cell types. I wouldn't say that the zygote had "prior knowledge" , except metaphorically.

 

Also, if genes needed for future populations were already present in ancestral populations wouldn't it be reasonable to assume that all DNA sequences should be almost entirely the same. Why would genes only code for certain changes and not others?

I'm not sure how you'd quantify "almost entirely the same", but scientists were surprised by how similar genomes are across diverse species. DNA is conserved.

 

It's all unitless. Would be a strange exponent if it wasn't.

 

How is that exponent derived? What determines its numerical value?

 

None of those links have an example of what you said.

 

Which one of those genes is unexpressed in the ancestral organism?

 

But it turns out that ancient species also carry genes that seem to anticipate the needs of descendants. A news article in Nature covering the sequencing of the genome of the Great Barrier Reef sponge Amphimedon queenslandica, reveals that the hoary creatures harbor a “tookit” of metazoan genes:

"The genome also includes analogues of genes that, in organisms with a neuromuscular system, code for muscle tissue and neurons."

A curious finding. The article continues:

"According to Douglas Erwin, a palaeobiologist at the Smithsonian Institution in Washington DC, such complexity indicates that sponges must have descended from a more advanced ancestor than previously suspected. 'This flies in the face of what we think of early metazoan evolution,' says Erwin."

"Charles Marshall, director of the University of California Museum of Paleontology in Berkeley, agrees. 'It means there was an elaborate machinery in place that already had some function,' he says. 'What I want to know now is what were all these genes doing prior to the advent of sponges.'"

The conundrum for normal evolution theory is clear. But, rather than propose that the genes needed by organisms with neuromuscular systems are in the sponge for the anticipatory purpose of providing those genes to descendants who will need them, the scientists invent an imaginary ancestor of the sponge that needed the genes. But the ghostly ancestor would have had to have arisen within a very narrow window. Fossil evidence of sponges goes back 650 million years; it constitutes, the authors note, “the oldest evidence for metazoans (multicellular animals) on Earth.” So, what use would any species even more primitive than sponges have for the neuromuscular genes? Nobody saw it coming. It was an empirical surprise.

 

But the sponge genome is only one example. Research is finding case after case of ancestral species that harbor genes essential for remote descendants. Another example: It turns out that a species of unicellular protozoan carries genes essential for metabolic processes specific to metazoans. The researchers who discovered the surprise genes and published their data (PNAS – 2010 107 (22) 10142-10147) explain,

"One of the most important cell adhesion mechanisms for metazoan development is integrin-mediated adhesion and signaling. The integrin adhesion complex mediates critical interactions between cells and the extracellular matrix, modulating several aspects of cell physiology. To date this machinery has been considered strictly metazoan specific. [. . . .]

Unexpectedly, we found that core components of the integrin adhesion complex are encoded in the genome of the apusozoan protist

Amastigomonas

sp., and therefore their origins predate the divergence of Opisthokonta, the clade that includes metazoans and fungi.

[. . . .] Our data highlight the fact that many of the key genes that had formerly been cited as crucial for metazoan origins have a much earlier origin." (emphasis added)

However, it is essentially a necessity that the ancestral organisms carried genes used by their descendants, new function or no, since the odds of entirely new genes appearing are rather slim.

I agree. But I connect the dots to argue that, if the genes are present from the get-go, then evolution looks like a developmental process.

[Ringer]

Yes I know this, though I think the "better suited " idea is needless. Some alleles proliferate through generations more than others. We can call them "suited," "lucky," "fated," or whatever.

I don't understand what you mean by saying it is needless. You mean the wording is redundant? Maybe so, but this redundancy wasn't seen as obvious so it was needed to be explained in the theory.

It is ??!! Then you agree with me. That's my point, the evidence suggests that evolution is a developmental process.

Only in the most vague sense. It is a developmental process, but that does not mean that it is planned. Any time something changes it develops something, this is what I mean when I say it is a developmental process.

 

 

Why are liver, kidney, skin, etc., genes present already in the zygote? Because they will be needed by those descendant cell types. I wouldn't say that the zygote had "prior knowledge" , except metaphorically.

But these genes are present in animals that use them. You don't find a dormant gene to develop kidneys in amoebas. The zygote has the DNA of it's parents that had those organs to begin with, that is why they are there.

 

I'm not sure how you'd quantify "almost entirely the same", but scientists were surprised by how similar genomes are across diverse species. DNA is conserved.

 

They were surprised that DNA was similar, but what I am saying is that if DNA encodes for future changes there should be no reason that all genomes should be coded for most possible changes. And if the genome was coded for changes in the environment then why is it that so many animals use different adaptations to deal with the same problem.

[Mr Skeptic]

How is that exponent derived? What determines its numerical value?

 

You put the numbers in a calculator and it will tell you the result.

 

But it turns out that ancient species also carry genes that seem to anticipate the needs of descendants. A news article in Nature covering the sequencing of the genome of the Great Barrier Reef sponge Amphimedon queenslandica, reveals that the hoary creatures harbor a "tookit" of metazoan genes:

"The genome also includes analogues of genes that, in organisms with a neuromuscular system, code for muscle tissue and neurons."

A curious finding. The article continues:

"According to Douglas Erwin, a palaeobiologist at the Smithsonian Institution in Washington DC, such complexity indicates that sponges must have descended from a more advanced ancestor than previously suspected. 'This flies in the face of what we think of early metazoan evolution,' says Erwin."

"Charles Marshall, director of the University of California Museum of Paleontology in Berkeley, agrees. 'It means there was an elaborate machinery in place that already had some function,' he says. 'What I want to know now is what were all these genes doing prior to the advent of sponges.'"

The conundrum for normal evolution theory is clear. But, rather than propose that the genes needed by organisms with neuromuscular systems are in the sponge for the anticipatory purpose of providing those genes to descendants who will need them, the scientists invent an imaginary ancestor of the sponge that needed the genes. But the ghostly ancestor would have had to have arisen within a very narrow window. Fossil evidence of sponges goes back 650 million years; it constitutes, the authors note, "the oldest evidence for metazoans (multicellular animals) on Earth." So, what use would any species even more primitive than sponges have for the neuromuscular genes? Nobody saw it coming. It was an empirical surprise.

 

But the sponge genome is only one example. Research is finding case after case of ancestral species that harbor genes essential for remote descendants. Another example: It turns out that a species of unicellular protozoan carries genes essential for metabolic processes specific to metazoans. The researchers who discovered the surprise genes and published their data (PNAS – 2010 107 (22) 10142-10147) explain,

"One of the most important cell adhesion mechanisms for metazoan development is integrin-mediated adhesion and signaling. The integrin adhesion complex mediates critical interactions between cells and the extracellular matrix, modulating several aspects of cell physiology. To date this machinery has been considered strictly metazoan specific. [. . . .]

Unexpectedly, we found that core components of the integrin adhesion complex are encoded in the genome of the apusozoan protist

Amastigomonas

sp., and therefore their origins predate the divergence of Opisthokonta, the clade that includes metazoans and fungi.

[. . . .] Our data highlight the fact that many of the key genes that had formerly been cited as crucial for metazoan origins have a much earlier origin." (emphasis added)

I didn't question whether genes were used by the descendants nor whether they were present in the ancestors, I asked which of those were unexpressed in the ancestors.

 

I agree. But I connect the dots to argue that, if the genes are present from the get-go, then evolution looks like a developmental process.

 

Not really. Development is a directional process. Evolution can go in circles or backwards, and genes are lost as well as created. And development involves inactive genes that exist specifically to be activated later in the development stage.

[starlarvae]

Natural selection isn't perfect. For example, the equation

[math]P(q) = \frac{1 - e^{-2N_esq}}{1 - e^{-2N_es}}[/math], where q is the initial frequency of the allele, Ne is the effective population size, and s is the selective advantage. This gives a probability for losing an allele, and note that a slight selective advantage is not even close to a guarantee that it won't be lost. See here for more details.

 

The result is that beneficial mutations could be lost

 

If they're lost, what makes them beneficial? The only way to determine whether an allele is "favorable" (the term used in the paper you cite), is to see whether it survives into future generations. A beneficial, or favorable, allele cannot be lost, because if an allele is lost, it is, by definition, not beneficial.

 

Really, let's say an allele arises, but fails to proliferate, and is lost. How would you determine whether it was lost because it was maladaptive or whether it was beneficial, but lost anyway, due to drift?

 

I don't understand what you mean by saying it is needless. You mean the wording is redundant? Maybe so, but this redundancy wasn't seen as obvious so it was needed to be explained in the theory.

All we know is that some alleles proliferate through generations more than others. Scientists then mystify the process with concepts like "adaptation", "fitness" and the like. Those concepts are mumbo jumbo. If we replace them with "luck" or "fate" nothing changes.

Only in the most vague sense. It is a developmental process, but that does not mean that it is planned. Any time something changes it develops something, this is what I mean when I say it is a developmental process.

No, I think that in biology "development" has a specific meaning that has a teleological dimension.

But these genes are present in animals that use them. You don't find a dormant gene to develop kidneys in amoebas.

Oh? They found a neuromuscular gene in a sponge. What was it doing there? See description of that case and links to others under heading 4 in my original post.

[Ringer]

No, I think that in biology "development" has a specific meaning that has a teleological dimension. [/size]

 

Thus why I said it is developmental in only the vaguest sense.

 

Oh? They found a neuromuscular gene in a sponge. What was it doing there? See description of that case and links to others under heading 4 in my original post.

[/size]

They found genes similar to ones that code for nerve cells and muscles; not the genes that we have. They could be doing many things, as I have said before, because our understanding of how genes interact with each other is still very limited. Just because there are genes that are similar to ones we have does not mean they interact and code for the same, or even similar, things. In the article it says that the ancestor of the sponge must have been more advanced than previously thought. It says nothing of the genes being dormant.

 

 

 

 

Edited December 27, 2010 by Ringer

[Edtharan]

All we know is that some alleles proliferate through generations more than others. Scientists then mystify the process with concepts like "adaptation", "fitness" and the like. Those concepts are mumbo jumbo. If we replace them with "luck" or "fate" nothing changes.

It is down to numbers. Replicating systems increase in population is geometric. This means that even a small advantage, over time, is massively amplified.

 

Luck is about chance. That is the process is inherently random by definition. But this process does not favour any component over another. In replicating systems, this would mean that the offspring of a replicator is no more likly to survive because it partent did than any other offspring of any other replicator. Thus, in a system based on "luck", you would not get any improvment over time. As living systems show improvment over generations tot heir environment, then it can be luck (btw: Evolution does not requier randomness, it can and does work in purely deterministic situations).

 

Adaption and Fitness are not "mysterious" at all. To put it simply: If a mutation gives an organism a greater chance of surviving, then that change will be passed on to their offspring.

 

This is because of two things:

1) When an organism replicates, it reproduces the genetics of itself.

2) If something dies before it reproduces, then it can't reproduce.

 

This is the basis of "Fitness" If an organisms surives to make a copy of itself, then that organism is "fit". If an ogranism reproduces more than another, then that organism is "more fit".

 

Adaptation is the result of this. Each mutation is only a small change and with each step the organism is "more fit". That is it has a higher reproductive sucess than others. But as many small steps occur, then this sequence of changes is called adaptation.

 

Oh? They found a neuromuscular gene in a sponge. What was it doing there? See description of that case and links to others under heading 4 in my original post.

Genes don't always just have a single function. Sure, some do, but they don't have to. Many genes are needed to get a specific function from them. The genes that go into our neuromuscular system are not just a couple of genes, but encompass quite a lot of the genes we have. Manay of these genes are also used by other parts of our bodies that are not related to neuro muscular activity.

 

Have a look at this video: http://www.youtube.com/user/cdk007#p/c/F626DD5B2C1F0A87/1/SdwTwNPyR9w

 

It is aimed at proponents of irriducable complexity, but it shows how the genes for one part of an organism can be co-opted for another part of the organism (in this case it is the genes for simple passive pores in the cell membrane can lead to a flagellum) The thing is, when it does this, the genes that the final system evolved from can still be mostly conserved and be found in organisms without that final function (but are relatged to the ancestral organism).

[starlarvae]

It is down to numbers. Replicating systems increase in population is geometric. This means that even a small advantage, over time, is massively amplified.

 

Some traits proliferate through future generations. In hindsight we call them "advantages", but all that's happening is that we are using the word "advantage" as an alternative name for traits that proliferate. Inventing the notion of "advantage" adds nothing to our knowledge, because all we know is that some traits proliferate.

 

In any event, we remain stuck with the problem of delineating a "trait". Is the lens of the eye a trait, or the whole eye? Or the eye and the optic nerve? There's no way to distinguish a trait from a non-trait.

 

 

Luck is about chance. That is the process is inherently random by definition. But this process does not favour any component over another. In replicating systems, this would mean that the offspring of a replicator is no more likly to survive because it partent did than any other offspring of any other replicator. Thus, in a system based on "luck", you would not get any improvment over time.

 

Improvement? what's that? Genes and species come and go. We can call it improvement, or attribute it to "advantages," or make up other abstractions. But we gain no explanatory or predictive power by doing so.

 

How is anything an "improvement" over bacteria? -- or cockroaches? Aren't they supposed to be so well adapted that they'd survive a nuclear war?

 

To put it simply: If a mutation gives an organism a greater chance of surviving, then that change will be passed on to their offspring.

 

The problem is that only by examining genes that get passed on can we hope to attribute to them bestowing their bearers with "a greater chance of surviving."

 

 

This is the basis of "Fitness" If an organisms surives to make a copy of itself, then that organism is "fit". If an ogranism reproduces more than another, then that organism is "more fit".

 

If it survives it survives. That's all we can observe. You can call it "fit" or "lucky" or "favored by God" or anything else. We can't observe any of those things.

[Edtharan]

Some traits proliferate through future generations. In hindsight we call them "advantages", but all that's happening is that we are using the word "advantage" as an alternative name for traits that proliferate. Inventing the notion of "advantage" adds nothing to our knowledge, because all we know is that some traits proliferate.

If you read what I wrote, then "advantage" is defined as being able to make more copies than others do. This is not limited to a single generation as it is about how many offspring the initial replicator's offspring have (as a replicator that replicates prolifically, but its offspring are non replicators will rapidly go extinct).

 

What aspects of a replicator are advantagious are not random or arbitary, so looking at these aspects and seeing if they provide an "advantage" to replication is not worthless. If such things were arbitary and only determinable in "hindsight" then there would never be a case of convergent evolution. As convergent evolution (that are traits that appear in vastly different species that don't share an evolutionary history of that trait - eg: flight in birds and flight in bats) does exist and there are thousands of instances of it, then this alone disproves your argument here.

 

In any event, we remain stuck with the problem of delineating a "trait". Is the lens of the eye a trait, or the whole eye? Or the eye and the optic nerve? There's no way to distinguish a trait from a non-trait.

Not at all. A trait is some quantifiable difference between organisms. If there were no differences between organisms, then all organisms would be identical. The fact that we can see differences between organisms means that the definition of "trait" is actually quite clear. A trait doesn't have to be good or even bad, they can be entirely neurtal as well having no impact, but if there is a difference we can call that difference a trait.

 

As an example, haivng blue eyes or brown eyes does not seem to convey any significant advantage or disadvantage, but it is a difference, so we call having blue eyes or brown eyes a "Trait". Having the ability to produce Vitamin C as part of the normal biological processes that go on in an organism is a trait, so is not having this ability (when compaired to having the ability to do so). Also a trait would be that an organism could break down cellulose by the aplication of a particular chemical secreted by them (or not having it).

 

So traits can be as big as large body changes, or as small as a variation on a chemical, but what they all have in common is that they present a difference between organisms.

 

Improvement? what's that? Genes and species come and go. We can call it improvement, or attribute it to "advantages," or make up other abstractions. But we gain no explanatory or predictive power by doing so.

You are just looking at a single word out of context and then finding that you can't make sense of it. This pretty much works for every single word in any language that exists, has existed or will exist. So you can't actually form an argument like that (it is actually an extreme form of "Quoting out of Context" logical fallacy).

 

What you have to understand, to actually be able to understand what is being discussed, is the context of a word as it is used. This is fundamental to any understanding of any language.

 

So, if you look at what I wrote and the context in which I wrote it, the meaning of "Improvment" is quite clear: It an increase in the reporoductive success of an replicator (organism in this case).

 

If a sexually reproducing species has a reproductive sucess of exactly 2 for each reproductive pair, then the population will remain stable. If this is even 0.00001% less than 2 (or even lower), then the population will decrease (and if the success does not rise, then the species will go extinct). However, if the reproductive success is any larger than 2 (no matter how small), then the population will experience geometric increase and if the success rate does not diminish, then in a short amount of time it will dominate.

 

So any change that increases the rate of reproductive success is an "Improvement". I defined it as such in the context, so your question about its meaning means that oyu were not actually reading what I was saying.

 

How is anything an "improvement" over bacteria? -- or cockroaches? Aren't they supposed to be so well adapted that they'd survive a nuclear war?

There is not just one solution to any problem, pluss, there are some limitations that can appear due to reproductive sucess that limits how successful any one species can be.

 

Looking at how there can be more than one solution to a problem, lets take a hypothetical example of being attacked by a lion. How many solution are there to this problem (that you will get out alive). Actually, the number of solutions is extremely vast, and I could not even hope to list them all (its not infinite, but large enough that it would appear to be without some other limiting factor). But for brevity I will list 3:

 

Speed: You could have the speed to outrun the lion

Defense: You could have the ability to defend yourself form it (and even here there are many, amny different options: Size, Strength, weapons, etc and all the variations of them there are too).

Heard: You could live in a group and thus are less likely to be selected as the victim, and even if you were, a heard can also help defend you where one is too weak, but many working together are strong.

 

So that is just 3 solutions to the problem of being attacked. And, remember, if you are killed by the lion, you probably won't get to reproduce (or reproduce more any way). If you live you can have offspring (or continue to have them). So this gives an "Improvement".

 

The next part of my opening paragraph of this section I mentioned that there are limits of being successful that can allow others to still exist. One that is obvious is the "niche". This where one organims expliots one area and does not compete with other organisms in other areas.

 

As you used bacteria as your example I will use it too: One species of bacteria might digest cellulose (plant matter) as their food source. Where as another bacteria might digest only sulfer compounds. These two bacteria can both happily exist without either of them ever compeating against each other and the incresased success of one does not mean that the other has to have decreased success.

 

Another situation is one of symbiosis, where the success of one species gives an advantage to another species. Take humans for example. If you count the number of individual cells, we have more bacterial cells than human cells. However, if we were to remove many of these bacterial cells, we will end up sick or even dying. Much of our ability to digest food comes not from us, but from the bacteria living within our guts. If you removed them then wwe coudl not digest food and we would starve to death.

 

But, the more successful humans are, the more successful these bacteria are. So any advantage we have gives an advatage to the bacteria living on us. This not only applies to symbiosis, but also to parasites however there is not a mutual gain as is with symbiosis (which is why I used symbiosis as the example).

 

Also, there is diverse or remote environments (this is kind of related to the first situation). If two species would normally compete, but live some distance form each other, then they effectivly don't compete and thus an improvemnt in one does not cause any damage to the other. A good example is Australia. In Australia there are mammals called Marsupials, and they have taken up many niches that typical mammals do in other countries. During the past, these animals were seperated and so did not compete, so an improvment in marsupials did not effect the survivability of mammals (and the other way aroudn too).

 

These are jsut 3 ways that organisms can gain advantages and improvements without it causing any problems for other speices (there are many others too).

 

The problem is that only by examining genes that get passed on can we hope to attribute to them bestowing their bearers with "a greater chance of surviving."

Not true at all. many of the genetic experiments that are performed are done to give the resulting organisms an advantage. For example, crop speices that can produce insecticide in themselves will give an advatage over the crops that don't produce insecticide. We can know this before we put the genes to produce the insecticide into the plants. So we don't need to know which will get passed on to know which will give their bearers "a greater chance of surviving".

 

If what you are saying was true, then gene terapy would just be a random act and no industry could ever be formed by using it. However there are many, very successful bio-tech industries that exist, and the only way these industries could be repeatedly successful is if we could determine how genes will effect the survivability of organisms before they are passed on.

 

The very existance of this industry proves your argument false.

 

If it survives it survives. That's all we can observe. You can call it "fit" or "lucky" or "favored by God" or anything else. We can't observe any of those things.

But the survivability is not random or arbitary. If it is "luck" then it is by definition random. If it is "fate", then it is favoured by the Gods by definition. But as it is neither fate, nor luck that determines survivability, then your argument is false.

 

Yes, even with the right genes there is a small amount of randomness to it, but it is not totally random (which is necesary for it to be considdered luck).

 

If we are defining "Fitness" as "the number of its offspring that survive to reproduce", then yes, all we will observe is survivabiltiy - because that is exactly what we are looking for. The only difference between what I am saying and what you are syaing is that you keep insisting on treating it as completely random or completely determinisitic. It is neither and both at the same time (that is it is neither completely random nor completely determinisitc, but it has some random aspects and some deterministic aspects).

 

Because it has both, you seem to want to think the whole must be one or the other. This is actually a logical fallacy (see: http://en.wikipedia.org/wiki/Fallacy_of_division ).

[starlarvae]

What aspects of a replicator are advantagious are not random or arbitary, so looking at these aspects and seeing if they provide an "advantage" to replication is not worthless. If such things were arbitary and only determinable in "hindsight" then there would never be a case of convergent evolution. As convergent evolution (that are traits that appear in vastly different species that don't share an evolutionary history of that trait - eg: flight in birds and flight in bats) does exist and there are thousands of instances of it, then this alone disproves your argument here.

 

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?

 

Not at all. A trait is some quantifiable difference between organisms. If there were no differences between organisms, then all organisms would be identical. The fact that we can see differences between organisms means that the definition of "trait" is actually quite clear. A trait doesn't have to be good or even bad, they can be entirely neurtal as well having no impact, but if there is a difference we can call that difference a trait.

 

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.

 

As an example, haivng blue eyes or brown eyes does not seem to convey any significant advantage or disadvantage, but it is a difference, so we call having blue eyes or brown eyes a "Trait".

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.

 

Having the ability to produce Vitamin C as part of the normal biological processes that go on in an organism is a trait, so is not having this ability (when compaired to having the ability to do so).

 

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.

 

Also a trait would be that an organism could break down cellulose by the aplication of a particular chemical secreted by them (or not having it).

 

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

 

What you have to understand, to actually be able to understand what is being discussed, is the context of a word as it is used. This is fundamental to any understanding of any language.

 

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.

 

So, if you look at what I wrote and the context in which I wrote it, the meaning of "Improvment" is quite clear: It an increase in the reporoductive success of an replicator (organism in this case).

 

If a sexually reproducing species has a reproductive sucess of exactly 2 for each reproductive pair, then the population will remain stable. If this is even 0.00001% less than 2 (or even lower), then the population will decrease (and if the success does not rise, then the species will go extinct). However, if the reproductive success is any larger than 2 (no matter how small), then the population will experience geometric increase and if the success rate does not diminish, then in a short amount of time it will dominate.

 

So any change that increases the rate of reproductive success is an "Improvement". I defined it as such in the context, so your question about its meaning means that oyu were not actually reading what I was saying.

 

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?

 

Looking at how there can be more than one solution to a problem, lets take a hypothetical example of being attacked by a lion. How many solution are there to this problem (that you will get out alive). Actually, the number of solutions is extremely vast, and I could not even hope to list them all (its not infinite, but large enough that it would appear to be without some other limiting factor). But for brevity I will list 3:

 

Speed: You could have the speed to outrun the lion

Defense: You could have the ability to defend yourself form it (and even here there are many, amny different options: Size, Strength, weapons, etc and all the variations of them there are too).

Heard: You could live in a group and thus are less likely to be selected as the victim, and even if you were, a heard can also help defend you where one is too weak, but many working together are strong.

 

So that is just 3 solutions to the problem of being attacked. And, remember, if you are killed by the lion, you probably won't get to reproduce (or reproduce more any way). If you live you can have offspring (or continue to have them). So this gives an "Improvement".

Wow. You're really good at telling stories.

 

The next part of my opening paragraph of this section I mentioned that there are limits of being successful that can allow others to still exist. One that is obvious is the "niche". This where one organims expliots one area and does not compete with other organisms in other areas.

 

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 )

 

 

As you used bacteria as your example I will use it too: One species of bacteria might digest cellulose (plant matter) as their food source. Where as another bacteria might digest only sulfer compounds. These two bacteria can both happily exist without either of them ever compeating against each other. . . .

 

These are jsut 3 ways that organisms can gain advantages and improvements without it causing any problems for other speices (there are many others too).

Right. It's not a zero-sum game.

 

Not true at all. many of the genetic experiments that are performed are done to give the resulting organisms an advantage. For example, crop speices that can produce insecticide in themselves will give an advatage over the crops that don't produce insecticide. We can know this before we put the genes to produce the insecticide into the plants. So we don't need to know which will get passed on to know which will give their bearers "a greater chance of surviving".

 

If what you are saying was true, then gene terapy would just be a random act and no industry could ever be formed by using it. However there are many, very successful bio-tech industries that exist, and the only way these industries could be repeatedly successful is if we could determine how genes will effect the survivability of organisms before they are passed on.

 

The very existance of this industry proves your argument false.

 

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.

 

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.

[Mr Skeptic]

Starlarvae, I note you have yet to give an example of your claimed unexpressed genes needed for later evolutionary steps. You gave examples of expressed genes instead.

[starlarvae]

Starlarvae, I note you have yet to give an example of your claimed unexpressed genes needed for later evolutionary steps. You gave examples of expressed genes instead.

I don't think it's clear from the published reports whether, what I call, anticipatory genes are expressed or not in the ancestral genomes. The researchers aren't explicit on that point, though the notion of "pre-adaptation" apparently is acceptable to mainstream researchers -- see example here http://www.biomedcentral.com/1471-2148/10/341/abstract/

 

But your point is taken. Nonetheless, I'm not sure that it's essential for my case that the "pre-adapted" genes be totally dormant in the ancestors.

[Ringer]

I'm fairly sure they mean pre-adaptation as in something that was developed before previously thought, not developed before use.

 

Theoretically if these genes were part of an organism before they were needed and were anticipatory, there is no reason to believe that they were only that way in early evolutionary stages; in fact most of your examples are, somewhat, complex. What Skeptic is asking is why we would not be able to find these anticipatory genes by experiment, and if we are able to do so why have none been seen.

[Mr Skeptic]

Evolutionary theory does contain concepts of pre-adaptation, and that is a major reason for the need for genetic diversity. There's two ways preadaptation might exist in species: 1) as a remnant from an earlier time when a situation similar to the current/future one had existed, or 2) genetic variability might cause pre-adaptation to a situation that hasn't happened before. So for your theory you not only need to show the existence of pre-adaptation but that it occurs far more frequently than can be expected by chance.

[starlarvae]

Ringer & Skeptic, additional examples of "anticipatory" genes are given here http://www.landesbio...ermanCC6-15.pdf

 

The author presents an unorthodox explanation, but one I mostly endorse, because it concurs with my position that evolution is not a directionless, purely contingent process, but, rather, the unfolding of an inherent life-cycle program -- though, at that, subject to environmental contingencies.

 

He suggests two experiments to test the "anticipatory" idea (tho I don't recall that he uses that term):

 

1. Find a way chemically to activate the "anticipatory" genes in the ancestral species, and see if the features coded for by those genes in the descendants appear in the ancestral.

 

2. Remove the genes from the ancestral species and see if the organisms are in any way compromised.

 

I've been meaning to set up a bioengineering lab in my garage. I suppose now I have an excuse to get started.

[Pavel]

If a sexually reproducing species has a reproductive sucess of exactly 2 for each reproductive pair, then the population will remain stable. If this is even 0.00001% less than 2 (or even lower), then the population will decrease (and if the success does not rise, then the species will go extinct). However, if the reproductive success is any larger than 2 (no matter how small), then the population will experience geometric increase and if the success rate does not diminish, then in a short amount of time it will dominate.

 

So any change that increases the rate of reproductive success is an "Improvement". I defined it as such in the context, so your question about its meaning means that oyu were not actually reading what I was saying.

 

Hi, I have a couple of questions about this - what I understand to be - central idea of the evolutionary theory. There are some cases, like cancer cells or bacteria colonies, in which excessive reproduction actually kills the population. While I don't have an example from an animal kingdom, I believe it's reasonable to consider an animal population, perhaps isolated and confined to some area, which reproduces itself to death, simply because the resources become unavailable due to the overpopulation of the species. So, introducing a gene that promotes a trait that actually decreases the reproductive success is beneficial to the population. The population thrives on. Therefore, contrary to the evolutionary thesis quoted above, a gene increasing the reproductive success is not necessarily an "Improvement". In fact, it has the opposite effect. First, am I proposing a reasonable thought experiement? Second, if so, how does the evolutionary theory adjust its principle to account for the possibilities I suggested.

 

Thanks,

 

Pavel.

[Mr Skeptic]

Hi, I have a couple of questions about this - what I understand to be - central idea of the evolutionary theory. There are some cases, like cancer cells or bacteria colonies, in which excessive reproduction actually kills the population. ... So, introducing a gene that promotes a trait that actually decreases the reproductive success is beneficial to the population. The population thrives on. Therefore, contrary to the evolutionary thesis quoted above, a gene increasing the reproductive success is not necessarily an "Improvement". In fact, it has the opposite effect. First, am I proposing a reasonable thought experiement? Second, if so, how does the evolutionary theory adjust its principle to account for the possibilities I suggested.

 

You are quite right, but you misunderstood the concept of fitness. Fitness means roughly what you think it should mean than what you seem to think it does mean. As your thought experiment shows, fitness is not just about having kids. You need your kids to survive and have kids too, and their kids need to have kids too, etc. However this cannot be done in an altruistic manner else those who are lacking this altruism will prosper at their expense. So for example we have huge denial of human overpopulation, and those who don't deny it largely aren't attempting to do anything about it, and yet we do have some built-in mechanism, a reduction in fertility when we go hungry. Many species have a solution that involves investing more effort in fewer offspring when food becomes scarce, and more offspring with less investment when food is plentiful. In some species its a somewhat unsolved problem, for example predators with over-reliance on a particular prey species can have cycles of population growth and population crashes. Anyhow, when people talk about fitness they often speak of surviving offspring. This is why.

[Pavel]

You are quite right, but you misunderstood the concept of fitness. Fitness means roughly what you think it should mean than what you seem to think it does mean. As your thought experiment shows, fitness is not just about having kids. You need your kids to survive and have kids too, and their kids need to have kids too, etc. However this cannot be done in an altruistic manner else those who are lacking this altruism will prosper at their expense. So for example we have huge denial of human overpopulation, and those who don't deny it largely aren't attempting to do anything about it, and yet we do have some built-in mechanism, a reduction in fertility when we go hungry. Many species have a solution that involves investing more effort in fewer offspring when food becomes scarce, and more offspring with less investment when food is plentiful. In some species its a somewhat unsolved problem, for example predators with over-reliance on a particular prey species can have cycles of population growth and population crashes. Anyhow, when people talk about fitness they often speak of surviving offspring. This is why.

 

Hi Skeptic, thank you for the explanation. But if you have to evolve mechanisms to counter the rate of reproduction (causing overpopulation), then how can an increased rate of reproduction be considered an "Improvement"? We developed a mechanism to fight cancerous mutations. We do not consider such mutations as an "Improvement". A gene increasing the reproductive success might or might not be an improvement. If it's not, a counter mechanism has to be invoked. If so, how can we use this fitness principle for anything meaningful, like make a prediction? If I insert a gene that increases a speciemen's libido (and therefore amount of sex), it then increases the rate of reproduction, but can you predict whether it is an "improvement", because, as you say, it involves the survival of offsprings' offsprings? If so, how many generations, specifically? If you say as many generations as it takes for the gene to be in the population, then the fitness principle doesn't seem to say much. You then basically say "the gene is an improvement if turns out to be an improvement while being expressed in the population". That's a tautology, is it not?

 

Thanks again.

 

Pavel

[Mr Skeptic]

Hi Skeptic, thank you for the explanation. But if you have to evolve mechanisms to counter the rate of reproduction (causing overpopulation), then how can an increased rate of reproduction be considered an "Improvement"?

 

Well it's much easier if you consider all the children equal, then more children=better, similarly if you consider the children superior when the parents have more. But if your can have more but inferior children things get complicated. Perhaps you would be interested in the difference between r-selected and K-selected species.

 

We developed a mechanism to fight cancerous mutations. We do not consider such mutations as an "Improvement".

 

Cancer significantly decreases your reproductive fitness, so it is not surprise there. Your cells aren't individual Homo sapiens.

 

A gene increasing the reproductive success might or might not be an improvement. If it's not, a counter mechanism has to be invoked. If so, how can we use this fitness principle for anything meaningful, like make a prediction? If I insert a gene that increases a speciemen's libido (and therefore amount of sex), it then increases the rate of reproduction, but can you predict whether it is an "improvement", because, as you say, it involves the survival of offsprings' offsprings? If so, how many generations, specifically? If you say as many generations as it takes for the gene to be in the population, then the fitness principle doesn't seem to say much. You then basically say "the gene is an improvement if turns out to be an improvement while being expressed in the population". That's a tautology, is it not?

 

Here's a little secret: the only things we know are true are tautologies (by "know" here I mean absolutely certain). To prove a math theorem is true it is quite common to prove that it is a tautology. Tautologies are always true...

[starlarvae]

Well it's much easier if you consider all the children equal, then more children=better, similarly if you consider the children superior when the parents have more. But if your can have more but inferior children things get complicated. Perhaps you would be interested in the difference between r-selected and K-selected species.

Right. So more progeny does not necessarily equal greater fitness, or adaptedness. So do "fitness" or "adaptedness" retain any coherent meaning in the theory? If they don't, then what remains of the theory?

 

Cancer significantly decreases your reproductive fitness, so it is not surprise there. Your cells aren't individual Homo sapiens.

But doesn't the cancer example demolish the "selfish gene" as the putative unit of selection?

 

Here's a little secret: the only things we know are true are tautologies (by "know" here I mean absolutely certain). To prove a math theorem is true it is quite common to prove that it is a tautology. Tautologies are always true...

All right. Break it up, or you'll be banished to the philosophy forum.

 

I just started Jerry Fodor's book, What Darwin Got Wrong, so far a good dissection of NeoDarwinian logic. He leans on evo-devo to make the case that evolution theory needs to make more room--much more room--for endogenous factors. I concur enthusiastically. Evolution continues to look increasingly like a developmental process.

[Pavel]

Well it's much easier if you consider all the children equal, then more children=better, similarly if you consider the children superior when the parents have more. But if your can have more but inferior children things get complicated. Perhaps you would be interested in the difference between r-selected and K-selected species.

 

I'm not sure how that answers my question. I'm trying to get a better definition of "Improvement" given a specific gene. How would you be able to falsify your answer?

 

 

 

Here's a little secret: the only things we know are true are tautologies (by "know" here I mean absolutely certain). To prove a math theorem is true it is quite common to prove that it is a tautology. Tautologies are always true...

 

Thanks, but it's not really a secret. It is also a mistake to think that "true" is used in our language only in the analytical sense you're referencing. I'm not trying to prove theorems here, but rather make an inference to the best explanation, something every scientist wants to be good at. What I'm trying to say is that if your claim is "it's an improvement only if turns out to be an improvement", such claim is useless. How can I falsify it or what can I do with it? So perhaps the claim needs to be unpacked to make it meaningful and useful. First, what specifically do you mean by "increased rate of reproduction"? Does it refer to an individual gene, every carrier of the entire genome in the population? Secondly, what do you mean by "improvement", specifically? And does the improvement apply to the individual, entire population, or the future populations? Then we can meaningfully evaluate the claim "increased reproduction rate is an improvement".

 

Following Dawkins' notion of "selfish gene", in which you have to consider the population driven dynamics (as opposed to the individual), I don't see how "increased reproduction rate" is an improvement. Genes survive by making copies of themselves in the population in the most optimal way. Sometimes, in order to have more copies of itself, you actually need to reduce the reproductive rate of the individual. So we can talk about "improvement" for the genes, not the individuals, as the poster I quoted suggested.

 

DJP

[Mr Skeptic]

Tautologies and definitions are not falsifiable. Tautologies are true because tautologies are always true. Definitions are true because we said they are. They might or might not be useless, because they don't "tell us something we didn't know" so you could consider them useless in that sense, like all the math theorems. Definitions don't make predictions. You're looking in the wrong place for predictions and falsifiability.