Degeneration > evolution

[Arikay]

Ok.

A follow up question,
In general, which is more likely to occur an insertion mutation or a deletion mutation? (again, if we know)

As you know, what an insertion or deletion mutation does is shift the reading frame. DNA is "read" for amino acids in groups of 3 bases -- the codon. BUT, there is no punctuation. So, when you insert or delete a base you change the entire reading frame and get a completely brand new protein downstream of the insertion/deletion. How extensive that will be depends on how far into the protein the insertion/deletion happened and when the new "stop" codon will appear. Yes, you do have special codons that say "start" and "stop".

We have used one insertion mutation that created the nylonase enzyme as an example of a "beneficial" mutation. But how many others there are out there compared to the number of proteins is quite simply unknown and therefore there are no probability calculations.

 

[lucaspa]

Ok.

A follow up question,
In general, which is more likely to occur an insertion mutation or a deletion mutation? (again, if we know)

I don't know offhand, let me check. I don't find the information in Futuyma or in my Biochemistry text. Insertion mutations are readily caused by acridine derivatives. These are 3 planar aromatic rings with a nitrogen in the middle. It looks similar to flavin. Deletion is caused by alkylating or deamination agents. Proflavin also induces deletions. Many of the carcinogens are alkylating agents.

So as far as I can see, it should be a toss-up.

 

[Arikay]

Ok, thanks for the info. Im not quite sure but I think our friends argument is that natural selection doesn't favor insertion over deletion, and that deletions are more common (I dont believe he has shown evidence for this point), thus evolution can not account for life going from small DNA to a large string of DNA.
(I believe he was calling the favoring of deletion, degeneration and the favoring of insertion evolution).
At least, thats what it seems like.

So the next big question is, why does it appear Evolution favors (even slightly) the addition of genetic code over the deletion of it.

 

[Saviourmachine]

An environment change

I suggest that there is fifth possibility:
e. Be at a selective advantage compared to individuals with 2c, because the environment changed and this enzyme that was once essential is now a drawback.

From one generation to another, is there really going to be an environment change? Since the environment is everything external to the organism, why would there be an environment change just at this time?

This was what I was thinking: if the environment is changing, there’s a bigger chance that a beneficial mutation will spread fast through the population. When there occurs a environment shift, the variation in the population comes more into play (and with variation mutation).

The definition of “Information”

I do not agree with you about information. Having more proteins does not necessarily mean more "information" in the colloquial sense. Again, a lot of the "information" to make an organism comes from how long the protein is expressed in embryonic development or how many of the protein molecules are made to set up a concentration gradient.

So, the definition of “Information” is still not correct. Would you like to give me a definition you like? I mean with “Information” the amount of information bearers that can be decoded from a DNA string. That bearer can be a biological catalysator, a biological clock, a biological counter and so on, it doesn’t matter for me.

Speed
Tooth fairy, nice example! If you want to define information in the terms I describe, I can talk about speed. (I’ve only to convince you that there is some kind of information that’s increasing with time).

Harmful & harmless

Every mutation that is not harmful is harmless.

I agree with you. I meant something different. I stated that harmful mutations nothing have to do with harmless mutations. I’m differing two types of harmless mutations, so the amount of harmful mutations doesn’t matter in that case. But, anyway, thanks for the information, because I need every piece of it.

The end of post 40 is corrupted. Thanks for your energy. I’m feeling it, we’re getting closer to the issue. What do you think about the question on the end, lucaspa? Because you see so much counterexamples, I think this question should help you answer me conveniently.

My argument

I think our friends argument is that natural selection doesn't favor insertion over deletion

That’s correct. With insertion and deletion in terms of information bearers that can be decoded from a DNA string.

Corruptions of old information is more likely

and that deletions are more common

Yes, without any proof out of practice, I based that on stochastics. Information out of the environment can be pushed in an organism by natural selection in adding new or deleting/corrupting old information. When speaking about a random process that handles these additions of new information and corruptions of old information, I think the last option is easier for her. For you, field men, it’s maybe utter nonsence, but for me it sounds very reasonable.

Another question

So the next big question is, why does it appear Evolution favors (even slightly) the addition of genetic code over the deletion of it.

Your speaking about deleting and adding a single base with new information as a result. I’m speaking about corrupting old information. But this is also a question, you’re right!

The big question

We have the genes that code for a tail, then we have more genes that STOP our body from making said tail.

This is a nice example of added information. What I’m stating is that it’s for me more assumable that a random proces would destroy “the old genes that code for a tail” then creating new genes. The big question is: why doesn’t that happen?

 

[Saviourmachine]

A little survey to clearify some of my questions.

The reason for an environment change

Whether a mutation is beneficial or not depends on environment. A mutation which helps the organism in one circumstance could harm it in another. When the environment changes, variations which once were counteradaptive suddenly become favored. Since environments are constantly changing, variation helps populations survive, even if some of those variations don't do as well as others. When beneficial mutations occur in a changed environment, they generally sweep through the population rapidly [Elena et al, 1996].

Sickle cell resistance to malaria

The sickle cell allele causes the normally round blood cell to have a sickle shape. The effect of this allele depends on whether a person has one or two copies of the allele. It is generally fatal if a person has two copies. If they have one they have sickle shaped blood cells.
In general this is an undesirable mutation because the sickle cells are less efficient than normal cells. In areas where malaria is prevalent it turns out to be favorable because people with sickle shaped blood cells are less likely to get malaria from mosquitoes.
This is an example where a mutation decreases the normal efficiency of the body (its fitness in one sense) but none-the-less provides a relative advantage.

How does nature filter these mutations? Ah, I see already, they can’t conquer the whole population, because it’s a recessive gen.

The role of duplication
http://www.ncbi.nlm.nih.gov/entrez/...ve&db=PubMed&list_uids=11682312&dopt=Abstract

A duplicate gene can have several evolutionary fates: first, it becomes a pseudogene; second, it maintains redundant functions; and third, it gains new functions. Walsh [43] examined the probability that a gene duplication evolves new functions under a simplified assumption incorporating only the first and third of these scenarios. He showed that a duplicate copy is in general much more likely to become a pseudogene instead of a new functional gene. He also showed that if a duplicated gene acquires an even slightly advantageous function, then it is unlikely to become nonfunctional in subsequent evolution. Ohta [44] proposed a probability model to examine the role of neutral mutation in the evolution of new gene functions. Gu [45] proposed a statistical method to detect potential functional divergence between duplicate genes.

Duplication doesn’t explain it? Or is this not a common opinion? I should read Ohta to examine her role.

Justifying question 1
Same article

Nurminsky et al. [58] investigated the origin of Sdic, an evolutionarily new gene in Drosophila. It originated in the single lineage of D. melanogaster, after its split only three million years ago from its sibling species. Sdic is one of the two youngest genes known (the other gene, Jingwei, also in Drosophila, is under 2.5 million years old) [59]. Remarkable in the early life of this gene are the unusual origins of various of its essential parts: deletion created the chimera; a new exon evolved from an intron of the Cdic parent; and the new testes-specific promoter formed from an exon in parent AnnX. As the resources for its various parts are so dissimilar to their eventual uses, both functionally and structurally, one could scarcely have predicted that they would be connected together. These changes provide evidence of tinkerism.

The deletion that created the chimera justifies question 1. By the way, why are the youngest genes known 2.5 million, resp. 3 million years old? It’s seems to me far to old if you take in account the amount of species and their number of genes.

Justifying question 2
http://www.gate.net/~rwms/EvoMutations.html

In the case of D-arabinose, Mortlock showed that the arabinose could be utilized if it could be converted to D-ribulose by an enzyme (an isomerase). Unfortunately, K. aerogenes has no such isomerase for the conversion of D-arabinose. However, the isomerase for L-fucose has a low activity for D-arabinose. But, the bad news is that the L-fucose isomerase is normally produced only when the cell is exposed to fucose. Nonetheless, in a few individuals, mutations occurred that allowed the fucose isomerase to be produced at all times - not just when L-fucose is present. This is normally a bad thing and would be selected against because it wastes the cells resources by constantly producing an unneeded enzyme. In this situation though, the mutation is a very good thing, and allows the cell to survive because it can now metabolize arabinose (albeit rather poorly). Although production of the fucose isomerase has been deregulated, the structure of the isomerase itself has not been changed. The next mutation was a change to the isomerase to make it more effective in the conversion of arabitol to ribulose. Finally (although I can't tell from Bell's description if this was actually done in the experiments), the culture could be selected to regain control of the expression of the isomerase - so that it is produced only when arabitol is present.

Is this the way evolution occurs? Is it always possible to regain the earlier abilities? Or can evolution destroy old abilities? They mention about Xylitol, and a evolution pattern that suggests this.

Don’t look at these examples as being used for evidence. It’s only to clarify mine questions. They can be out of context, whatever. I’m still searching for a better example for question 2. Firstly, because this one is destroying a function within the same environment (with the chance of ‘back-mutation with gained abilities’). Secondly, because I think there exists mutations where this ‘back-traveling’ isn’t probable at all, because the mutation gives rise to another mutation and another and so on until it’s almost impossible to retain the anterior function.

 

[Saviourmachine]

Before we go on…

I admit that I didn’t proof my hypothese. So, I didn’t proof that Degeneration > Evolution. Nonetheless, I didn’t see any proof to the anti-hypothese. That’s why I’ve still these questions (see above). If anybody thinks he can prove that Evolution > Degeneration, please, give it a try.

So, let’s wait until somebody appears with some (stochastical) information about real life.

 

[ForeRunner]

How does nature filter these mutations? Ah, I see already, they can’t conquer the whole population, because it’s a recessive gen.

Nature filter's these mutations via natural selection. The article you posted explained it perfectly in regard to sickle-cell anemia. All mutations are random and neutral, the enviroment is what determines whether it is beneficial or not. It might help if you tell us exactly what it is about selection you don't understand.

Duplication doesn’t explain it? Or is this not a common opinion? I should read Ohta to examine her role.

Again, the article you posted answers your question, it explained exactly how gene duplication adds information. As for a common option... common compared to what? It seems to me it happens often enough.

The deletion that created the chimera justifies question 1. By the way, why are the youngest genes known 2.5 million, resp. 3 million years old? It’s seems to me far to old if you take in account the amount of species and their number of genes.

Not my field of expertise, so I'll leave this one alone. Without reading the whole article I am not certain of the context.

Is this the way evolution occurs? Is it always possible to regain the earlier abilities? Or can evolution destroy old abilities? They mention about Xylitol, and a evolution pattern that suggests this.

I still think you you don't quite understand how eveolution works. Usually it doesn't "destroy" old genes, but instead new genes supress them. And yes, old "abilities" can evolve again, what is to stop it if the enviorment selects for that?

Secondly, because I think there exists mutations where this ‘back-traveling’ isn’t probable at all, because the mutation gives rise to another mutation and another and so on until it’s almost impossible to retain the anterior function.

Not if there are 2 genes and the original still retains its function.

 

[ForeRunner]

If anybody thinks he can prove that Evolution > Degeneration, please, give it a try.

No offense, but your terminology is still terrible. Evolution is the change in a population over time, that is it. this whole evolution/degeneration thing shows that you don't really understand what evolution is. There is no forward or backward, only change. No species is "better" than another unless they occupy the same ecological niche, and one invariably goes extint. I "think" you mean does gene deletion happen more often to gene addition when it comes to evolution.

I say no. As evidence I present the genome of every complex creature on the planet. Complex creatures all have genes that supress older genes, we have genes to supress our tails, birds have genes to supress teeth, and so on. Thousands(or more) of examples can be found. Why would this happen if deletion was so much more common, it wouldn't.

 

[Saviourmachine]

Sure, my terminology is terrible, I'm struggling with my definitions. I should prefer to use biological ones, but what I'm understanding by Degeneration doesn't exist in ordinary Darwenian theory. Call it "beneficial mutations for the individual that reduce the DNA length (1) or the function set (2) of an organism". Or something like that.

I don't say anything about such an evidence, spare me. I want to know the 'how', besides.

 

[SanDiegoAtheist]

Sickle cell resistance to malaria


How does nature filter these mutations? Ah, I see already, they can’t conquer the whole population, because it’s a recessive gen.

Just addressing this one point: Whether it's a dominant or a recessive isn't really important here - though a dominant would presumably increase the penetration level more rapidly in an environment which favored it, and reduce the speed at which its penetration level would decrease in an environment which was hostile to it.

How natural selection works is based on fitness to the current environment. In other words, in middle Africa, where Malaria is a common scourge, sickle cell anemia is selected FOR, because individuals within the population which have the sickle cell genetic mutation are more likely to survive longer, and leave more offspring (with that gene), than individuals within the population that do NOT have the sickle cell mutation.

In northern Europe, where Malaria is pretty much unknown, natural selection will work in the complete opposite way - since the sickle cell mutation carries with it also the negative factor of increasing the likelihood of anemia, and this negative factor is no longer counterbalanced by the positive factor of increased protection against a dangerous and prevalent disease, individuals that have the sickle cell genetic mutation will be selected against, because they are less likely (all other factors being equal) to live as long, or parent as many offspring, as those without it.

That is why you find a very high incidence of sickle cell mutations in those of African descent, yet a much lower incidence of sickle cell in those of European descent.

BTW, it's important to state that the "populations" we're talking about are NOT the entire population of humanity, but simply the populations that reside in that one particular environment, and that are likely to interbreed with each other. This was especially important until very recently, as, say 1000 years ago, it would have been very unlikely for a person born in SE Asia to interbreed, and thus share genetic material, with someone born in N. America at the time - indeed, at that time, they were effectively reproductively isolated.

It's important to realize, I think, that filtering of genes through natural selection can take a great deal of time in many circumstances, and there are several factors which affect the rate in which this happens. For example, reproductive isolation plays a large part - if the Europeans had been completely reproductively isolated for long enough from the Africans, it's possible that the sickle cell mutation might have been completely eliminated from the gene pool for the Europeans. Similarly, if the Africans had been reproductively isolated for long enough in an environment which contained the malaria disease, sickle cell may have come to completely dominate the gene pool. As it is of course, there are some areas of Africa with little or no malaria, thus even if they had been isolated from the Europeans, sickle cell would not likely have become completely dominant.

Cheers,

The San Diego Atheist

 

[Saviourmachine]

BTW, it's important to state that the "populations" we're talking about are NOT the entire population of humanity, but simply the populations that reside in that one particular environment, and that are likely to interbreed with each other.

I think this is the most important point you're addressing. It states that a beneficial mutation will spread only through a part of the population in the particular environment what makes it beneficial. Although you didn't say so, mutations which are beneficial for more environments will more likely conquer the whole population. Mutations that are globally beneficial have a greater chance to endure time!

So a next question is: can a specie spread fast enough around the earth, before being conquered by a locally/temporary beneficial mutation?

And to repeat my old question in another way: what is the chance that after an temporary beneficial mutation the organism evolves to the old situation or jump-evolves over the old situation to the new situation?

 

[Saviourmachine]

I still think you you don't quite understand how eveolution works. Usually it doesn't "destroy" old genes, but instead new genes supress them. And yes, old "abilities" can evolve again, what is to stop it if the enviorment selects for that?

Please, do you want to prove that 'usually'? Do you have numbers?

Don't you see the point of re-evolving old beneficial abilities when overwritten by temporary beneficial abilities (and further evolution of a organism!)?

 

[Jet Black]

well yes, see, when one looks at flightless beetles and so on, one finds that rather than lose the gene that starts the wings growing, they have another one that stops them growing later. The same is true for whales legs, and human tails. it is actually extra layers of instructions, rather than the removal of old ones that causes these sorts of changes.

 

[Saviourmachine]

You've to come up with a range of experiments where the role of adaption in regard to adding/deleting instructions is surveyed.

For me, it's now still possible that it started with a beetle with many layers of instructions, and that they pelled of like from an onion in a relatively short period.

 

[Jet Black]

as I said, we already know that it is extra instructions that do these things.

 

[ForeRunner]

Please, do you want to prove that 'usually'? Do you have numbers?

Don't you see the point of re-evolving old beneficial abilities when overwritten by temporary beneficial abilities (and further evolution of a organism!)?

I did a pub-med search and found no studies for the overall deletion of mutations. The only way I can think of to get a good number is to compare our geneome with that of a direct ancestor. I am pretty sure we don't have a direct ancenstors genome to compare ours to. However, we do have cousins, so we can get an idea of how often it happens

My point, however, is still valid. Frequency is irrelevant. The proof lies in the genes that code for our tail, that code for birds teeth, whales legs, etc. Gene addition occurs, and with enough frequency as to cause geneomes to have many, many old genes that are supressed. And that occurs in ALL organisms.

 

[Saviourmachine]

My point, however, is still valid. Frequency is irrelevant. The proof lies in the genes that code for our tail, that code for birds teeth, whales legs, etc. Gene addition occurs, and with enough frequency as to cause geneomes to have many, many old genes that are supressed. And that occurs in ALL organisms.

It isn't valid, every being can be devolved from a superbeing, with wings, teeth, legs, tail and so on, with everything else possible supressed.

The only way I can think of to get a good number is to compare our geneome with that of a direct ancestor.
...
many old genes that are supressed

No ancestors, and you're speaking about old genes? Are they really old? Or should we aspect in the future human with tails, wails with legs, birds with teeth and so on?

Anyway, I'm not doubting that evolution can occur, in the cases above. But I'm still not sure about the 'common' adding feature of natural selection.

 

[ForeRunner]

It isn't valid, every being can be devolved from a superbeing, with wings, teeth, legs, tail and so on, with everything else possible supressed.

This completely contradicts all evidence we observe, and is completely preposterous. Technically anything is posssible, but we are trying to be reasonable here.

No ancestors, and you're speaking about old genes? Are they really old? Or should we aspect in the future human with tails, wails with legs, birds with teeth and so on?

What on earth are you talking about? I said we compare our genome with that of a direct ancestor. Then we document the changes and determine if additions or deletions happen more frequently, that would be the best way to determine exact percentages.

Anyway, I'm not doubting that evolution can occur, in the cases above. But I'm still not sure about the 'common' adding feature of natural selection.

Well, it doesn't matter if you are sure or not. The proof is as plain as day. It is in your geneome as well as mine.

 

[Saviourmachine]

My point, however, is still valid. Frequency is irrelevant. The proof lies in the genes that code for our tail, that code for birds teeth, whales legs, etc. Gene addition occurs, and with enough frequency as to cause geneomes to have many, many old genes that are supressed.

My problem with the term 'old' is that this assume that once they were 'current'. I'm not supposing that whales had once functional legs. Maybe if they are degenerating further, they can get them.

There are now regulatory genes that suppress the forming of
1. human tail
2. bird teeth
3. whales legs
Can you provide me information about these three examples?

I've been searching for beneficial mutations with side-effects, but that's very, very difficult. There are rearly beneficial mutations! I've found the cave fish, cave salamander, all evolved under less-demanding environmental circumstances.

 

[lucaspa]

This was what I was thinking: if the environment is changing, there’s a bigger chance that a beneficial mutation will spread fast through the population. When there occurs a environment shift, the variation in the population comes more into play (and with variation mutation).

The probability of a mutation being fixed is the same whether the environment is changing or not. It's just that, if the environment is changing, a mutation giving a change in form will be the one selected since that change in form will fit the new environment. When the environment is stable, most mutations will move the population off the fitness peak and are therefore not advantageous.

So, the definition of “Information” is still not correct. Would you like to give me a definition you like? I mean with “Information” the amount of information bearers that can be decoded from a DNA string. That bearer can be a biological catalysator, a biological clock, a biological counter and so on, it doesn’t matter for me.

I don't think there is any definition of information that can be applied to the subject. All our intuitive notions of "information" fail here. The problem is that the DNA codes for an individual organism and that organism goes thru a developmental process that amplifies what is in the DNA in ways that don't allow a linear correlation from DNA to individual. And it is the "complexity" of the organism on which we base our ideas of "information", with the more "complex" individual representing more information.

I know that isn't a satisfactory answer, especially since anti-evolutionists claim that evolution can't provide the necessary "information", but it is going to have to do. Any attempt I have seen to define "information" in an evolutionary sense has failed.

Speed
Tooth fairy, nice example! If you want to define information in the terms I describe, I can talk about speed. (I’ve only to convince you that there is some kind of information that’s increasing with time).

Again, that doesn't work. If you look at the speed an enzyme catalyzes a reaction, is that "information"? When a reaction proceeds "slowly" but very specifically, is that more or less information than a non-specific enzyme that catalyzes a reaction that proceeds faster?

What do you think about the question on the end, lucaspa? Because you see so much counterexamples, I think this question should help you answer me conveniently.

When hte environment shifts and what was an essential enzyme is no longer essential, what we see is not a "loss of information" but rather an addition of information. What happens is that a mutation appears that shuts the gene off. This is a positive action, not a negative one. And because the individual with the mutation saves the energy that would go into making and maintaining the enzyme (or structure), that positive action is selected for.

My argument

That’s correct. With insertion and deletion in terms of information bearers that can be decoded from a DNA string.

You and Arikay are talking apples and oranges. Insertion and deletion mutations simply scramble the gene and give you a different protein. What you are talking about is deletion of an enzyme or a feature, such as teeth in birds or leg bones in whales.

As I say, what we see at the detailed genomic level is not deletion, but addition of a step that says "keep this gene turned off".

Corruptions of old information is more likely

Yes, without any proof out of practice, I based that on stochastics. Information out of the environment can be pushed in an organism by natural selection in adding new or deleting/corrupting old information. When speaking about a random process that handles these additions of new information and corruptions of old information, I think the last option is easier for her. For you, field men, it’s maybe utter nonsence, but for me it sounds very reasonable.

Usually, when you screw with a sentence, you end up corrupting that sentence and losing meaning. This is what you are thinking of. However, that is in terms of the individual sentence. Instead, look at population of sentences, each having some form of variation. Then you select only those sentences that have meaning. It's tough on the individual sentence, but for the population you end up increasing information.

You are continuing to confuse what happens in an individual with what happens to a population. Evolution is what happens to populations.

Another question

Your speaking about deleting and adding a single base with new information as a result. I’m speaking about corrupting old information.

Same thing. Most of the time, for the individual, adding or deleting a single base will corrupt the old information. But those individuals die! Tough on the individual, but it does remove the corrupted information from the population. When the insertion or deletion results in new information, natural selection guarantees that this new information will become part of the population.

The big question

This is a nice example of added information. What I’m stating is that it’s for me more assumable that a random proces would destroy “the old genes that code for a tail” then creating new genes. The big question is: why doesn’t that happen?

It does. If you look at the population, the random process does, in some individuals, destroy the old genes for a tail. Spina bifida babies have genes for forming a brain destroyed. But what happens to those spina bifida babies, especially in the absence of modern medical care? They die and don't have babies of their own. So, for the population, that corruption doesn't count.

Let's try another example. You make 100 copies of the Windows XP CD. In one of them, the information is corrupted and the CD won't work. What do you do with it? You throw it away! And then make the next copies from one of the copies that was fine.