I'm looking for...

[RufusAtticus]

UWO,

Here is something I have written previously on this topic. (Note that I'm not actually addressing you or your comments in this.)

Individuals don't evolve. Populations do. So in linking information theory to evolution, you must consider the information in the population, which you do not do. Biologically, information can refer to different things. Pseudogenes, contain information about evolutionary history but not information that can be selected for. In the context of this discussion, it would be better for us to consider the genetic information underlying traits, with an interest in adaptable traits. It is difficult to determine a way to measure the amount of this information, but one possibility is the size of the proteome. This is the number of unique proteins produced in the population and includes all loci and alleles. Whenever a mutation produces a novel allele, it adds information to the population. In other words, there is a new trait for selection to act upon. Here are two examples of the effects of information in a population.

Jeff knows something about Gina: "Gina is neat." Thus he has information about Gina. Before he leaves town, Jeff replicates this information by telling it to two people, Nick and Randy. Because neither of them pays attention, they don’t replicate the information exactly. Nick thinks "Gina is sweat," and Randy thinks "Gina is near." We can measure the about of information about Gina by the number of non-redundant attributes people ascribe to her. Here, the amount of information about Gina has doubled: from "neat" to "sweat and near." Clearly when we remember that it is the population that’s important to evolution, it is obvious how mutations can add information for selection to act upon.

Take this example retrieved from LocusLink [7], the only difference occurs in the 7th codon (6th amino acid because the first one, 'm,' gets cut off). The letters refer to amino acids [8].

Human Beta-hemoglobin (HBB)
  1 mvhltpeeks avtalwgkvn vdevggealg rllvvypwtq rffesfgdls tpdavmgnpk
 61 vkahgkkvlg afsdglahld nlkgtfatls elhcdklhvd penfrllgnv lvcvlahhfg
121 keftppvqaa yqkvvagvan alahkyh

HBB-S
  1 mvhltpveks avtalwgkvn vdevggealg rllvvypwtq rffesfgdls tpdavmgnpk
 61 vkahgkkvlg afsdglahld nlkgtfatls elhcdklhvd penfrllgnv lvcvlahhfg
121 keftppvqaa yqkvvagvan alahkyh

HBB-C
  1 mvhltpkeks avtalwgkvn vdevggealg rllvvypwtq rffesfgdls tpdavmgnpk
 61 vkahgkkvlg afsdglahld nlkgtfatls elhcdklhvd penfrllgnv lvcvlahhfg
121 keftppvqaa yqkvvagvan alahkyh

Each allele does not encode the same information since each one produces a distinctly different product. A single point mutation has enough effect on the information contained in the genome that it can determine whether an individual dies from malaria or not. In the presence of malaria, HBB-S is maintained because of heterozygote advantage. However, HBB-C also offers resistance to malaria, but the most fit genotype is the homozygote.[9] It is expected to become the most common allele in parts of Africa if the environment stays the same. These mutations have clearly added new information to the population. Selection then acts on this new information, changing the make up of the population. Thus, evolution happens.

It is important to realize that evolution occurs even if information is lost. It also occurs when information is gain or without any change in the amount of information at all. Thus no-new-information arguments do not actually address evolutionary theory. By focusing on individuals and not populations, no-new-information claims never even get close to disproving evolution. In fact, the actual claim, when applied to biology, is that the information capacity of an individual's genome cannot increase. However, this claim is false because there are known types of mutations that can increase the length of the genome and thus its capacity to hold information. Ernst Mayr discusses this origin of new genes in his latest book.

“Bacteria and even the oldest eukaryotes (protists) have a rather small genome. . . . This raises the question: By what process is a new gene produced? This occurs, most frequently, by the doubling of an existing gene and its insertion in the chromosome in tandem next to the parental gene. In due time the new gene may adopt a new function and the ancestral gene with its traditional function will then be referred to as the orthologous gene. It is through orthologous genes that the phylogeny of genes is traced. The derived gene, coexisting with the ancestral gene, is called paralogous. Evolutionary diversification is, to a large extent, effected by the production of paralogous genes. The doubling sometimes affects not merely a single gene, but a whole chromosome set or even an entire genome.” [10]

7. http://www.ncbi.nlm.nih.gov/LocusLink/
8. http://www.chem.qmul.ac.uk/iupac/AminoAcid/AA1n2.html
9. Modiano D. et al. (2001) Haemoglobin C protects against clinical plasmodium falciparum malaria. Nature: 414 pp 305-308
10. Mayr E. (2001) What Evolution Is. Basic Books.

 

[Jerry Smith]

How we get from this:
...
To this:
...

Let me point out that you are looking at two different levels of magnification. Bacterial DNA would look much like the human model of DNA at the same level of magnfication.

Human DNA would look like a little "X" at the level of magnification that your picture shows for bacteria...

Regardless....

The short answer is: you don't. The common ancestor was not modern bacteria, though it had many traits in common. To anticipate the next question - how to get from the common ancestor's DNA to modern bacterial or human DNA, the other short answer is 3 & 1/2 billion years of evolution. One gene at a time for the most part.

 

[unworthyone]

Originally posted by RufusAtticus
It is important to realize that evolution occurs even if information is lost. It also occurs when information is gain or without any change in the amount of information at all. Thus no-new-information arguments do not actually address evolutionary theory. By focusing on individuals and not populations, no-new-information claims never even get close to disproving evolution. In fact, the actual claim, when applied to biology, is that the information capacity of an individual's genome cannot increase. However, this claim is false because there are known types of mutations that can increase the length of the genome and thus its capacity to hold information. Ernst Mayr discusses this origin of new genes in his latest book.

Thanks for your explanation RA.

Are there any practical observations of information being added where the loss of information is less than or equal to the gain?

 

[unworthyone]

Originally posted by Jerry Smith

Let me point out that you are looking at two different levels of magnification. Bacterial DNA would look much like the human model of DNA at the same level of magnfication.
Human DNA would look like a little "X" at the level of magnification that your picture shows for bacteria...
Regardless....
The short answer is: you don't. The common ancestor was not modern bacteria, though it had many traits in common. To anticipate the next question - how to get from the common ancestor's DNA to modern bacterial or human DNA, the other short answer is 3 & 1/2 billion years of evolution. One gene at a time for the most part.

Yes Jerry I know the magnification was different. I was merely trying to illustrate complexity. LOL.

and now....

A practical observation in which new gene information is added to a DNA strand without killing more then whats added is ______.

 

[Jerry Smith]

Weren't you satisfied with what you found at LFOD's link? If not, why not? Did you check the link and the sidebar links of the one I sent you?

 

[unworthyone]

Maybe a real-life example with a graphical illustration would help me understand???

 

[unworthyone]

Originally posted by Jerry Smith
Weren't you satisfied with what you found at LFOD's link? If not, why not? Did you check the link and the sidebar links of the one I sent you?

I understood somewhat. I'll look at it again.

 

[Jerry Smith]

Ok, man.. it isn't simple, and I cannot claim to understand it very well myself.

I'll tell you something else, though. There was a time when scientists didn't even know what a mutation was. This was a big puzzle to them. The evidence for evolution was strong enough even then, that they accepted it, and went looking for the genetic mechanisms that it implied. Not having the answer to every detail about how evolution occurs, doesn't mean that we can't know it occurs, and it doesn't even mean that we can't know a lot about how it occurs.. It just happens that this detail you ask about is one that has recently been figured out.

 

[unworthyone]

Originally posted by Jerry Smith
Ok, man.. it isn't simple, and I cannot claim to understand it very well myself.

I'll tell you something else, though. There was a time when scientists didn't even know what a mutation was. This was a big puzzle to them. The evidence for evolution was strong enough even then, that they accepted it, and went looking for the genetic mechanisms that it implied. Not having the answer to every detail about how evolution occurs, doesn't mean that we can't know it occurs, and it doesn't even mean that we can't know a lot about how it occurs.. It just happens that this detail you ask about is one that has recently been figured out.

Yes I agree its quite confusing, but I do have a hard time agreeing with the logic of the theories because they are using examples that are not related to phylogenetic evolution which is what all my questions are about.

He says it doesn't weaken the argument but in fact it does because the argument is not using phylogenetic evolution observations. If it was a viable theory, at least they could come up with an example directly related to the topic in question.

 

[Jerry Smith]

Do you think phylogenetic mutations must be so different?

Let me ask you: are you trying to ascertain whether it is reasonable to attribute the genetic variation that is observed when we observe various evolutionary events (either micro evolution in the laboratory or the field, or macro-evolution from genomic studies, the fossil record, etc) to mutations?

Or are you trying to prove without doubt that all of the variation we observe is due to mutations?

Or are you merely trying to assess the creationist claim that "mutations can't add information."

As far as I can tell, the links you have been given should be sufficient for the first and third options, and the middle may not even be correct, much less absolutely provable.. (for all I know - Rufus knows a lot more about that subject than I).

 

[Sauron]

Originally posted by unworthyone

Humans have more genetic information then plants.

They do? Based upon what?  The world leader in number of chromosomes is a fern, something like 120 chromosomes.  Humans have only 22.

The creature with the least number of chromosomes?  A species of ant, with 7.

Because so far, the only thing you have offered is that somehow "information" means a beneficial mutation.  The problem with that definition is that some of the things you excluded (eye color, wings/lack of wings, hair color, etc.) could be beneficial mutations, depending upon the environment.

So:

1.  how are you defining "genetic information", and

2.  how are you measuring it? 








 

 

[unworthyone]

Originally posted by Jerry Smith
Do you think phylogenetic mutations must be so different?

In the antibody example the antibodies are the same antibody. No change or addition of a new type of antibody.

Let me ask you: are you trying to ascertain whether it is reasonable to attribute the genetic variation that is observed when we observe various evolutionary events (either micro evolution in the laboratory or the field, or macro-evolution from genomic studies, the fossil record, etc) to mutations?

Or are you trying to prove without doubt that all of the variation we observe is due to mutations?

Or are you merely trying to assess the creationist claim that "mutations can't add information."

As far as I can tell, the links you have been given should be sufficient for the first and third options, and the middle may not even be correct, much less absolutely provable.. (for all I know - Rufus knows a lot more about that subject than I).

Actually I'm not trying to ascert anything. I'm really just trying to understand and thus far the creationists seem to have the upper hand. I've yet to see a single example of phylogenetic mutation that has been observed that resulted in NO LOSS of DNA information. Change is not addition.

 

[unworthyone]

Originally posted by Sauron
They do? Based upon what?  The world leader in number of chromosomes is a fern, something like 120 chromosomes.  Humans have only 22.

Sorry. Bad example. Change it to some plants.

Because so far, the only thing you have offered is that somehow "information" means a beneficial mutation.  The problem with that definition is that some of the things you excluded (eye color, wings/lack of wings, hair color, etc.) could be beneficial mutations, depending upon the environment.

So:

1.  how are you defining "genetic information", and

2.  how are you measuring it? 

A simple DNA strand verses a complex DNA strand such as ours. How do we get from simple (1 penny) to complex (The USA Federal Reserve).

First forms of life are like a penny. 1 tiny purpose.

to......

Our known life as it exists now like the US Federal Reserve. Many purposes.

But lets start simple. How do we get from the penny to the nickel? Size, color, and purposes are now increased, so.....more information.

The penny changing color is not "more info" but it is taking pre-existing characteristics and mutating them. Size and purpose are what I'm looking for.

I'm looking for phylogenetic examples where the penny does not lose its original value in any shape or form whatsoever.

I don't want a euro, I don't want a dollar, I don't want 10 pennies, but just a nickel will do for now.

 

[seebs]

UWO: I think you have been fed a line of... (I can't use this word here) about what it means to talk about "more" information.

It is fine if we "lose" some information, as long as we gain more than we lost. Some of the "lost" information wasn't very useful.

Essentially, if you randomize and then select, you end up with a lot of information after a while. It's hard to look at a given mutation and say how much information was "added" - but after a while, you can tell that there's more information than there used to be.

The problem is, it's very hard to decide what ought to count as "new" information. A change of coloration doesn't sound like new information, until you realize that melanin affects Vitamin D production and resistance to sunburn.

 

[unworthyone]

Originally posted by seebs
UWO: I think you have been fed a line of... (I can't use this word here) about what it means to talk about "more" information.
It is fine if we "lose" some information, as long as we gain more than we lost. Some of the "lost" information wasn't very useful.
Essentially, if you randomize and then select, you end up with a lot of information after a while. It's hard to look at a given mutation and say how much information was "added" - but after a while, you can tell that there's more information than there used to be.
The problem is, it's very hard to decide what ought to count as "new" information. A change of coloration doesn't sound like new information, until you realize that melanin affects Vitamin D production and resistance to sunburn.

Seriously I don't think you know what I'm saying. DNA strands obviously started basic and turned much more complex.

It's fine if we lose information as long as the information gained outweighs it like this...

12345678 duplication to 1234567878 and loses a 7 in the process.

123456878 mutates to 1234587Z

Understand?

Anybody have a pic of the most basic DNA strand to the most complex?

 

 

 

[Jerry Smith]

Actually I'm not trying to ascert anything. I'm really just trying to understand ...

Worthy -- When I said "ascertain" I meant "determine" (for yourself)... so yes I meant more or less what you are trying to do. I was just trying to find out what you were trying to ascertain..

. I'm really just trying to understand and thus far the creationists seem to have the upper hand. I've yet to see a single example of phylogenetic mutation that has been observed that resulted in NO LOSS of DNA information. Change is not addition.

You have fallen victim to one of the most recent (and sophisticated) creationist ploys. They use a term "information" that they generally won't define. (Occasionally, they will define it as "specified comlexity" which opens a whole other can of worms.)

The kind of "increase in information" that you are looking for, I believe, is large scale anatomical or physiological change. This doesn't occur due to one mutation. It occurs over the evolutionary "long term".

I will use the term just as loosely as the creationists use it for a moment. "Information" capacity of the genome is increased everytime the DNA chain gets longer. Gene duplications and insertions are common observed mutations, so the DNA chain can get longer relatively often. (This is obvious because no matter how you define information, the bigger the chain of nucleotides that encodes it, the more capacity there is for added information) That capacity is filled every time an old gene takes on a new function without depriving the organism of some essential old function. The globin family of genes is a relic of this. Where once one or two globins regulated oxygen transport, now many globins carry out specialized tasks of oxygen transport. The globin genes are all homologues that most likely originated from duplication events, then evolved specialized function while the original gene was still functioning as normal. Phylogenetic analysis of the globin family of genes supports this view.

But it isn't certain that we have ever actually observed "the addition of new information." Well, we don't really have to. The theory of evolution has nothing to do with the mechanism of mutation. It requires that variation enter a population (this has been observed), that such variation may at times enhance survival prospects (this has been observed), and that natural selection favors those variations which enhance survival and eliminates those variations which are deleterious for survival. This has been observed.

For creationists to ask for further proof of "information increasing mutations" is really begging the question. Perhaps not all evolution and increase in complexity is even due to mutation. We have several lines of evidence from several fields that evolution does and has occurred, and that it is the correct explanation for the diversity of life we observe today. Even if we do not fully understand the mechanisms at the genetic level that introduce that variation (and we don't fully understand them), we know that something is causing all of that evolution. What you are seeing when you see a creationist demand "a single example of phylogenetic mutation that has been observed that resulted in NO LOSS of DNA information," is just another "creationism of the gaps."

Unfortunately, they are just wrong even in this attempt to disprove what has been observed and proven by fine analysis of the "gaps" they suppose in science knowledge. Gene duplication happens, and it happens in the stem lines that produce gametes. Gene duplication is a mutation that often increases genetic variability (aka DNA information capacity). Genome duplication, as you can guess actually DOUBLES that capacity, and has also been observed. Consider:

ATCAGTCAAGATCC - codes for protein 1 (lets pretend it codes for clotting factor A, which works ok)
Duplication event... now we have
ATCAGTCAAGATCC
ATCAGTCAAGATCC
both coding for clotting factor A.
Point mutation in gene #2:
ATCAGTCAGGATCC - no harm, no gain either. gene# 2 does nothing, and gene#1 still makes clotting factor A
ATCAGTCAGGATGACCC - Translocation from another point on the chromosome, which was, like sequence 2 a non-useful segment.. But now this gene still does nothing.
TCAGTCAGGATGACCCG - Frame shift mutation. Now this gene codes for clotting factor B, which works better than clotting factor A.

You can't point to a single one of the above mutations that "added information", but after they were finished, the organism that carried them has new, and better abilities, and it will not harm the organism (at this point), even if Gene #2 is deleted right now. This is an oversimplification. Add another hundred steps, and take into account all of the other changes that are taking place in the organism's genome, and you start to get the idea...

Here are some good links re: gene, chromosome, and genome duplication:

http://linkage.rockefeller.edu/wli/duplication/
http://www.sciencemag.org/cgi/content/full/293/5535/1551a
http://www.skeptics.com.au/journal/dawkins1.htm

And of course, the ones that I and LFOD pointed you to. Mutations are mutations, whether or not they occur in the gamete stem line, so the issue of whether they contributed to "phylogenetic evolution" in this case, is kind of irrelevant, unless something magical happens that prevents mutations of these kinds from occurring in stem cell DNA.

 

[Morat]

  Let me add something: Strictly speaking, the length of the genome denotes information capacity. Now, it's not exactly true (bacteria do some really nifty stuff genetically, which would increase the amount of "information" their genomes could express), but it's close enough for jazz.

   Say our chromosomes represent a finite amount of information capacity. You're looking for an increase in capacity by asking that it be lengthened. Which may or may nor be an increase in information.

   Because, and this is important, the information encoded in our DNA does not fill it's capacity. We have more capacity than we have information. Long strenches of our DNA do nothing (they are turned off, or broken).

   Further, you're using a really simplistic definition of information. One that is not at all accurate. A new allele for eye color appearing would be new information. Humans have green, blue or brown eyes. Now, you can get mixes (like hazel), and different intensities (dark green, a blue so light it's gray, etc). But only the three colors.

   Suddenly, a girl is born with purple eyes. A mutation in the genes that would originally have caused blue eyes turns them purple instead. Did she lose information? She can no longer make "blue eyes". Did she gain it? She can make purple ones. Is it a break even thing? (Lose one allele, gain another?).

   It doesn't matter for her. Because, if she manages to reproduce, the human race now has four eye colors. Green, Blue, Purple and Brown. Information has been added to the human genome.

    Now, there are strict definitions of information. Shannon, for instance, did the first work on it at Bell Labs about 5 decades ago. He's considered the father of information theory (which would be important to the phone company). Information can be measured, just like entropy can. And, like with "evolution violates the 2nd Law of Thermodynamics" no one seems willing to show their work.

 

[unworthyone]

Originally posted by Jerry Smith

You have fallen victim to one of the most recent (and sophisticated) creationist ploys. They use a term "information" that they generally won't define. (Occasionally, they will define it as "specified comlexity" which opens a whole other can of worms.)

The kind of "increase in information" that you are looking for, I believe, is large scale anatomical or physiological change. This doesn't occur due to one mutation. It occurs over the evolutionary "long term".

I will use the term just as loosely as the creationists use it for a moment. "Information" capacity of the genome is increased everytime the DNA chain gets longer. Gene duplications and insertions are common observed mutations, so the DNA chain can get longer relatively often. (This is obvious because no matter how you define information, the bigger the chain of nucleotides that encodes it, the more capacity there is for added information) That capacity is filled every time an old gene takes on a new function without depriving the organism of some essential old function. The globin family of genes is a relic of this. Where once one or two globins regulated oxygen transport, now many globins carry out specialized tasks of oxygen transport. The globin genes are all homologues that most likely originated from duplication events, then evolved specialized function while the original gene was still functioning as normal. Phylogenetic analysis of the globin family of genes supports this view.

But it isn't certain that we have ever actually observed "the addition of new information." Well, we don't really have to. The theory of evolution has nothing to do with the mechanism of mutation. It requires that variation enter a population (this has been observed), that such variation may at times enhance survival prospects (this has been observed), and that natural selection favors those variations which enhance survival and eliminates those variations which are deleterious for survival. This has been observed.

For creationists to ask for further proof of "information increasing mutations" is really begging the question. Perhaps not all evolution and increase in complexity is even due to mutation. We have several lines of evidence from several fields that evolution does and has occurred, and that it is the correct explanation for the diversity of life we observe today. Even if we do not fully understand the mechanisms at the genetic level that introduce that variation (and we don't fully understand them), we know that something is causing all of that evolution. What you are seeing when you see a creationist demand "a single example of phylogenetic mutation that has been observed that resulted in NO LOSS of DNA information," is just another "creationism of the gaps."

Jerry. I am not supporting creation OR evolution. Please get this into your head. UWO does not know the answer, hence he asks. Ok? Cool.

Thanks for your explanation. Now....Why don't you have to show me an example of something that is accepted as necessary to happen for evolution to occur?

I understand its complex, but from reading evolutionist and creationist sites I have gotten the impression that no one truly has any proof that additional (lets call it "length") was added to a DNA strand (whats the correct term here???). All we have is unsupported theories which mean didly squat to me. Until I see a beneficial mutation that results in added length to a DNA strand that does not die or return to original form, I'm probably not going to have any "faith" in this theory whatsoever.

An amino acid turning into a human. All I want is one example that the DNA strand was lengthened and survived the entire process.

Why is that so much to ask for?

Oh. One more thing...

It would be necessary that this be able to be passed to another host or being through a natural process.

 

[Morat]

  That's all? Polyploidy in plants. Happens all the times. Generally results in a more vigorous plant.

Evidence that a species of fireweed formed by doubling of the chromosome count, from the original stock. (Note that polyploids are generally considered to be a separate "race" of the same species as the original stock, but they do meet the criteria which you suggested.)

(Test for speciation: cannot produce offspring with the original stock.) Mosquin, T., 1967. "Evidence for autopolyploidy in <I>Epilobium angustifolium</I> (Onaagraceae)", <I>Evolution</I> 21:713-719

&nbsp; Or, better yet, in humans. From the Human Genome Project. Mentions olfactory and globin genes.

&nbsp;Gene Duplication, if you want a bit more info.

&nbsp;

 

[Jerry Smith]

Uw, I will reply to you this evening or in the a.m. Right now, Clark Kent has just shown up, and I must give a sinister laugh and dig out my Kryptonite...