RE: Regulating Evolution (Full Version)

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essentialsaltes -> RE: Regulating Evolution (4/18/2008 3:51:27 PM)

quote:

ORIGINAL: Jhud

Oh, looky here - this just came out:

...

Oh, yeah, a prediction fulfilled in one hour!

Go ID, go ID, go ID...


This thread is expanding too rapidly for me to be sure what you're replying to or crowing about, but this study deleted genes, not junk. The mouse study deleted noncoding DNA. I don't think evolution predicts that deleting a critter's genes won't have an effect.



drj11 -> RE: Regulating Evolution (4/18/2008 4:10:08 PM)

quote:

ORIGINAL: benelchi
When those like Dawkins acknowledge the appearance of design, they are talking about the appearance of "sentient" design. Their contention is that although life appears to be designed by a "sentient" being, they do not believe this to be true. You can contend that "forces of natural selection, random mutation, sexual selection etc..." leave the impression of intelligent design, but you cannot honestly contend that Dawkins was referring to these "forces of natural selection, random mutation, sexual selection etc..." when he said life had the appearance of an intelligent designer; if this is is the designer he had in mind he would have acknowledged a designer, not called into question the appearance of one.


Well, I'm not all that familiar with what Dawkin's contends. I haven't read his books, except for a few excerpts of the God Delusion, and a few youtube clips of him.

What I have heard, is the argument that we, and other organisms are perfectly designed to fit our environment. This is a bit of a tautology and a failing to acknowledge the anthropic principle.

It reminds me of the Douglas Adams quote:

". . . imagine a puddle waking up one morning and thinking, 'This is an interesting world I find myself in, an interesting hole I find myself in, fits me rather neatly, doesn't it? In fact it fits me staggeringly well, must have been made to have me in it!' This is such a powerful idea that as the sun rises in the sky and the air heats up and as, gradually, the puddle gets smaller and smaller, it's still frantically hanging on to the notion that everything's going to be alright, because this world was meant to have him in it, was built to have him in it; so the moment he disappears catches him rather by surprise. I think this may be something we need to be on the watch out for."



Jhud -> RE: Regulating Evolution (4/18/2008 5:08:20 PM)

quote:

This thread is expanding too rapidly for me to be sure what you're replying to or crowing about, but this study deleted genes, not junk. The mouse study deleted noncoding DNA. I don't think evolution predicts that deleting a critter's genes won't have an effect.


This directly addresses that point:

However, because complete deletion of most yeast genes (80%) has no obvious phenotypic consequence in rich medium (that is, they appear under normal circumstances to be non-coding), it is difficult to study their functions. ...
We found that 97% of gene deletions exhibited a measurable growth phenotype, suggesting that nearly all genes are essential for optimal growth in at least one condition.

Despite the fact that 80% of the genes in yeast could be deleted with no harmful effect under normal circumstances, under certain various conditions, they were almost all found to be essential. This speaks directly to the two points you made:

Although actual and potential functions have been found for some noncoding DNA, I think it's still the case that there is plenty of functionless junk in the genome. Far be it from me to disparage the noble Amoeba dubia, but it's hard to see why it needs a genome 200 times larger than mine.

Researchers have also deleted millions of base pairs of noncoding mouse DNA, and produced seemingly healthy mice.



essentialsaltes -> RE: Regulating Evolution (4/18/2008 6:30:36 PM)

quote:

ORIGINAL: Jhud

quote:

This thread is expanding too rapidly for me to be sure what you're replying to or crowing about, but this study deleted genes, not junk. The mouse study deleted noncoding DNA. I don't think evolution predicts that deleting a critter's genes won't have an effect.


This directly addresses that point:

However, because complete deletion of most yeast genes (80%) has no obvious phenotypic consequence in rich medium (that is, they appear under normal circumstances to be non-coding),


If it's a gene, then it's a coding sequence. Just because the gene has no obvious effect doesn't make it non-coding.



Jhud -> RE: Regulating Evolution (4/18/2008 8:33:49 PM)

quote:

If it's a gene, then it's a coding sequence. Just because the gene has no obvious effect doesn't make it non-coding.


So the many science articles referring to non-coding gene sequences are referring to what?



Bettawrekonize -> RE: Regulating Evolution (4/18/2008 9:03:51 PM)

Notice what just happened. essentialsaltes made a prediction based on evolutionary presuppositions and we made a prediction based on ID presuppositions. Our prediction was further confirmed. Will essentialsaltes acknowledge evolution was wrong? I predict he, and other evolutionists, will not acknowledge evolution is wrong. Instead, they will accommodate the evidence into evolution and then claim this is what evolution predicts and not ID and they will find some lone evolutionist who predicted this many years ago and point to him (despite the fact that this was not the evolutionary consensus). This further demonstrates the postdictive power of evolution and the predictive power of ID. If evolution were allowed more criticism in public schools and opposing views were allowed exposure, evolution would simply fall apart.



essentialsaltes -> RE: Regulating Evolution (4/19/2008 12:57:04 AM)

quote:

ORIGINAL: Jhud

quote:

If it's a gene, then it's a coding sequence. Just because the gene has no obvious effect doesn't make it non-coding.


So the many science articles referring to non-coding gene sequences are referring to what?


In my ignorance of biology, I may have not quite got it right. Apparently a 'gene' has "regulatory regions in addition to regions that explicitly code for a protein or RNA product". So I guess I should have said, "If it's a gene, then it includes a coding sequence." So in the yeast study, they were deleting genes, and necessarily were deleting coding sequences. The mouse study involved deleting only noncoding sequences.



essentialsaltes -> RE: Regulating Evolution (4/19/2008 1:05:41 AM)

quote:

ORIGINAL: Bettawrekonize

Notice what just happened. essentialsaltes made a prediction based on evolutionary presuppositions and we made a prediction based on ID presuppositions. Our prediction was further confirmed. Will essentialsaltes acknowledge evolution was wrong?


Could you be specific about what this prediction was, and where mine was disconfirmed?

I said, "I don't think evolution predicts that deleting a critter's genes won't have an effect."

This is sort of an anti-prediction, and Jhud's evidence confirms it, such as it is.

I said, "I think it's still the case that there is plenty of functionless junk in the genome"

Jhud's evidence was about deleting yeast genes, which no one considers to be functionless junk.



Bettawrekonize -> RE: Regulating Evolution (4/19/2008 1:12:21 AM)

quote:

ORIGINAL: essentialsaltes
In my ignorance of biology, I may have not quite got it right. Apparently a 'gene' has "regulatory regions in addition to regions that explicitly code for a protein or RNA product". So I guess I should have said, "If it's a gene, then it includes a coding sequence." So in the yeast study, they were deleting genes, and necessarily were deleting coding sequences. The mouse study involved deleting only noncoding sequences.


Introns generally refer to DNA sequences between stop codons and start codons where as exons refer to the opposite. Exons generally code for proteins, introns do not. The definition of a gene is more complicated than that.

quote:


So I guess I should have said, "If it's a gene, then it includes a coding sequence."



quote:


In cells, genes consist of a long strand of DNA that contains a promoter, which controls the activity of a gene, and coding and non-coding sequence.


http://en.wikipedia.org/wiki/Gene

The problem with the word "gene" is that it's an ambiguous word, different people refer to it differently. I'd probably have to read the article to figure out what they meant, but genes do not exclusively mean coding sections (the word for that is generally exon but even here that gets confusing depending on the context).

Exon definition
quote:


This definition was originally made for protein-coding transcipts that are spliced before being translated.


http://en.wikipedia.org/wiki/Exon

If you read on, even that definition has been confused over time.



Bettawrekonize -> RE: Regulating Evolution (4/19/2008 1:25:15 AM)

quote:

ORIGINAL: essentialsaltes
Could you be specific about what this prediction was, and where mine was disconfirmed?

I said, "I don't think evolution predicts that deleting a critter's genes won't have an effect."

This is sort of an anti-prediction, and Jhud's evidence confirms it, such as it is.

I said, "I think it's still the case that there is plenty of functionless junk in the genome"



The point is that we are discovering that less and less of DNA is useless and more and more of it is useful, which further disconfirms the notion that a substantial quantity of DNA is junk. It might still be the case that we haven't found the function of much of this alleged junk DNA, but the point is that we continue to find function as time goes by which further disconfirms your point.

quote:


Jhud's evidence was about deleting yeast genes, which no one considers to be functionless junk.


Oh, so now that we found more function than was previously known, you are no longer labeling it functionless junk. The point still stands, we are finding out that less and less useless DNA exists and more DNA that was previously thought to be junk is now considered useful (or at least we are finding out the functions of more and more DNA which means that we learn that less and less of it has no function).



essentialsaltes -> RE: Regulating Evolution (4/19/2008 1:35:44 AM)

quote:

ORIGINAL: Bettawrekonize

quote:


Jhud's evidence was about deleting yeast genes, which no one considers to be functionless junk.


Oh, so now that we found more function than was previously known, you are no longer labeling it functionless junk.


Dude, no one ever called genes junk DNA.



Bettawrekonize -> RE: Regulating Evolution (4/19/2008 1:41:32 AM)

quote:

ORIGINAL: essentialsaltes
Dude, no one ever called genes junk DNA.


The point is that we are finding out that more and more sections of the genome are really genes (ie: useful) and not junk.

Where we define a gene as

"A gene is a union of genomic sequences encoding a coherent set of potentially overlapping functional products"
http://en.wikipedia.org/wiki/Gene

and we're finding out that more and more of the genomes are useful and hence not useless. We simply call the useful sections genes, so you could say that we are finding out that more and more of the genome are composed of genes (or useful dna) and hence not junk. We are finding out the functions of more DNA which means we now know that more of this DNA is composed of (useful) genes and not junk and hence we know less of it is composed of junk. This further disconfirms your prediction.



Bettawrekonize -> RE: Regulating Evolution (4/19/2008 3:40:26 AM)

quote:

ORIGINAL: essentialsaltes
but this study deleted genes, not junk.


It deletes something that might have been mistaken for junk (useless) had we not found them to be (probably) useful.

quote:


I said, "I think it's still the case that there is plenty of functionless junk in the genome"


This helps demonstrate why ID is useful. Instead of assuming it has no function, we assume that it was probably designed to have function and hence we would try to search for its function. Now only if ID advocates weren't so discriminated against by the tax funded secular community, maybe then they can get research grants. They would love to find function and would be eager to look.

Assuming it has no function, we would assume that it probably was originally designed to have a function and that original function broke (and that it's not just random DNA from unguided processes). We would put effort into researching what those original functions could have been and then see if we can use them to our advantage. You can read Post 7 here for a possible example of this. We might find that a gene used to code for something that could be of benefit to us before it broke and we could figure out what it was used for (and possibly synthesize and use it). For instance, if we find that a gene is triggered under certain conditions but it doesn't seem to do any good, perhaps what it codes for is broken and it doesn't function properly. Knowing when the gene is triggered, we can get an idea of what it was supposed to do and possibly figure out what it coded for. Then, if we can synthesize or get a hold of what it originally coded for, we can possibly use it under certain conditions. Or, maybe it coded for something that we already have access to and are aware of its existence, but we didn't know it could be beneficial under certain specific conditions until we find out that cells are trying to code for a broken version of it under these conditions (or they're trying to code for something similar but not identical because its broken. We could notice the similarities and determine what it's trying to code for. [added in edit] From a creationist standpoint it makes sense that some people may have the original gene and it just broke down in certain lineages. In this case, we can look at more members of the population to look for variances and see if one of the variances are beneficial under the conditions that activate the gene).



essentialsaltes -> RE: Regulating Evolution (4/19/2008 12:17:58 PM)

quote:

ORIGINAL: Bettawrekonize

quote:

ORIGINAL: essentialsaltes
but this study deleted genes, not junk.


It deletes something that might have been mistaken for junk (useless) had we not found them to be (probably) useful.


No. Since the coding sections have start and stop markers (and intelligible amino acid coding sequences in between), we can easily spot genes.

quote:


quote:


I said, "I think it's still the case that there is plenty of functionless junk in the genome"


This helps demonstrate why ID is useful. Instead of assuming it has no function,


I'm not suggesting that we already know all the functional stretches of DNA in the genome. As all these studies show, we are indeed learning more and more of them all the time. And there's no way we could ever go backward and find less functionality (we thought this gene produced hemoglobin, but we were wrong, it's actually useless.) So yes, as our knowledge increases, we will find more function. However, I think there will be nonfunctional residue. I'm not an expert to say what proportion. Also, since I'm not an expert, I base my thinking on the writings of people who are experts:

quote:

Many non-genic sequences that are conserved across taxa or which exhibit characteristics consistent with regulatory regions or binding sites or structural components may be treated in the same way as finding an open reading frame as noted above. For most non-coding DNA, there is no such evidence of probable function, however. In fact, as the Sandwalk series on "junk DNA" notes, most non-coding DNA is of a type for which there is little reason to expect function. Inactive vestiges of transposable elements and pseudogenes may occasionally be functional, but there is no reason to assume that they all are given what we know about how they form. Moreover, the massive differences in genome size (i.e., amount of non-genic DNA) among taxa, including species that would be expected to have similar regulatory, mutational buffering, or structural requirements, suggests that much of it is indeed lacking in a universally applied function.


quote:

Now only if ID advocates weren't so discriminated against by the tax funded secular community, maybe then they can get research grants. They would love to find function and would be eager to look.


The concept of 'junk DNA' as it has changed and evolved, never stopped science from progressing. I've already shown that there was no more than a 9 year gap between the first use of the phrase "junk DNA" (1972) and the proposal of a regulating function for it. And Jhud agrees that this whole field took off in the 1980s, apparently unhindered by any discrimination from the tax funded secular community. This is how science progresses. 'Science' did not monololithically announce that noncoding DNA was all junk and no one may study it.



Bettawrekonize -> RE: Regulating Evolution (4/19/2008 12:59:16 PM)

quote:

ORIGINAL: essentialsaltes
No. Since the coding sections have start and stop markers (and intelligible amino acid coding sequences in between), we can easily spot genes.


Depends on what definition of a gene you use. The point is that we are finding out that more and more of the genome is useful (because we are finding their functions), which means we know less and less of it is useless. This further confirms ID and disconfirms your point.

From Jhud's article (quoted from his post)
quote:


However, because complete deletion of most yeast genes (80%) has no obvious phenotypic consequence in rich medium...


From an evolutionary standpoint, there is no reason to assume function.

From Jhud's article (quoted from his post)
quote:


it is difficult to study their functions.


This statement was written after it was known it probably has function, it's not that they predicted or knew it would have function.

quote:

ORIGINAL: essentialsaltes
However, I think there will be nonfunctional residue.


I think ID predicts that things break over time and hence we would expect some no longer functional information. However, we generally expect more functionality than evolutionists have argued to be the case, so we would probably be more inclined to look for functionality.

quote:


The concept of 'junk DNA' as it has changed and evolved, never stopped science from progressing.


The point is that it could have progressed faster had we not assumed it was junk based on evolutionary presuppositions.

At the very least, ID or creationism would not hinder science so there is no reason why the secular community should discriminate against creationists or ID proponents. They do discriminate against them (they teach only that which is consistent with naturalism and censor criticisms and opposing views) and it is dishonest for them to do so. There is nothing about creationism or ID that would stop science from progressing, if anything (as I have demonstrated) it could help us look at things in a different way which can cause us to discover things sooner. Despite the fact that Darwin was wrong about a lot (and ID and Creationism were right about a lot), you argue this hasn't hindered science. Likewise, even if ID or creationism are wrong about some things, there is no reason it should hinder science.

Many organs that were once thought to be vestigial (examples Darwin used to use to argue for evolution) are now known to be more useful than Darwin thought. Our knowledge and research just weren't sophisticated enough to know the functions at the time. Yet creationists have long argued that these organs probably contain function. Likewise, our knowledge may still not be sophisticated enough to know the functions of much of this alleged junk DNA, yet we still argue that it probably contains more function than evolutionists propose (and as time goes by, we discover more and more function).

http://www.answersingenesis.org/home/area/magazines/TJ/TJv14n2_Vestigial.pdf



Real_Solitude -> RE: Regulating Evolution (4/19/2008 8:29:01 PM)

This has only slight relevancy to anything that's being said, but it's in the general ballpark, so I'll let fly.

It may be my ignorance on many of the involved subjects, but I never really understood why it would be assumed that there should be a lot of useless DNA. To my understanding, evolutionary processes tend to weed out things that are either negative or have no function, simply because it expends excess energy. If this only applies a the organism-level, then junk DNA would be understandable, but if it applies at the DNA level, then shouldn't the expectation be to see a lot of useful DNA with a relatively small percentage of junk DNA.
For instance, the human appendix is thought to have been, sometime in our evolutionary history, used in the process of plant digestion. Since it has long been thought that the appendix is useless, and only recently found to have a small part to play in our immune system, we assume that this function is a secondary one. (Note that the example doesn't really matter, only the general point). If this is true, and the appendix does more harm (in the form of appendicitis) than it does good (with its role in the immune system) we should expect the appendix to eventually do one of two things. Be reduced to such a point that it does not matter at all, to the point of being eliminated. Become more important in the immune system. We should expect this because if the appendix is useless, it is taking up energy. If it is harmful, then it is less beneficial to have one than to not, or more beneficial to have less of one than more of one.
Again, it may be due to some oversight in my knowledge of the relevant processes, but shouldn't the same thing apply to DNA? We should expect a lot of things that contribute to the survival, and therefore propagation of DNA, along with relatively few things that are either useless or harmful, that don't contribute to propagation. If this is correct, only things that have recently become useless or harmful should be in the DNA, and those should be weeded out as time goes on.
Of course, this is all moot speculation if there's no cost for waste at the genetic level.



Jhud -> RE: Regulating Evolution (4/19/2008 9:47:08 PM)

The point here is if, as the yeast studyindicates, the genes in question have "no obvious phenotypic consequence" then they would be effectively 'junk' because they don't do anything. It's exactly the same as the mouse study in this respect.

However, the study found that in various genes are important in less than optimum circumstances - 97% of them in fact.

So if we follow essentialsaltes prediction, that, "there is plenty of functionless junk in the genome." then we would not expect that this percentage of normally inconsequential genes would be shown to be important; but they have been shown to be and so his prediction, based on evolution, is wrong.



essentialsaltes -> RE: Regulating Evolution (4/20/2008 10:49:13 AM)

quote:

ORIGINAL: Jhud

The point here is if, as the yeast studyindicates, the genes in question have "no obvious phenotypic consequence" then they would be effectively 'junk' because they don't do anything.


You're being disingenuous. Genes are never considered junk DNA.



Jhud -> RE: Regulating Evolution (4/21/2008 2:57:01 AM)

quote:

You're being disingenuous. Genes are never considered junk DNA.


Never?



essentialsaltes -> RE: Regulating Evolution (4/21/2008 9:51:45 AM)

quote:

ORIGINAL: Jhud

quote:

You're being disingenuous. Genes are never considered junk DNA.


Never?


That 'new kind of gene' "does not produce a protein". It doesn't meet the definition of gene that either Betta or myself have been using.



Bettawrekonize -> RE: Regulating Evolution (4/21/2008 10:02:49 AM)

quote:

ORIGINAL: essentialsaltes
That 'new kind of gene' "does not produce a protein". It doesn't meet the definition of gene that either Betta or myself have been using.


Did you not read my posts? The word you are referring to isn't "gene" it's "exon" but even then (thanks to the unfortunate ever changing evolution of language) there is some ambiguity. The word exon is more representative of the word you are looking for than gene is.



Jhud -> RE: Regulating Evolution (4/21/2008 11:04:46 AM)

quote:

That 'new kind of gene' "does not produce a protein". It doesn't meet the definition of gene that either Betta or myself have been using.


But scientists still refer to it as a gene, correct?



essentialsaltes -> RE: Regulating Evolution (4/21/2008 12:39:03 PM)

quote:

ORIGINAL: Jhud

quote:

That 'new kind of gene' "does not produce a protein". It doesn't meet the definition of gene that either Betta or myself have been using.


But scientists still refer to it as a gene, correct?


This does seem to be the case. I hate to be in the position of Humpty Dumpty, declaring that a word "means just what I choose it to mean, neither more nor less". So I grant that there are genes that I didn't know were genes.

quote:

So if we follow essentialsaltes prediction, that, "there is plenty of functionless junk in the genome." then we would not expect that this percentage of normally inconsequential genes would be shown to be important; but they have been shown to be and so his prediction, based on evolution, is wrong.


You are mis-stating my prediction. Yeasts must make some proteins, so some of its genes must code for them, and these are genes that I would have previously recognized as genes. I never meant to imply (and I really don't think I did imply) that coding genes were going to contain plenty of functionless junk.

Rather, I said that in the stuff commonly called junk DNA (which excludes all the stuff that we already know has function, even an 'inconsequential' function) we would continue to discover functional stretches (and even genes, as your link demonstrates), but a residue of functionless junk will remain.



Jhud -> RE: Regulating Evolution (4/21/2008 1:07:54 PM)

quote:

You are mis-stating my prediction. Yeasts must make some proteins, so some of its genes must code for them, and these are genes that I would have previously recognized as genes. I never meant to imply (and I really don't think I did imply) that coding genes were going to contain plenty of functionless junk.

Rather, I said that in the stuff commonly called junk DNA (which excludes all the stuff that we already know has function, even an 'inconsequential' function) we would continue to discover functional stretches (and even genes, as your link demonstrates), but a residue of functionless junk will remain.


And how long could we continue to discover 'functional stretches' befire we abandon the idea of 'funtionless junk'.

And why would we bother to keep looking if we expect to find functionless junk?



essentialsaltes -> RE: Regulating Evolution (4/21/2008 2:20:01 PM)

quote:

ORIGINAL: Jhud
And how long could we continue to discover 'functional stretches' befire we abandon the idea of 'funtionless junk'.


I don't know. Maybe we'll find out.

quote:

And why would we bother to keep looking if we expect to find functionless junk?


None of the discoveries that you have mentioned or that are in the SciAm article were made by people who didn't bother to look. Go ask them why they bother. They may respond that it's part of science to test our understanding of nature. Or they may respond that they had a hunch. Or they may respond that a piece of data jumped out at them, violating their expectations and inspiring a closer look. Despite the pejorative term 'junk DNA', scientists haven't stopped looking into the matter.



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