Is all TRUTH scientifically knowable?

Answer to the retroviral insert argument:

From this site:

http://www.trueorigin.org/theobald1e.asp

Listed as prediction 19... contains a more detailed answer to the common ancestory argument.

UT, At a minimum, this negates your argument that common ERV's provide certain evidence that man and ape evolved from a common ancestor.

 

Phillip, I think the target of UT's clarification was me, not Meyer.

I am citing someone who is not YEC to support YEC. Willingly acknowledged.

If he thinks Meyer's ID beliefs disqualify his authority then that tells a whole different story about who is close-minded to the evidence.

 

"Did you not read the other post? That citation comes from evolutionists writing in the Proceedings of the National Academy of Science. They say that the greatest genetic complexity occurred at the beginning and has since been simplifying."

I have read it. I will be getting to it eventually.

"It is more consistent than macroevolution."

No, there are certain things you would expect to see if your assertions were true. We do not see those things.

"Meyer's quotes are further confirmation of this trend."

Meyer is ignoring evidence of transitions before the cambrian and is stretching by saying the all amphibians, reptiles, birds, mammals and fish are just minor variations on the bilateral body plan. If you are willing to accept that all tetrapods are merely minor variations that came from a single bilateral ancestor let me know.

"All of the things you list above are ultimately speculation... educated guesses."

Nope, there are several examples of recently observed instances of new genes and functions.

Did you read the two papers above and the abstract exerpts I posted for you?

"The few that are deemed beneficial would never amount to anything close to the ascendency of a new biological system."
Is this an admission that new "information" does arise?

What is information?

What would you accept as an example of new "information?"

 

"BTW, Have you found the number of shared ERV inserts between men and apes? I would be interested in how many there are compared to those shared between apes species as well.

Again, the only one I have seen you post as shared between man and ape is the one effecting Vitamin C production. "

You are talking apples and oranges.

The vitamin C gene is an example of a shared pseudogene.

I have given a link to a paper that details twelve specific ERVs. My impression from what I have read is that there are on the order of magnitude of dozens of inserts that are unique to the apes.

Some of the ones in the paper are HERV-K HML6.17, HERVK-18, HERV-K(C4), RTVL-la, RTVL-Ha, RTLV-Hb, RTLV-H.

I can only remember coming across one insert that is in humans but not the other apes.

 

"No more nor less than the Cambrian bottleneck proposed by evolution. "

You will have to explain that one.

If all lines have to go through the ark, then they all go through a bottleneck of two individuals with at most four different copies of each allele. We do not observe such a lack of genetic diversity.

What bottleneck are you proposing at the Cambrian explaosion?

 

"First, that isn't a necessary outcome of a rich genome..."

Yes it is.

If there were many different genes that were capable of giving different lines different abilities, then we would see remnants of these genes scattered about as pseudogenes. We don't. And I do not know of a mechanism to neatly snip out all of these unused genes. Do you? Especially since many (most I think) genes are not continuous sequences. They are scattered about and are assembled by the cell. YOu'd have to snip all the pieces and their markers without getting any of the surrounding sequences.

"Second, it isn't the closely related descendents that are most in question. "

Let me define close as those that you would say came from the same "kind." (Just what is a "kind?")

THose that came from the same "kind" should see that there differences are in what genes are turned on or off. Instead we see the differences as being changes in functional genes.

 

"That's not at all true. There should be significant connection but also disconnects... and that is what the fossil record shows."

No. Think about it. Fossil trees show a bushy, branching pattern going back. You propose a case where you have all these parallel branching lines. Then you cut off all branches but one in each line. Then they start branching again. Not what we see.

"I have read some well educated men who disagree with you. "

You need to read up on a field called taphonomy. It is the study of how fossils are made from death until the fossil is found.

The fossils we find are incompatible with being formed in a large flood. For example, how do you have scavenging of an animal that drwoned in a big flood by scavenging land animals?

http://paleo.cortland.edu/tutorial/Taphonomy&Pres/taphonomy.htm

"...naturalism does for explaining complexity or the origin of information."

YOu did not read all that I provided for you, eh? People who are familar with the subject have no problem expalining where the genetic diversity comes from. I have given you at least a couple dozen examples of the processes in action. You simply deny it.

 

"UTEOTW, I find this statement quite enlightening. I spend a lot of time analyzing testimony and statements and this one has disturbed me.

You claim to believe in God and God's hand in creation (even if it is through evolution), you claim to believe in the virgin birth, Jesus as diety and His miracles, and miracles of the disciples.

Then you make a blatant open ended statement that says that "Meyer is an ID advocate". Setting the tone that "Meyer" obviously has a problem with his theories because he uses an intelligent design factor in his studies."

It was simply informative. The readers may not know who he is. I thought it might be beneficial data. I did not comment on this fact either positive or negative.

I have tried to be very polite and patient in these discussions. YOu should have known that was not an attack.

While we are on the subject of Meyer, you may want to congratulate him for being one of the few IDers to get a paper published.

Meyer, Stephen C. 2004. The origin of biological information and the higher taxonomic categories. Proceedings of the Biological Society of Washington 117(2):213-239.

 

"Answer to the retroviral insert argument:"

Apples and oranges.

That is talking about retrotransposons. I am talking about endogenous retroviral inserts.

 

"Oh... I ran across a very interesting piece of info today. You claim that my contention for "descent" from a rich genome is without basis. Read the story "Genes evolving downward" on this site: http://creationsafaris.com/crev200502.htm "

Before tackling this, it might be of some use to explain just what introns are. This also has bearing on something I posted above.

Most eukaryotic (cells with a nucleus: plants, animals, fungi, etc.) genes are broken into many little pieces. Prokaryotes (bacteria, archaea) are not so arranged. In prokaryotes, there is no nucleus and so when DNA is transcribed into mRNA it is almost immediately then turned into proteins. In eukaryotes, the mRNA is made in the nucleus which then travels out into the cell to make the proteins.

Now, in eukaryotes, most of the genes are divided into little bits. The bits that code for proteins are the exons. The "junk" in between in introns. This works for eukaryotes because there is time for the introns to be removed from the mRNA before the proteins are made. This does not work for prokaryotes because there is not time to snip the introns and they would disable the function of the proteins.

So to begin with you are talking about how much junk there is in between the functioning parts of the genes.

This is also where I point out that you have intimated that perhaps the extra genes in your rich genome scenario could have been simply deleted. To do so, you would need a mechanism that could track down all those exon and neatly snip them without leaving a trace or damaging surrounding cells. Well, even if you did htis, you still have the problem of the differences between species being variations in existing genes mostly and not differences in which genes they have or that they express.

An aside is needed here. This in itself may be considered evidence for evolution and may shed light on the mechanisms. That the genes are formed from scattered pieces of DNA is thought by some to be an indication that they are combinations of earlier, simpler genes. More importantly, there is a process called exon shuffling where organisms make new genes by combining these exons into new combinations to make new genes. The individual exons are like pieces of a toolkit that the organism can then use to make different things. This is another way to generate new genes and new functions. You likely would not consider it new "information" because it is merely using what is already there in a new way, but it shows that such definitions of "information" are at odds with what happens in reality.

Back to the story. Look at your quotes again closely.

This sounds to me like he is saying that the the ancestors had fewer introns than the descendants but this is still more than expected.

Next issue is the complexity one. Let's consider closely what he means here. He means that his study shows that early eukaryotes had more introns breaking up thier gene sequences than was expected. Hardly a groundbreaking discovery for ID or a young earth. This is a key point.

Instead what we see is a fair amount of variety in the number of introns among the species. His paper shows that some early eukaryotes had more introns than expected, but when you look at the total picture, you still see an increasing percentage of such junk as you get to what you would consider more complex organisms. There is, however, a lot of variety in this as some lines may have experienced duplications or losses that others did not.

Now, there is another point that should be raised about introns. Some ARE useful. In short, some of the introns are coded into RNA which then controls the expression of genes and is considered to be a part of how eukaryotes control their increasing complexity.

This, again, has bearing on evolution. This time going all the way back to abiogenesis. It is thought that one stage along the development of life was the RNA world. This was a time where life depended on RNA for both information carrying and for carrying out cellular function. It turns out that RNA can do most of the roles of proteins if not as well as proteins. So there is thought to have been a time when RNA served both roles before evolving to make DNA and proteins as better alternatives. Anyhow, if the RNA world was true, it should come as no surprise that bits of RNA would still serve important cellular functions.

This brings us to another reason why you could see such variation and loss. Ne intorns could be created by varous mutations. But only these few that serve a purpose would be conserved. The others could be made, mutated, and deleted without harm. This also explains why some introns are actually very ancient. Those that are involved in regulation would tend to be conserved.

So, just how do you think this supports your ideas?

Why would an intelligent designer throw a bunch of extra junk in between the exons just for it to be deleted with time?

 

The only thing I can think of is that you are so determined not to give in on evolution that you are intentionally not seeing things.

It was the conclusion of these writers, evolutionists, that genetic thought must be reconsidered since the evidence supports the idea that the ancestors were more genetically complex and have moved toward more simplicity.

You aren't arguing with me but with people who are trained in this field... and who you would otherwise agree with if their conclusions supported evolution.

This does have to do with abiogensis... it is strong evidence that it did not occur. If all we see from the very beginning to now is a process of simplification then that precludes the idea that life arose from inanimate chemistry.

As far as mechanisms are concerned, that isn't necessary for this information to weigh against macroevolution. This information demonstrates to a very large degree that speciation did not occur as animals acquired new, useful information through mutation or any other known mechanism.

By the way, they weren't claiming that some past eukaryotes had more introns. They indicated this condition as the norm.

I know you would rather not consider the implications of this information but your post seems to be an effort to bend/conform this evidence so that it does not contradict what you required to be true.

First, just because someone said it is junk does not mean it does not have a function.

Second, just because it doesn't have a currently known function does not mean it was useless in the past... especially if there was an exceptionally rich genome that does not exist today. That condition could have necessitated functions that fixed species do not require.

Third, your question is rhetorical. Why did God save me... or you? He could have chosen not to. As far as the grand plan is concerned, you and I could rightly be considered "junk". He doesn't need us. We are actually worse than junk- we don't deserve to exist.

To question God's motive on this is to question God's sovereign ability to do whatever He wants. Maybe His purpose is to test Christians' faith in His Word. Maybe it is specifically to see if we would trust His wisdom or man's wisdom.

 

What am I not seeing? The complexity that they are talking about is that the older eukaryotes had more junk between their exons than were expected. You own quote shows that the further back you go that there was less of the junk just more than expected.

I think you fail to understand what an intron is. Introns are the bits of junk between the exons. The exons are the functional bits that when combined make up the functional gene sequences. Did you even read my whole post? That was pretty clear. Feel free to google if you doubt that basic statement. Introns have to be trimmed out before the gene can be put together. I was also clear that a limited class of introns do have regulartory function.

"You aren't arguing with me but with people who are trained in this field... and who you would otherwise agree with if their conclusions supported evolution."

Their conclusions are not contradictory. I fail to see where you have made a case that they are.

"This does have to do with abiogensis... it is strong evidence that it did not occur. If all we see from the very beginning to now is a process of simplification then that precludes the idea that life arose from inanimate chemistry."

You do not understand what the authors meant. They were not meaning complexity in the sense of being able to do more. They meant it in the sense of a higher ratio in introns to exons than expected.

And there is a case to be made for this being relicts of the beginning of life. The way the exons are scattered and then assembled into functional genes shows that they are likely combinations of simpler, earlier genes. Why would a designer starting from scratch divide all those sequences up only to have to go through a process of putting them back together? The use of RNA from a class of introns in cellular function is also a single that the RNA world hypothesis is on the right track.

"This information demonstrates to a very large degree that speciation did not occur as animals acquired new, useful information through mutation or any other known mechanism."

YOu will have to explain that one. Exon shuffling is a key related bit here and is a mechanism for generating new function. The intron losses are losses of junk between the functional bits.

"I know you would rather not consider the implications of this information but your post seems to be an effort to bend/conform this evidence so that it does not contradict what you required to be true."

There is no bending necessary. They found that ancestors had a bit more junk between the functional bits than expected. There is nothing to twist.

"First, just because someone said it is junk does not mean it does not have a function."

Then why did we waste bandwidth on a paper about how useless introns can get trimmed with time?

"To question God's motive on this is to question God's sovereign ability to do whatever He wants. Maybe His purpose is to test Christians' faith in His Word. Maybe it is specifically to see if we would trust His wisdom or man's wisdom."

This logic I cannot stand! God faking evidence to test us? You believe in a different god if you think that IMHO.

 

You need to go read the whole article. I only posted portions of it but it isn't very long. The meaning wasn't that more introns have not accumulated but rather there even more of them present in the past. From the same quote: " Intron losses outnumber gains over a large range of eukaryotic lineages."

So it isn't less "junk" in the past (although that it would be a completely unjustified assumption to call it "junk") but rather more complexity. In fact, I found an article that suggests that introns may be useful error prevention/correction.

Again, this was their conclusion- not mine alone... My theory however did predict this to be true, did it not?

I won't claim to have a complete knowledge but I did do some self education after reading the article and before posting it here. I understand basically what introns and exons are and the basic functions.

They said this was proof that eukaryotes had more genetic complexity in the past and that the trend is toward simplification. They did not have a means of assimulating that information adequately into TOE so they left it open ended. Their conclusion is contradictory to the notion that eukaryotes have been becoming more and more complex.

On the contrary, I am pretty sure I do understand what they meant but have no reason to deny the implications.

If they meant something different than what they wrote then they could have expressed it differently.

Here is what they concluded with: "These results contradict the assumption that genome complexity has increased through evolution. Instead, species have repeatedly abandoned complex gene structures for simpler ones, questioning the purpose and value of intricate gene structures. These results suggest a reconsideration of the genomics of eukaryotic emergence [sic]."

Whether they think the complexity meant more function is completely irrelevant especially since they didn't speak to it.

What is relevant is that descendents with less complexity are going to have no better than equal function/variability than the ancestor... unless there is a strong, persistent mechanism for adding new, useful information. The information of course isn't just the simple matter of a small mutation of a genetic pair with no beneficial effect but rather the kind of information that suddenly gives rise to complex biological systems that give the species a survival advantage. This is something that evolutionists would love to find but fail. Even the Cambrian evidence I posted from Meyer weighs against such a notion.

The better question is why do you assume a speculative explanation by men as truth then question God's purposes based on that assumption. It should be obvious that God's creative genuis far surpasses ours and even our ability to understand.

To submit our inability to understand why He might have done something as evidence against His having caused it is ridiculous.

Nope. There are way too many other problems with that view to be saved by something that doesn't directly support it any way.

It is far superior and infinitely more biblical than suggesting that human understanding places a limit on what could or could not have done or even would or would not do.

And yes, God does allow us to be tested by things in this natural world... things that to our natural sensibilities seem good, right, and beneficial. If the evidence for corruption and descent evident in nature causes you to look for an explanation based on the wholly unbiblical concept that everything is and always has been evolving into something better, greater, and more organized then that is your problem, not God's.

However the Bible is clear that this world is in a process of general decay and is getting worse- not better. The best it has ever been is when God called it "good".

 

Where did you find the whole article? There are just snips on the link you provided. Since you said you read the whole thing, can you provide a link to where it is found? I looked this morning and could not find it.

 

I was referring to the article on that page and if you thought I was referring to the whole original article, I apologize for the misunderstanding.

They do provide the reference and you can go to the PNAS website for the whole article... but I do not have a subscription.

 

I think about the only thing to do at this point is to send you to other writings by the same authors and see if you cannot get a sense from them what is actually being talked about.

Let's try this one first.

http://www.pnas.org/cgi/content/full/95/9/5094

The summary would be that many of the introns were formed just after the split between prokaryotes and eukaryotes. Many new genes were formed through exon shuffling and in the process many introns were formed. One bit of evidence for this is that genes that are found in both groups are continuous in the prokaryotes and are split by introns in the eukaryotes. This might also help convince you that the complexity spoken of is simply in how many introns are splitting up the exons.

You will also find a section on predictions if this is true and what has been found and what still needs to be examined.

You can also find some of Gilbert's other papers here.

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&db=pubmed&term=Gilbert+W[au]&dispmax=50

Roy is just one of his grad students.

Here is a different listing of his papers.

http://mcb.harvard.edu/gilbert/pubs.html

 

Very interesting! All this demands is a presuppositional belief in evolution and it is palpable. Otherwise, it is not great science.

 

Do you care to explain what is wrong with this science? This material has all been peer reviewed. What did you find wrong with the papers that the reviewers missed?

Maybe you would like to assert yourself into the discussion we have been having about ERVs and furnish a mechanism that explains the observations.

 

Sure it has been peer reviewed. Reviewed by scientists with the presupposition that evolution is a fact and not a theory.

I ask for the seventh time:

How can you believe in your heart that an omnipotent God exists, and not allow for a supernatural variable within the creation? Without this variable you must admit that you have bad science.

 

"Sure it has been peer reviewed. Reviewed by scientists with the presupposition that evolution is a fact and not a theory."

You are free to read the paper yourself. The full article is available through the link I provided. If you can find where their methods were incorrect then you can spell it out for us here or send your concerns straight to them.

"How can you believe in your heart that an omnipotent God exists, and not allow for a supernatural variable within the creation? Without this variable you must admit that you have bad science."

And I have answered you more than once.

I DO allow for the supernatural. But I think it demeans God to invoke the supernatural at every opportunity. When there are natural explanations, I find it easier to accept that it is the correct explanation and that it is a part of God's will.

You sound as if you would leave us in the precarious position of never knowing what is real and what is supernatural. Does the earth really orbit the sun because of gravity or are there angels pushing the earth around the sun just so? Do acid-base reactions really happen naturally and repeatably or does God take a personal interest in every molecule of acid or base that come near to one another?

In the case of evolution, there is no problem with the natural explanation. It works well without the need for intervention. The data points to it. The mechanisms explain it and can be seen. There is no need to invoke a supernatural cause for any of it. To do so becomes arbitrary and capricious. Common descent explains precisely what we see with regard to ERVs. Could God make things look that way? Sure! But I do not accept that He would supernaturally intervene to make it look like evolution happened when it really did not. If you think that He would, then I gues we are at an impasse. If you do not, then we are back to the natural explanation.

This is why I have tried hard in the past to get you to come down on one side of the fence or the other. Either you think the world is young and the data shows it. Or you think the world is young and God made it appear to be the product of long term processes for some unknown reason. If the former, then we can get back to the data. If the latter, well we have nothing to discuss once you admit that everything supports OE yet you still reject it.