Douglas J. Bender

scigirl,


No, it is you who once again misunderstand me. (Hanging my head down, and shaking it slowly and sadly, and suddenly noticing that I need to get a new shoelace in one of my trusty "Wolverine" workboots.) I was not thinking that you thought that that one specific gene (or whatever) was the only difference between humans and chimps - I was trying to highlight the fact that it ISN'T the only difference (the "fusion point"). I was trying to get you to be the one to "'fess up", as it is more dramatic that way.

I caught that part waaay back.

I'm good with numbers - I understood that part right off. (But what's a "gamete"? )

I understood this part, too. Am I on top of things, or what?

I noticed that in that picture. But initially I thought it was some kind of abstract painting.

I understood this point, as well, first thing. I amaze myself, sometimes.

And is it known for a fact that the new "non- functioning" centromere plus telomere does not have some new function, given its placement in the chromosome?

So, is that where transvestites come from? But, I kind of gathered all the above, some time ago.

No, it's NOT. What you actually should say, to be precise and completely accurate, is: "So, the idea that the hypothesis that our chromosome 2 came from a fusion of two chimp chromosomes is possible is well-supported by the evidence."

That's not what I said. The way you phrase it, it makes it sound like God intentionally decided, "Now, how can I get a human chromosome to look like a chimp chromosome? I know - I'll fuse two chimp chromosomes. It'll be so cooool." I had said that perhaps those particular "parts" (which are unfused in chimps, and fused in humans) are necessary for both chimps and humans, and for whatever functional or other reason, God chose to fuse them in humans, and to not fuse them in chimps - they no more indicate "common ancestry" than would similar parts on two different robots, for example.

I wasn't making an "inference", scigirl - I was pointing out a contrary "hypothesis", one which is consistent with the evidence, and which shows that your "inference" is not a "necessary" one, unless one starts out with a purely "naturalistic" set of assumptions.

No need to. I KNEW that you were "talking about one specific phenomenon in the chimp-human evolution, not the entire genome". I was trying to get you to be the one to "admit" that you were not talking about the "entire genome", and that thus there are other "pieces to the puzzle". Thus, the "fusion" point is just one piece of evidence, and one which can be just as easily explained, in the context of a "Designer", by seeing it as simply the Designer's decision to perhaps more efficiently use two "parts".

You miss the point. The point is, scigirl, that UNLESS ONE STARTS OFF WITH A PURELY NATURALISTIC SET OF ASSUMPTIONS, one can no more conclude "common descent" from the "fusion point" evidence you describe than one could deduce that two robots who shared similar parts, fused in one and unfused in the other, had "evolved" from a common robot ancestor (perhaps designed by a really clever robot designer, who could design his robots to "evolve").

It would only possibly be "faulty" IF it was proven that the "extra telomeres and the centromeres" didn't actually do anything. But, you tacitly admit that this is not known for certain, when you say, "...the extra telomeres and the centromeres don't APPEAR to be doing anything". You know, I seem to recall how evolutionists, even less than a month ago, were trumpeting God's incompetence in having a genome with so much "junk DNA" - turns out that that "junk DNA" actually serves a function, apparently (or at least, a fair portion of the "junk DNA" does, which would suggest that the rest of it does as well, we just don't know what it is yet).

Oh? And why not?

Be careful not to speak too soon, as did so many earnest but mistaken evolutionists when they proclaimed the genome to be "full" of "junk DNA". And, if our genome is such a "mess", then why is it that that particular chromosome (which appears to be a fusion, in the human, of two chromosomes in the chimp) happens to have been spared all the "random mutation" messiness which has so affected our genomes? (If I'm understanding you correctly.)

Sounds like a form of "redundancy"/"plasticity", kind of thing (sort of like the brain - damage a part, and there's another part which can take over...not everything necessary for a particular function is lost if a small area is damaged). Sounds like a good idea to me, actually. And, how would evolution explain this? I mean, how could it "evolve" the encoding of a protein complex by genes "on several different chromosomes"?

There might be other reasons why this would not be so advantageous, and which would indicate you would not have made a very good "glorious creator". Of course, I can't comment on the specifics, as this is not my area of expertise.

Okay. So, why would this not be evidence of a very flexible "design" pattern or style, but rather it would be evidence of inefficient and stupid evolution?

Maybe because there's a function or importance to them that we silly humans just don't understand yet. Or are you claiming that scientists now know everything?

I hope you didn't give in to the temptation to insult or attack me, scigirl. You've got to learn not to take my disagreements with your conclusions personally.


In Christ,

Douglas

[ June 15, 2002: Message edited by: Douglas J. Bender ]</p>

lpetrich

Sex cell; egg or sperm cell.

That former centromere may have become co-opted into having some other function, but one thing is clear: it is no longer serving as a centromere.

Is that supposed to be a joke?

DJB can barely conceal the fact that he does not have a real answer; "Goddidit" can explain essentially anything. Also, DJB's scenario reminds me rather strongly of Philip Gosse's "Omphalos" hypothesis of created appearance, which states that God had created the Earth only about 6000 years ago, but with the appearance of having been much older. Though PG argued that that had been a logical way for God to create, his hypothesis was often considered divine fraudulence.

Robots don't grow and reproduce, so that analogy is a poor one.

From this argument, one could argue that DJB had not come from two human parents, but instead, that he had miraculously popped into existence into thin air, having been miraculously created.

I wonder if DJB understands how this conclusion was reached. The short bumper-sticker answer is that it was reached with the help of knowledge of patterns of evolution.

To expound in detail, this was a result of comparing our genome with other genomes, such as those of chimps, mice, dogs, and fish. Some parts are strongly conserved (close sequence matching), while some parts are not. Protein-coding parts are generally conserved, which is a result of being selected for specific functions, but the big surprise is the finding of a large number of conserved noncoding parts. These most likely have other functions, such as gene regulation and coding for functional bits of RNA; exactly what functions many of these parts have is unknown.

But much of our genome has poor sequence conservation, meaning that it evolves with little or no selective constraint. This suggests that those parts either have no function or have some function that imposes very little sequence constraint, like being "stuffing" or mutagen sinks or whatever.

I think that SG is trying to avoid the Philip-Gosse created-appearance hypothesis.

Being multipart, maybe, but scattered all over the genome?

Dr Rick

Mr. Bender:

Do you accept?

Rick; moderator of the FD&D forum.

scigirl

Ok here we go again,

Sperm or egg cell. We have 23 chromosomes in our gametes, but 46 in our somatic (body) cells.

To my knowledge, no known function has been found for the extra centromere. Note - it is not just an extra centromere, it's a sequence that sure looks like the chimp centromere.

from <a href="http://www.gate.net/~rwms/EvoEvidence.html" target="_blank">the evolution evidence page</a> again:

Bold added by me. Note - the 2q chromosome is the chimp one.

About function of the telomeres:
Are these telomeres functional? I think not, they are in the wrong direction (which makes sense, if you think about how the fusion must take place. It helps to look at the picture again.)

I believe the burden of proof is on you to prove their function. Evolution provided an testable explanation, the evidence supported this explanation, and it is the answer I'm sticking with, until someone can show me that the centromeres and telomeres are 1) doing something AND 2) explain how they got there in the first place.

Well, basically, yeah that is what you are saying, although I don't think you realize it. The sequences coupled with their location are just too similar for me to believe anything but a chromosome fusion. It just makes logical sense.

No, your robot analogy is not good enough. First of all, you have to demonstrate that the extra centromeres/telomeres have a function. It appears right now that they don't.

This is from another chromosome (chromosome number 4), but here's some preliminary work addressing your question whether extra telomeres are functional.
<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=117319 35&dopt=Abstract" target="_blank">A cascade of complex subtelomeric duplications during the evolution of the hominoid and Old World monkey genomes.</a>
So in this case, one of the duplicated genes in the telomere appears to be functional, whereas the other one became useless (but this has not been conclusively proven yet).
Well Douglas, that is what scientists do. All of them - the ones that study cancer, the ones that study black holes, the ones that study evolution. In this case, they started out with a natural assumption that the chromosomes fused. Their data supported this hypothesis. Furthermore, other data indicate that chromosome fusions do indeed happen and can be observed (they can and have been observed in our lifetimes). So there was no need to invoke the chromosome fairy. There still could be a chromosome fairy, but it is useless to include her in the Science paper, because you don't need her to do anything for the fusion to work.

Obviously, just because there is a naturalistic explanation for planet orbits, or for thunder, that doesn't mean there is no supernatural deities. Why do you object to evolutionary biologists looking for natural explanations, but not other scientists? Or do you object when a scientist looks for a natural cause of cancer, rather than a satanic one? I'm very confused as to why evolutionary biologists get 'special' treatment, out of the long list of scientists who attempt to study and explain the natural world in order to improve it.

You asked why your explanation doesn't explain the locations? Well, when you do genetic engineering (say, you insert a gene in a mouse), usually you just throw it in there, and it integrates into any old spot in the DNA. And usually, it works just fine. Actually, you can stick it in a bacterial plasmid, insert that plasmid in the eukaryotic cell, and the gene usually works without ever being integrated into any of the euk chromosomes!

It seems that the locations of genes do not seem to matter much - this is an assumtion based on the fact that multi-subunit proteins are encoded by genes that are scattered around the DNA (in what looks to us a haphazard fashion).

So, if genes don't need to be in a particular order (as evidenced by genetic engineering AND just common sense observations about proteins), than why are so many genes from so many different organisms lined up in a pattern that is consistent with evolution?
I was not talking about redundancy here, I was only talking about order. Where the genes are (not how many, or what shape they are in). Why are they so scattered around, not only what looks like to be a haphazard pattern in terms of function for that particular organism, but also in a pattern consistent with evolutionary trees? In nearly every organism we have sequenced? Again, God either set evolution into motion, or He wanted it to look like we evolved.

Gene duplication, transversions, jumping genes, transposons, etc etc. Many different genes tell interesting evolutionary stories. I'll dig one up for you and tell you about it next time, for this post is already too long.

Hey, be nice to evolution, what did it ever do to you? Plenty, actually!

What I am trying to impress upon you is this:
1) Genes do not appear to need a particular location in order to function. This is true with gp91 that I study in my lab--one of the 5 genes in NADPH oxidase (you can introduce it as a plasmid and it still works).
2) Genes do not have a particular order if you analyze them according to what they do in a given organism (again, the NADPH oxidase genes--there's 5--are all on different chromosomes).
3) These same exact genes are in that same weird haphazard order in related organisms. For example, gp91 is on the X in humans, and lo and behold, it's also on the X in all the animals that evolution says are our relatives.

If #1 is true, than why do we see #3, if not for evolution? If each animal were separately created, this to me seems like a pretty amazing coincidence that gp91 is always on the X, even though we can show it doesn't need to be on the X.

Why?

But the evolution explanation works!

Should we abandon all of our working theories and models about the universe because we might be wrong? Or should we keep using the ones that work fairly or really well to explain the evidence, until data surfaces that shows our models are wrong?

I vote for the former. So out with it, prove that the extra centromere and telomeres in chromosome 2 are necessary, and show me where they came from.

Here's some more evidence for you:
<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=118630 72&dopt=Abstract" target="_blank">Direct evidence for the Homo-Pan clade.</a>
Again, another amazing coincidence, or evidence for evolution?

The thing is Douglas, there is no way to prove to you that evolution happened, if your answer is to say, "well all that evidence just means that God wanted it that way." Why is it that all this data just happens to align with our evolutionary trees that we made just from fossil records and other types of data? Is that just an amazing coincidence too? The ordering of the genes (even though they don't need to be in that order), the ordering of the "junk," the extra centromeres and telomeres, the transposition data in the Y, etc, etc. This data is piling up higher and higher, and nearly every time, the data supports our trees that we made before genetic experiments. Coincidence, God wanted it that way, or evolution?

I wonder, if evolutionary theory is such a good predictor of where genes are going to be in an organism, even if it didn't really happen, why does it matter to you? You might as well accept the predictions/conclusions of evolution anyway, since so far, here's the score as I see it:

* Specific predictions about genes made by evolutionary theory that just happened to come true: thousands
* Specific predictions about genes made by the 1st chapter of Genesis that just happened to come true: zero

So why not just accept evolution, and say, "God set it into motion" or whatever, since you are forced to accept the conclusions anyway (instead of saying 'humans have very similar chromosome patterns as a chimp that in fact look like evolution but are not at all from evolution')??

scigirl

Douglas J. Bender

lpetrich,

Oooooo - ya' caught me there, lp. I was hoping nobody would notice. Drat.

I am NOT here arguing anything similar to "appearance of age". I have simply pointed out that if a Designer (whether God, or simply a really sophisticated and advanced human being who is capable of creating robots which self-replicate) created two similar things or robots with similar or exactly the same parts, that in one case He/he could have fused two of those parts for some purpose (efficiency, perhaps?) in one of those things/robots, and left them unfused in the other. Very simple. So, if someone was to find, say, two such robots, they COULD NOT conclude, just from the fused parts, whether those two robots were created that way, or had "evolved" that fusion during their history of self-replication.

So, is there any reason why robots will never be able to be designed such that they "grow and reproduce"? If not, then the analogy is a very good one.

No. Because we KNOW that human beings are created through two "parents", and have never observed human beings being "miraculously created" out of "thin air". On the other hand, we HAVE observed robots being designed, and we have observed robot designers using exactly the same parts, and sometimes "tinkering" very slightly with those parts, and we have observed science increasing in knowledge, and we deduce/extrapolate that one day science will be able to design robots which self-replicate. (Here, the argument is like scigirl's to me in the "Formal Debate": "Prove to me why microevolution over time cannot result in macroevolution". In this case, it's: "Prove to me why advances in robotic design, over time, could not result in robots which self-replicate". Granted, it might be very difficult to do, and might take many, many years of research, but in principle, that's no real limitation.)

In Christ,

Douglas

scigirl

ROFL! Oh, Douglas, can I quote you on that? Pretty please?

scigirl

lpetrich

DJB, as I understand you, you are claiming that fused vs. separate chromosome 2 parts are something that is appropriately functional in each species. However, there is nothing known that suggests any such functionality, and there is an abundance of nonfunctional parts of genomes, like pseudogenes, copied-in retroviruses, and "parasitic DNA".

Sorry if I misunderstood you on that point; I was extrapolating from present-day robots. DJB, you seem to be claiming that we ought to take special creation seriously because we can never rule out the hypothesis of special creation that looks exactly like evolution.

Sorry if I was not being clearer. I was illustrating the possibility of having been created with the appearance of age.

scigirl

All right, I'll play the robot game. Let's say we are watching a junkyard wars marathon, and we tune in to find the following robot had been constructed:

1. A robot with a one-piece arm. This part had a hook on it that attached it to the main frame, and also had a characteristic blemish on it--say, a big red stain.

Now, let's say that the old creations get left in the junkyard, and can be used in future shows.

Next week we find this robot:

2. This robot is much different from last week's robot. The arm is composed of two pieces this time. The piece that attaches to the main frame (the "upper arm) has a different hook from the first robot arm. But then we notice that there's a piece that was welded by the team to the upper arm (i.e. the "forearm) that, strangely enough, looks just like the main arm from the first robot. In fact, the hook is still there, but is not hooking to anything. Also, this forearm has the same red stain, and is the same size.

Would you conclude the following?

A. The junkyard wars team constructed the second robot arm from scratch, they stuck a hook on the forearm even though it wasn't hooking to anything, and also put a red stain on it.

B. The team found the first robot in the junkyard, took the arm, and stuck it on their new robot?

That, I believe is a better analogy. Robot A's arm represents one of the chimp chromosomes (how about 2q), robot B's arm represents human chromosome 2. A piece of chromosome 2 looks just like 2q - same size, same blemishes, same non-functioning hook (at least it looks non-functional). The centromere does actually function as a hook--the microtubules attach to it to pull chromosomes apart during meiosis and mitosis. Chromosomes only need one. We have not observed any known function for the extra centromere in the human chromosome, but yet, there it is, looking just like the centromere from 2q, blemishes and all.

scigirl

daemon

Actually, this is not an unreasonable assumption. Given several near-identical designs, it is probable all are modifications of an intial base design, which may or may not be one of the given designs. This is not a terribly bad analogy for evolution, really.

scigirl

Douglas,

Well? Anything to add about the human/chimp chromosome fusion event?

scigirl