Being an engineer and not being a biologist/geneticist, some honest questions have come to my mind after reading through the references above:
- Are the remaining 22 chromosones identical between humans and primates?
- Are the experiment conditions listed in the paper comparable to "actual" conditions? [I'm still trudging my way through the paper, but I find reading biologist-ese difficult; I require a translator ;) ]
This an open invitation to civil discussion on the above references. Ad hominem comments are not welcome and will be deleted.
Side note: this appears to be along the lines of what Dr. John A. Davison is proposing, that macroevolution occured in the chromosones, not the genes.
Are the remaining 22 chromosones identical between humans and primates?
ReplyDeleteDepends on the primate. If you are talking about chimpanzees, they are not "identical", but nearly so. It also depends on whether you are talking about the order of genes on the chromosomes, or the exact DNA sequences. If the former, yes, the chromosomes LOOK almost identical, with genes in the same places on chimp and human chromosomes. If you are talking about DNA sequences, there are obviously quite a few differences. I know that there are some differences in the Y chromosome, not the order of the genes on the chromosome, but sequence divergence in the 5-6 million years since we had a common ancestor with chimps. Since that paper was published in 1991, there have been lots of advances in genome sequencing. Here's a more recent paper (Ebersberger I, Metzler D, Schwarz C, Paabo S; AMERICAN JOURNAL OF HUMAN GENETICS, 70(6): 1490-1497 Published: JUN 2002). I can send you a PDF if your library doesn't have access.
Are the experiment conditions listed in the paper comparable to "actual" conditions?
I'm not sure what this question means. The experiments in the paper cited were basically standard DNA isolation, cloning, sequencing and such. Those are "actual" conditions... I'm sure that, given the vintage of this paper, the conditions for doing all of those experiments might have improved in the interim, but I don't think that the experimental conditions themselves have been implicated as any sort of problem for the conclusions reached.
I have a feeling that is not what you are asking about, however. Can you be more explicit?
It's sort of amusing that this primate example is THE example of a prediction made by common descent. Scientists test predictions made by common descent on a daily basis; DNA cloning and almost all of molecular biology would be impossible to do if you didn't have common descent as a baseline assumption. So far all of those predictions seem to have generated fruitful experiments, papers etc. But the idea of primates giving rise to US is probably controversial in the minds of some at TT, so it was a good choice by Dave Heddle.
dave, please do send the Ebersberger et al (2002) pdf.
ReplyDeleteWhat I mean by "conditions" is this: is the "environment" provided by this and other experiments showing similar results applicable (to put it very roughly) to the insides of a primate where the fusion would have to occur.
PDF is on the way, along with another recent and elevant publication in the area.
ReplyDeleteRe this What I mean by "conditions" is this: is the "environment" provided by this and other experiments showing similar results applicable (to put it very roughly) to the insides of a primate where the fusion would have to occur.
The fusion occurred millions of years ago. The paper cited was NOT attempting to reproduce that fusion event, rather it was merely looking at the sequences (clues, in your parlance) to see if telomeric sequences (characteristic of the ends of chromosomes) could be found within human chromosome 2, and also whether that human chromosome had 2 centromeric sequences, consistent with its origin from two separate functional chromosomes. Both of those predictions were borne out by the data, and subsequently refined by several other labs. They did not attempt to fuse chromosomes at all. There are, however, LOTS of ways that chromosomal fusions can occur, so i don't know what that would prove, exactly...
"They did not attempt to fuse chromosomes at all."
ReplyDeleteLike I said in my post, I found it tough to understand what the authors did in their experiment since my biologist-ese is rusty. ;) That said, thank you for the mini-translation in your second comment.
Next question:
I would think that it would take at least some energy to fuse the chromosones and that the fusion process would emit energy. (In a sense, this sounds a little like what Shapiro mentioned in this SciAm article.) So the question now becomes what is/are the effects of this fusion (if any) on the surrounding environment (primate body - both local and global)?
Local = immediate area where chromosone fusion occurs ("educated guess": ova/sperm)
Global = adjacent body parts and/or entire body structure.
I would think that it would take at least some energy to fuse the chromosones and that the fusion process would emit energy. (In a sense, this sounds a little like what Shapiro mentioned in this SciAm article.) So the question now becomes what is/are the effects of this fusion (if any) on the surrounding environment (primate body - both local and global)?
ReplyDeleteWow, you really are an engineer. :-)
If you are thinking that this is like nuclear fusion (or even cold fusion), you are mistaken. It all is a logical outcome of the structure of DNA and the base-pairing rules. Think about the structure of DNA; long strands of nucleotides. Think about how it is replicated; first it is unwound, then the strands are separated, then new strands are made using complementary base-pairing with the old strand.
So if a strand of DNA with a particular sequence happens to be in the vicinity of another strand of DNA with a similar sequence (e.g. telomeric sequences, which are quite similar on all the chromosomes), that strand might stick to the other strand and the two would become joined after the other strands were completely replicated. It wouldn't require a massive release of energy; it's not like they were slammed together with great force. It merely requires base-pairing and DNA replication, two processes that occur all the time in every cell, pro- or eukaryotic. And DNA replication actually REQUIRES energy, rather than releasing it.
As for where these fusions occur, you're right, it had to occur in a germ (sperm or ovum) cell. But I'm not a geneticist, and it has been a long time since I had a genetics course, so I'm not going to guess (and I don't think it really matters, for the purposes of this paper).
I have a bunch of introductory college textbooks sitting around the office; I review textbooks a lot. If you'd like one, let me know. I think it might be useful for you as you learn a bit more biology.
dave said:
ReplyDelete"So if a strand of DNA with a particular sequence happens to be in the vicinity of another strand of DNA with a similar sequence (e.g. telomeric sequences, which are quite similar on all the chromosomes), that strand might stick to the other strand and the two would become joined after the other strands were completely replicated. It wouldn't require a massive release of energy; it's not like they were slammed together with great force. It merely requires base-pairing and DNA replication, two processes that occur all the time in every cell, pro- or eukaryotic. And DNA replication actually REQUIRES energy, rather than releasing it."
I believe that I did point out that energy input would be required:
"I would think that it would take at least some energy to fuse the chromosones ..."
So now the question becomes where does the energy come from and how is it utilised?
I like talking about "niggles" in the back of my head that tell me something is wrong even if I don't have an explanation at this time. Right now, the "niggle" is due to the experiment in question not fusing the chromosones in question. Have any other experiments demostrated this fusion explicitly? Describing how processes could work is one thing; showing experimentally that is works that way is another.
So now the question becomes where does the energy come from and how is it utilised?
ReplyDeleteThe initial "fusion" (base-pairing of similar DNA sequences") requires no input of exogenous energy. Hydrogen-bonding between the bases (A to T, G to C) occurs spontaneously; the base-paired structure, in fact, has lower energy than the unpaired strands.
After that DNA replication does require energy. Like all DNA replication processes, the energy comes from hydrolysis of nucleoside triphosphates. There are no mysteries here, just basic DNA chemistry.
I like talking about "niggles" in the back of my head that tell me something is wrong even if I don't have an explanation at this time. Right now, the "niggle" is due to the experiment in question not fusing the chromosones in question. Have any other experiments demostrated this fusion explicitly? Describing how processes could work is one thing; showing experimentally that is works that way is another.
The paper is question simply searched for evidence of the predictions, and found the evidence. It seemed sufficient to get that paper published in PNAS, a fairly prestigious journal. So if you were expecting explicit fusion research in that paper, I'm sorry that you are disappointed. But the paper stands on its own.
In addition, as alluded to previously, chromosomes are just DNA. Adherence of similar DNA sequences to each other is simple chemistry, and the process has been well studied since the 1950's. Assuming that this process will occur is an underlying assumption for MANY molecular biology techniques, including PCR, gene cloning, etc. It's so non-mysterious that molecular biologists barely think about it at all; they take it for granted. Ditto for DNA replication. So both of the processes required for chromosome fusion (base-pairing and DNA replication) are well-understood, and can occur in test tubes. They do not require a cell at all, just the proper conditions and components and enzymes. I'm sorry if that is not clear, but I don't know how I personally can make it any clearer.
Chromosome fusions happen in cells all the time. Google Robertsonian translocations to learn about fusions of cellular chromosomes, or retroviral insertions to learn about fusion of viral chromosomes with cellular chromosomes. It's ubiquitous!
My niggling meter goes off when I wonder WHY you are fixated on this process. Are you concerned that this process cannot have happened as suggested by the authors of that paper? Or do you have some other reason to doubt this basic molecular biology?
dave said:
ReplyDelete"...the base-paired structure, in fact, has lower energy than the unpaired strands."
IOW, the energy "flows" from the unpaired strands to the base-paired structure, correct? This I have no problems with as it is a simple law of nature: energy always flows downstream (from high potential to low potential).
"My niggling meter goes off when I wonder WHY you are fixated on this process. Are you concerned that this process cannot have happened as suggested by the authors of that paper? Or do you have some other reason to doubt this basic molecular biology?"
Just trying to cover all bases and trying to learn more, dave. It's what I do for a living. :)
It's not that I "doubt ... basic molecular biology", it's just that I'm wondering since the paper didn't display the specific process of fusing the primate chromosones to make the human chromosone whether it is a warranted extrapolation.
Tell you what: until I look into this more, I'll give you and the authors the benefit of the doubt wrt chromosone fusing, k?
I hope you don't take this the wrong way, but the focus on this well-understood and ubiquitous process (DNA base-pairing and replication to generate fused chromosomes) is getting in the way of real understanding. I don't know if I have an analogy that will work for you, but I'll try. It is similar to me looking at a building that was built using concrete, and asking why the builders didn't explicitly explain the chemistry of concrete-setting during the architectural and construction phases. Hopefully you would say that the process is well-understood, ubiquitous, and taken for granted by architects and builders alike. It's that basic. My question might be seen as an ignorant question...
ReplyDeleteI am certain, given your education and willingness to seek understanding, that your ability to focus on the important questions would be improved by a re-introduction to basic biology. As noted before, I have many college-level introductory biology books here in the office. I'd be glad to ship one to you. You have my email address from the PDFs that I sent you. if you are interested in getting a modern biology textbook, send me an email with a mailing address, and I'll pack one up for you.
thanks