Oolon Colluphid

<sigh> Oh, okay Vanderzyden.... I apologise for my sour disposition. Can we do a deal? I promise to be as sweet as a very sweet thing to you, if you will please answer my questions.

With all best wishes, Oolon

Oolon Colluphid

To remind you, as they got buried pretty quickly:

1. Why can chromosomes not fuse? We thought we had evidence that they can and do. So let's be scientific about it. Could you offer some counter evidence to refute our claim, some information about chromosomes and their operation that indicates that fusion is impossible? Thanks .

2. Why are the numerous articles cited not evidence and observations of fusion?

3. Why is the presence of extra telomeres and centromeres in the human chromosome 2 not good evidence
(a) that chromosomes can indeed fuse, and
(b) of human evolution from a common ancestor with chimpanzees, especially in the context of every other piece of evidence about these species, which this agrees with?

Many thanks for listening. I hope you can forgive me enough to have a go at these.

Cheers, Oolon

beausoleil

While there may be issues of copyright infringement, accusations of plagiarism on an internet bulletin board strike me as more than faintly ridiculous.

If Vdz misrepresented an original source, that has been pointed out and was both wrong and silly of him. If he did this because he borrowed a quote or qutoes from another place or places, the only consequence of the 'plagiarism' is that he can't now publicly blame someone else for the mistake and has to suck up the criticism himself.

Mageth

Perhaps you could explain the last sentence further. This "operator discretion" would appear to leave data collection open to very broad configuration and interpretation.

There is a universal nomenclature for describing chromosome banding. Any cytogeneticist could point out "2q13" on an image of a chromosome he/she captured (or that some other lab had captured) or on an idiogram he/she is using or that some other lab is using.

There is variation in the appearance of karyotypes and chromosome banding patterns between individuals.

Different techniques and procedures may cause some variation as well. Someone mentioned R-banding in addition to Q-banding. Some techniques show relatively short, "fat" chromosomes with fewer visible bands (e.g. 400), some long, skinny chromosomes with lots of bands (e.g. 800), and some "in between" (550).

Even different equipment setups can make a difference. The karyotype images are captured under microscope, and there is a lot of equipment involved (microscope, lens, light (there are several different types of bulbs that may be used, and even the age of the bulb may cause variation in lighting), camera (digital or film), etc.)

I looked at thousands of karyotypes on my job. Comparing the karyotypes of two individuals with "normal" karyotypes, a trained technician or scientist can identify the bands (as illustrated in idiograms of the proper resolution) in the chromosomes of both individuals. "There's 2q13." But the trained individual can also (usually) identify the karyotypes as being from different individuals (that's harder at low resolution (e.g. 400), easier at higher resolution (e.g. 550 and 800), and trivial if they're not of the same gender ).

At the job I mentioned, I developed automated chromosome classification algorithms for karyotyping. The software would analyze hundreds of manually-generated normal karyotypes to generate a database of "average" chromosome classification metrics (centromere location, arm lengths, major band positions in relation to centromere, etc.) We generated several of these classification databases for different band levels, staining techniques, an even "custom" ones for particular labs to better work with their particular technique. Note that these databases are "averaged" data and are roughly equivalent to a manually-generated idiogram (which may be considered an "average" representation.)

In use, a technician or scientist prepares a slide, search for nice metaphase "spreads", and captures an image of a good "spread" with a digital camera connected to the microscope and coupled to the computer system. A metaphase "spread" is a group of 46 chromosomes in a rough circle. The captured image of the metaphase is displayed on the computer. Typically, there are a few overlappiing chromosomes. Any overlapping chromosomes are separated (manually and/or automatically). The image may be further digitally manipulated to improve appearance (background flattening, image sharpening, contrast enhancement, etc.) The chromosomes may be manually or automatically karyotyped. To automatically karyotype, "Classify" is selected and the chromosomes are moved to (hopefully) the right positions in a karyotype window (using a pre-selected classification database to identify the chromosomes). Errors in classification, if any, are manually corrected.

One use of idiograms is to train technicians on chromosome banding and recognition. Karyotypes are used, for example, in detecting "gross" genetic errors (monosomy, trisomy, fusion, major translocations, "circle" chromosomes, etc.). Other techniques have been developed that are more sensitive for detecting some errors such as translocations (e.g. using fluorescent "probes" to "mark" chromosomes; probes have been developed that are specific to each chromosome, and even to segments of chromosomes). Note that AFAIK in all of these other "staining" techniques, bands that show up in banding techniques (G, R, etc.) don't appear.

Why do I say all this? Perhaps to educate you on the process. And to point out that technicians and scientists routinely share information, at conferences and such, and, although different ones may use different techniques, they have a common nomenclature and knowledge of cytogenetics that allows them to understand each other. There's no disagreement that I know of on where centromeres are located, where bands are located, where genes are located, etc.

[ September 06, 2002: Message edited by: Mageth ]

[ September 06, 2002: Message edited by: Mageth ]</p>

pangloss

Maybe I missed it or something, but I was wondering if Vander had posted his references regarding molecular clocks.

Skeptical

Yes, I meant to get back to it last night but I turned in early. I assure you I will reply and apologize for my tardiness in doing so, I promise I am not avoiding your post. Take your time in asessing the information I provided, but I would also suggest looking at some of the information provided by others. I am _not_ an expert in this field and I don't want to overstate my ability to discuss this topic as there are clearly others on this list much more qualified than I.

WRT fusions, I think the examples posted by Scigirl regarding Robertsonian fusions as well as the links I posted earlier in the thread clearly show evidence where fusions have occured. If your argument is that we don't have a specific example of end to end fusions _other_ than that believed to have occured in human chromosome #2, I don't have enough knowledge to know whether that's true or not, it very well may be. However, that fusions occur is known (Robertsonian for example) and that it certainly _appears_ as if a fusion occured in human chromosome #2 is also known. Given these two facts, it seems to be that this places the burden on someone who says a fusion cannot have happened _in this particular way_ to give a reasoned argument backed by data as to _why_ it couldn't have occured.

In other words, if we cannot think of a good reason this particular fusion could not occur and we know different other types of fusions occur and we see what certainly looks like clear evidence of a fusion, it only seems prudent to at least tentatively conclude that a end-to-end fusion has occured in the absence of contradictory data.

You seem to be arguing that because you personally have not witnessed a end-to-end chromosome fusion with your own eyes then it couldn't have happened. But surely you don't approach everything in your life in this manner. You may not know the exact physics behind why airplanes fly (I can't say that I do), but you probably have still taken a plane flight. By the criteria you keep requiring for evidence of an end-to-end fusion, you would have to have a degree in physics and personally have seen the plane assembled at boeing before you would accept that the plane is flight worthy. If you saw a Sesna built and fly and then a 747 rolled up, would you claim that the 747 couldn't possibly be flight worthy since you personally didn't see it built? Obviously not, but this seems to be the level of evidence you are requiring.

At some level you have to have a certain amount of trust in the scientific process or no amount of evidence provided by scientists will suffice. One can always argue that a particular experiment was faked or rigged. However, we know that much of science is correct because it produces working results, we use the products of science every day. We have the past two hundred years of demonstrated success of science as overwhelming data that the scientific methods and processes work. The level of "proof" you are requiring from genetics seems to me to require a degree in genetics and several years of chromosome fusion field study to get to the point where you would accept the findings of geneticists. If you took this approach with things like vaccines, you'd never get a vaccination without having a degree in medicine and years of personal research in the specific areas of immunology. I'd guess you and your family have had vaccinations and never thought twice about them and are no doubt better off for it.

I'm not saying we should have blind faith in science, we should not and we should require hard data for any explantions. What I _am_ saying is that as a layman, at some level you have to examine the long track record of the success of scientific explanations, accept that based on this evidence that science in the vast majority of cases works and that scientists are "playing fair" with their data.

Based on this, it seems only logical that in the absence of specific information to the contrary, we should at least tentatively accept findings such as chromosome fusion when it goes through the rigors of peer review and withstands the test of repeated results in varying conditions by scientists all over the world who are specialists in their field.

There is always the potential for problems with specific research in science, but the more experiments that are done the stronger the evidence gets. Just from the sparse information presented in this thread it seems that there are many scientists working on various areas of chromosome fusion and there doesn't seem to be much disagreement in the field of genetics regarding its occurence. There are no doubt many contentious issues in genetics, but whether or not chromosome fusions occur does not seem to be one of them. It seems to me that it is a bit presumptive for anyone, including you and I, who are not geneticists to question some of the basic findings of a field of specialists without a lot of solid data to back it up.

This is a bit of a catch-22, since we pretty much have to be a specialist in the field to collect the data and gain the knowledge in the first place, but this is part of my point. I have a layman's understanding of quantum mechanics and some of the findings seem extraordinarily odd (for example, stochastic ooze). However, I don't think I am in a position to tell a physicist specializing in quantum theory that "what you claim cannot happen" without having a lot of data to back me up. I don't necessarily absolutely accept all the findings. However, given that thousands of physicists have worked on these topics, examined the evidence, argued and hashed it out through scrupulous peer review, I at least tentatively accept that the conclusions are probably correct with the provision that future data may make revions necessary.

You seem to take the approach that you provisionally reject the data barring evidence you personally find utterly irrefutable. The problem with this is that in order to be qualified to make such a conclusion, you pretty much need to be a specialist in the field or at the very least have enough background to thoroughly discuss it _with_ an expert. (I don't know that anyone on this list is a genetics expert, I believe even Scigirl is not a geneticist) In my opinion, it would take years of research for a layman to get to such a point, and you'd still have the problem of needing to do research requiring expensive equipment not generally available to the public. I'm not saying only an expert in a particular field can critique another expert, but I do feel you need a high degree of understanding and very solid data to make strong assertions regarding particular findings, qualities it can be very difficult to attain as a layman. It's difficult even for scientists in the same field who may not be specialists in the particular area of question!

All I am saying is that in my view, a non-specialist should at least grant the same amount of respect to the research and ideas in scientific fields they are not experts in that I grant to quantum mechanics: "Seems a little strange, but there seems to be a lot of data and based on the past proven track record of science I give it at least tentative acceptance barring strong data to overturn it."

[ September 06, 2002: Message edited by: Skeptical ]</p>

Blinn

This <a href="http://www.faseb.org/genetics/ashg99/f2062.htm" target="_blank">abstract</a> describes a child, whose parents had normal karyotypes, that was born with a telomere-telomere fusion of chromosomes 7 and 22. Some of the chromatin was lost, resulting in clinical abnormalities for the child.

Mageth

I posted that abstract several pages ago, Zetec. If it wasn't read and understood the first time, I doubt if it will be this time.

<a href="http://iidb.org/cgi-bin/ultimatebb.cgi?ubb=get_topic&f=58&t=001305&p=3" target="_blank">(Here's the page)</a>

Blinn

Oops, I missed that Mageth. You're right that it'll probably be ignored.

Vanderzyden

The reason I didn't pay much attention is that it's yet another example of a supposed fusion in the context of a tragic abnormality.

Please tell me where I can find the entire paper. "Program Nr: 2062" isn't very helpful. Google searches for the authors and the laboratory only produce the link to which you are pointing.

Vanderzyden