Free Republic
Browse · Search
News/Activism
Topics · Post Article

To: VadeRetro; Doctor Stochastic; edsheppa; LiteKeeper; Fiddlstix; AndrewC
Many thanks to all of you for your posts!

I had no idea using the term "lawn" would generate such a lively discussion. Jeepers!

I am aware that a device known as "the Tree of Life" is used in the Kabala (new age version) and Tarot reading. My understanding is the Kabala originally was rooted from the Torah (Spanish) and of course the Tree of Life is mentioned in Genesis and Revelation as being in the center of Eden and Paradise respectively. That's one reason why I believe Eden is in the spiritual realm - but I digress...

Several of you seem to believe my "lawn" choice has already been disputed. But I'm not convinced by your assertions. I visualized a "lawn" when I saw this article:

What it really means to be 99% chimpanzee (excerpts:)

We are accustomed to imagining scales of similarity ranging from 100% similar – that is to say, identical – to 0% similar, that is to say, totally different. This is the conceptual framework within which we interpret the 98.6% or whatever similarity of human and ape. They are really, really similar, almost identical.

But in fact, DNA similarity is not structured in quite that way. There are, as everyone knows, only 4 bases in DNA. And this places an odd statistical constraint on the comparison of sequences. No DNA similarity at all – that is to say, two random sequences that share no common ancestry – are still going to match at one out of four sites. In other words, the zero mark of a DNA comparison is not zero percent similar, but 25% similar.

Once again, the DNA comparison requires context to be meaningful. Granted that a human and ape are over 98% genetically identical, a human and any earthly DNA-based life form must be at least 25% identical. A human and a daffodil share common ancestry and their DNA is thus obliged to match more than 25% of the time. For the sake of argument let’s say 33%.

The point is that to say we are one-third daffodils because our DNA matches that of a daffodil 33% of the time, is not profound, it’s ridiculous. There is hardly any biological comparison you can make which will find us to be one-third daffodil, except perhaps the DNA.

In other words, just as Simpson argued in the 1960s, the genetic comparison is exceptional, not at all transcendent. DNA comparisons overestimate biological similarity at the low end and underestimate it at the high end – in context, humans are biologically less than 25% daffodils and more than 98% chimpanzees.

The focus on base-pair mismatch itself is misleading, for it encodes a number of archaic assumptions about genetics and evolution. In fact, it ignores what is quite possibly the most significant development in biology in the last quarter-century – namely, the complexity of genome structure.

If humans and chimpanzees are over 98% identical base-for-base, how do you make sense of the fact that chimpanzees have 10% more DNA than humans? That they have more alpha-hemoglobin genes and more Rh bloodgroup genes, and fewer Alu repeats, in their genome than humans? Or that the tips of their chromosomes contain DNA not present at the tips of human chromosomes?

Obviously there is a lot more to genomic evolution than just nucleotide substitution. But the percentage comparison renders that fact invisible, and thus obscures some of the most interesting evolutionary genetic questions.

Once you recognize that there are easily identifiable differences genetically between humans and chimpanzees – the presence of terminal heterochromatin is 100% diagnostic – you can begin to see that the pattern of relationships between the species is actually the same genetically as anatomically. Humans and chimps are simply very similar to, yet diagnosably different from, one another.


31 posted on 11/23/2002 10:30:42 AM PST by Alamo-Girl
[ Post Reply | Private Reply | To 24 | View Replies ]


To: Alamo-Girl
I visualized a "lawn" when I saw this article...

You also visualize a lawn when you see the fossil record represented as vertical parallel lines. (You have posted such pictures.) That's a question-begging reconstruction which assumes what it tries to show, that nothing is related to anything else.

The scale of similarities appears non-linear, yes, but that's because nothing is a zero. Common descent and all that. The daffodil is not totally unrelated to you. Nevertheless, nothing is as related to you as the chimp.

33 posted on 11/23/2002 10:46:50 AM PST by VadeRetro
[ Post Reply | Private Reply | To 31 | View Replies ]

To: Alamo-Girl
Once again, the DNA comparison requires context to be meaningful.

A curious link you found there, Alamo-Girl, and you seemed to have missed the significant details in it.

It may be helpful to know just a little bit about how sequence comparisons are done. One can come up with a uniform lawn if each individual base in one genome is compared to any base in another genome. It will be completely non-informative and all organisms will stand alone as single blades. But people who like to think instead of lawyer aren't this stupid and will, instead, look for ways to find meaningful information from a sequence comparison. The first task is to align matching genes. Do you see immediately that the 25% random match is eliminated? That's how sequence comparisons are done in real life. (Even the lawn in your analogy would be a spotty one. It would be similar to the effect of representing each branch on the tree of life by a light and then projecting this light onto the ceiling. You've eliminated the time dimension.)

The next task is to set an estimate of expected matches just by chance. That's the base line. The actual match will be compared to the baseline. But it gets tough because mismatches between gene segments are usually not just single base mutations. They include inversions and deletions. Scores of biostatisticians and biomathematicians have created algorithms to turn that meaningless lawn into something significant. Important information does emerge. Core genes, like histone genes, are similar between daffodils and humans. Other genes don't find any match at all. You may not be aware that the chimp genome has not been sequenced. Comparisons are estimates based on the information we do have. (Don't worry, those estimates are not based on godless bayesean priors.) What emerges is a visual representation of the relationship between species. It's, roughly, a tree. The rooting isn't at a single point. The trunk is fuzzy. But as you move up the branches, distinct clarity emerges. Naturally, it would, because we have DNA sequences from extant species.

60 posted on 11/23/2002 3:44:02 PM PST by Nebullis
[ Post Reply | Private Reply | To 31 | View Replies ]

To: Alamo-Girl
There are, as everyone knows, only 4 bases in DNA. And this places an odd statistical constraint on the comparison of sequences. No DNA similarity at all – that is to say, two random sequences that share no common ancestry – are still going to match at one out of four sites.

A statistically meaningless question. That's like saying that uncorrelated two binary sequences match at half their locations. The guy's article is just nonsense mathematical ly.

More relevant would be the correlation between sequences.

76 posted on 11/23/2002 8:35:41 PM PST by Doctor Stochastic
[ Post Reply | Private Reply | To 31 | View Replies ]

To: Alamo-Girl
A human and a daffodil share common ancestry...

This would seem to explain my neighbor's behavior. ;~)

420 posted on 11/26/2002 8:14:58 AM PST by verity
[ Post Reply | Private Reply | To 31 | View Replies ]

Free Republic
Browse · Search
News/Activism
Topics · Post Article


FreeRepublic, LLC, PO BOX 9771, FRESNO, CA 93794
FreeRepublic.com is powered by software copyright 2000-2008 John Robinson