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03-27-1999, 01:22 AM
Newspapers keep printing the percentages of commonality of genome we other species share with the human ideal (?). I believe it goes something like:

chimpanzee 99.7
round worm 70
yeast 30

I know very little about how genotypical
structures and sequences are translated in nature into the physical features and behaviors of correlate phenotypes. I'm not really fearful of being mistaken for a bit of yeast, or even for a chimp, now that the scores are known. However, given all the possible parametric differences that must exist as reasonable candidates to be selected for the measuring of some recognizable similarity among different species' genomes, what sort of algorithm might I suppose they have selected to produce all these nice catchy numbers every time a news reporter calls them up? (No need to show your work.)

03-27-1999, 03:15 AM
I meant also to include the tidbit that someone bestowed upon me (the truth of which I don't know), that variation in commonality of genome ranged, within the species Homo sapiens, over a range of 0.5-0.7% from the stereotype (more that the stated human-chimp disparity.

03-27-1999, 06:09 AM
The 99.7% figure (and a quick search of the internet by me found numbers ranging from 97 to 99.9% with no clear concensus) is not based on the genetic code itself, although a couple on non-geneticists on the internet say it is, but is a comparison of the proteins between chimps and humans. Some proteins are exactly the same in chimps and humans (cytochrome c for example) and some differ slightly. Actualy genes are a different story because humans have 23 pairs of chromosomes, chimps have 24. This means there is going to be at least an 4 to 5% difference in genetics off the top.

The variation in actual human genes in far, far less than 1% and is less than the variation between man and any of his closer relatives.

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Jim Petty
A Snappy message should appear here

03-28-1999, 12:20 AM
So, are you saying that, in order to get those percentages, they just count up the number of identical proteins (whatever their relative abundance or application in the two species, forget the similar proteins, count up the total number of proteins in the species they want to reference the percentage to, and then print the result of the calculation? Similarity in proteins and relative complexity in the dedication of the like proteins don't count for anything?

What do those chimps do with that extra pair of chromosomes that leaves us in the dust anyhow?

Ray Chamberlin

03-28-1999, 12:38 AM
>>>What do those chimps do with that extra pair of chromosomes that leaves us in the dust anyhow?<<<

Those would be the chromosomes that hold the "we-have-sense-enough-not-to-come-down-from-the-trees-and-worry-about-genetics" gene.



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Aon Dia.
Aon Tir.
Aon Ite.

NanoByte
01-28-2000, 09:54 PM
Since our (US) President repeated a figure for "genome" commonality among all human races in his State of the Union speech last night, perhaps its time to bring up this old thread again from last March. The figure he gave for this commonality was 99.9%.

Jim "Jimpy" Perry, above, found the Web to give figures for "genome" commonality between humans and chimpanzees anywhere from 97 to 99.9%. See his post above under "jimpy". But Jim claimed these percentage figures, the ones AP and others throw around all the time as measures of the commonality between different species and different strains within them, don't really pertain to the genomes, but rather to proteins resultant from them, in the respective genotypes. See his post under "Jimpy" above.

Maybe there's more or more reliable info around today. Although I have no formal training in biology, it appears to me that, even if the particular percentages are accurate and properly defined, when they're very close to 100%, it's likely to be pretty hard to relate them reasonably to functional differences we might otherwise feel are significant.

Ray (Vote for Washoe's offspring to replace some of those Republicans in Congress.)

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LIFE: Those sparse nanoseconds between downloads of software upgrades.

Jois
01-28-2000, 10:02 PM
What do those chimps do with that extra pair of chromosomes that leaves us
in the dust anyhow?

Aren't those the two they are holding in reserve for after the humans kill each other off?


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Oh, I'm gonna keep using these #%@&* codes 'til I get 'em right.

Alphagene
01-28-2000, 10:27 PM
Dang. I'm on vacation away from my 80-lb. textbooks when all these questions come up.

First of all chromosome number, like total DNA length has little to do with the "complexity" of an organism. Many amphibians have a longer genome than humans. IIRC, the genome of the lily is one of the largest known.

I'm actually unsure how they get the percentages exactly, but remember that the human genome is around three billion base pairs in length. A 99% similarity means that 30 million base pairs are different. Changing just one nucleotide in a gene can drastically change the activity of a protein. That 30 million base pair difference can include entire genes which define an organism.

I'll come back with more info as I find it.

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I used to rock and roll all night and party every day. Then it was every other day. Now I'm lucky if I can find a half an hour a week in which to get funky.

01-28-2000, 11:48 PM
Actually, what's being mentioned here is degree of protein homology. To determine this, Hemoglobin A, for example, from humans would be laid side-by-side hemoglobin A from chimps, and the amino acid sequences would be compared. If the protein had 300 amino acids, and 6 amino acids differed, they would be 98% homologous.

There could be 100% homology between the proteins of different individuals, or of individuals from different species, however, and some much lower figure for homology between total DNA.

One reason for this is that only part of our DNA actually codes for the amino acid sequences of the proteins. The rest of the DNA plays regulatory roles in determining which genes get transcribed when (Promoter regions), or codes for sections of RNA (introns) which gets cut out as the RNA transcript gets processed into messenger RNA.

The number of chromosomes has nothing at all to do with protein homology (which is what most of these figure cite). You can take the genes (and their regulatory sequences) and arrange them any old whichway on any number of chromosomes without affecting the degree of homology between the proteins these genes code for compared with the original arrangement. This is critical to being able to do gene therapy - we don't have to get the gene in the exact right place on the right chromosome; we just have to get it into the nucleus where it can be transcribed...

Adding to this difference is the fact that small differences in DNA bases may or may not affect which amino acid in inserted into the protein. There are 64 possible sequences of 3 bases (4 bases, 3 positions = 4&sup3 = 64 combinations). These sequences of 3 bases are called codons, and each codon codes for one specific amino acid. But there are only 20-something different amino acids coded for by these 64 possible codons. So, several different codons may code for the same amino acid. The net result is another mechanism where differences in DNA might have no difference in the protein coded for.

Or, if the non-coding regions were "highly conserved" (there is little difference between species), there could be MORE homology between DNA than between proteins...

Obviously, when comparing one species to another, one pitfall is the degree of intra-species variation. Ray, I don't know what kind of algorithm is used to "average" all human proteins and all chimp proteins and then compare these averages, but I hope the information I provided above helps.



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Sue from El Paso

Experience is what you get when you didn't get what you wanted.

Jois
01-29-2000, 01:58 AM
Try this:

This is a pretty good article from Science.

Volume 281, Number 5382 Issue of 4 Sep 1998, pp. 1432 - 1434 The American Association for the Advancement of Science

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For the moment, no one can tie the few known molecular variations with the familiar litany of chimp-human differences, such as body hair, language,or brain size.

"This is one of the major questions that those of us interested in our own biology would like to ask--what does that 1.5% difference look like?" says Francis Collins, director of the National Human Genome Research Institute.

"That question was first raised in print in a landmark 1975 paper by geneticist Mary-Claire King and the late biochemist Allan Wilson, both then of the University of California, Berkeley. They surveyed protein and nucleic acid studies and found that the average human protein was more than 99% identical to its chimpanzee counterpart; the coarse DNA hybridization methods of the time showed that the average nucleic acid sequence was almost as similar (Science, 11 April 1975, p. 107).

"Thus, King and Wilson concluded, humans
and chimpanzees were genetically as similar as sibling species of other organisms, such as fruit flies or mice.

"This left a great paradox: Our DNA is almost identical to that of our chimp cousins, but we don't look or act alike. "The molecular similarity between chimpanzees and humans is extraordinary because they differ far more than many other sibling species in anatomy and way of life," the pair wrote.

"What's more, much of the DNA in any organism is so-called "junk DNA" that has no apparent function, and mutations in these regions do not change the function of genes. Thus, many of the genetic differences between humans and chimps probably don't affect the organisms at all. (I thought someone just came up with a good understanding of "Junk DNA" but I can't remember it right now.)

"The challenge is to find those few mutations that do make a difference--either by altering genes that code for proteins or by changing how genes are regulated, King and Wilson said.

"But although many labs have since confirmed that our nuclear DNA is 98% to 99% identical to that of chimpanzees, few have taken on the quest to find the differences that matter. "It was one of those fields that fell through
the cracks," says Ajit Varki, a glycobiologist at the University of
California, San Diego (UCSD), who has recently surveyed the known differences between humans and apes.

"What's different? What makes us human?"

"One way to answer that question is to start with biochemical differences, and then trace them back to their genetic origins. That approach has yielded its first big payoff, to be reported in the October issue of the American Journal of Physical Anthropology.
After studying tissues and blood samples from
the great apes and 60 humans from diverse ethnic groups, Varki and his colleagues Elaine Muchmore and Sandra Diaz at UCSD were surprised to find that human cells are missing a particular form of sialic acid, a type of sugar, found in all other mammals studied so far, including the great apes.

"Now you've got something that is changing the surfaces of all cells in the body," says Varki.

"...There are even hints that sialic acid may
be involved in cellular communication during brain development and function, says Varki.

"...But the human form is simply the basic acid, lacking the additional oxygen atom. That changes the shape of the molecule in a region that could alter how it is recognized by other molecules, whether pathogens or cellular messengers, says Varki.

"Yet the question still remains: Does this biochemical difference matter? No one has yet identified a specific function altered by the loss of this particular version of the molecule.

"But others, such as Pääbo, think that chromosomal rearrangements at influential sites are rare and so are skeptical that they play a major role in the differences between chimp and human.

"Pääbo and King think instead that the most promising research avenue is to identify small sequence differences that subtly change the expression of genes that regulate the timing of development, such as those that code for transcription factors that might lengthen the growth period of the brain and, hence, allow more complex brain structure in human fetuses.

"Pääbo's group in Munich and Leipzig has sequenced a 10,156-base pair segment of DNA in the X chromosome of humans and chimpanzees, confirming again that they are about 99% similar. Now they're seeking differences in the expression of the identified genes in the brain and in the immune system.

"And at GenoPlex Inc., a Denver-based company founded last year by University of Colorado Health Sciences Center geneticists Jim Sikela and Tom Johnson, researchers have come up with a rapid method to find meaningful
sequencing differences between humans and chimps. After sequencing a stretch of DNA in each species, they count two different types of nucleotide differences: those that change the structure and function of a protein product, and silent substitutions that don't.


"If the ratio of replacement to silent
substitutions is high, they consider that the gene sequence is likely to have undergone
a functional change that was selected for in humans.

"Preliminary results suggest that they have found uniquely human genes involved in AIDS susceptibility and learning and memory, says Walter Messier, an evolutionary biologist at the company. The firm has submitted patents on novel uses of these gene sequences, which they hope may become targets for drugs."
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Note: I added more paragraphing and have greatly condensed this article.
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Additionally: That extra chromosome is not DNA no one has ever seen before. They can
tell from the gross structure of it (in karyotype -like assays) that it's made up of bits of rearranged dna that can be found in the 23 chromosomes ... it's sort of a piece that came off and ended up as a chromosome.
Presented at a...thesis defense.



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Oh, I'm gonna keep using these #%@&* codes 'til I get 'em right.

NanoByte
01-29-2000, 04:37 PM
Here's the take of a Tasmanian mathematician (dunno how many chromosomes they have) on the subject:
http://www.abc.net.au/rn/science/ockham/stories/s163.htm

Ray (And so mah fellow American citizens, y'all gotta get along together, 'cause y'all're missing the same full-blown sialic acid molecules; otherwise ya woulda been some other kinda ape. Remember, it's whatcha don't have that counts. (And if ya don't get along, we'll mutate ya aa' throw ya in the zoo.))

RobRoy
01-29-2000, 05:13 PM
This discussion points out that the "blue print" analogy that is popular is woefully inadequate. Genes are not blueprints - a static plan for the finished product, but something (obviously) more organic, in that these "blue prints" are ain large part chemical formulas for the materials for the "house" and if actually building instructions, wouldn't say, "build a limb that is so long and has these features", but says "build a 'bud' in that direction, and keep working with these time tested builing materials, until told to stop or given some more details".

The old blue print mindset makes it counter-intuitive to think that we have so much in common with chimps etc. No surprise after 1000's of years of deliberately looking for what makes us different...

Interesting also is the fact that variation between members of a species can be greater than that between the most closely related species, yet humans never produce chimps, etc.

To the potential visitors from outerspace (another string) humans may all be seen to be shades of beige, light to dark (esp. if they are blue or green), and may be grouped with chimps based on visual inspection alone.

Jois
01-30-2000, 09:05 AM
Seems like, Ray, you kind of had your answer before you asked the question?

From the OR article you offered for reading:
"That is, that we share 98% of our genes with chimpanzees. A strong and convincing statement, and true. But why is it convincing,and..."

And is that really what is being said?

For example, Most of the early homology info between human and chimp is inferred from the annealing temperatures of chim and humanDNA to themselves and each other. Differences between the sequences screws up the annealing temperature and you can caculate percent identity from that in a way that I couldn't begin to tell you. That technique is very old fangled in these days of DNa sequencing. But they did get the number of 99%.

The quote I gave you above had at least 3 references to groups who have have separately studied human to chimp or human to ape DNA, but this Tasmanian Devil Math Man is willing to say all of them put their shoes on the wrong feet?

It's okay if you or I get a little sloppy (Ray, wipe your feet outside on the mat) with our wording here but here's Jared Diamond, physiologist mentioned in the above article, listen to his wording: "A quarter-century of genetic studies has consistently found found that for any given region of the genome, humans and chimpanzees share at least 98.5% of their DNA..."

Maybe he is just saying only mathematicians know how to do math?

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Oh, I'm gonna keep using these #%@&* codes 'til I get 'em right.

NanoByte
01-30-2000, 03:16 PM
Whatever keeps the economy going. I see they have a court case going now as to whether a genetic mix that is "almost" human can be patented.

I'm looking over the list of educated chimps to see if I can find one that can tell Slovenia from Slovakia, so that maybe we can get the White House properly staffed this time with the right stuff.

Ray (Would be just my luck to end up with one that smoked marijuana in its youth.)

Jois
01-30-2000, 03:23 PM
Find one that's potty trained. (See above Not THE E coli

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Oh, I'm gonna keep using these #%@&* codes 'til I get 'em right.

ZenBeam
02-01-2000, 01:36 AM
For another perspective, consider the person with Down's syndrome. He has the same DNA (although an extra copy of one of the chromosomes), and presumably 100% "protein homology" that Majormd was talking about. Yet there are signicicant developmental differences. Humans are more than the sum of their genes and/or proteins.

Aside: IIRC, it's the 22nd chromosome which has an extra copy. Are there cases where there is an extra copy of some other chromosome (not the 23rd, for this question!)? Are they all lumped into Down's syndrome, or is the impact too great, and they don't survive.?

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It is too clear, and so it is hard to see.

Jois
02-01-2000, 03:20 AM
QUOTE: "Aside: IIRC, it's the 22nd chromosome which has an extra copy. Are there cases
where there is an extra copy of some other chromosome (not the 23rd, for this question!)? Are they all lumped into Down's syndrome, or is the impact too great, and they don't survive.?"

From my biology text - Down's Syndrome is the example and probably because they do survive, other errors are large/small occur but, as you said, the impact in too great for survival.

It lists Down's, abnormalities in the sex chromosomes (a short paragraph), and chromosome deletions - mentioning only Wilm's tumor - a small deletion on the short arm of chromosome 11 is assoc. with Wilm's turmor, a cancer of the kidney also assoc. with the absence of the iris of the eye.

For Down's it says that the individual has three, rather than two copies of chromosome 21.



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Oh, I'm gonna keep using these #%@&* codes 'til I get 'em right.

02-01-2000, 03:30 AM
Trisomy 21 is Downs.

Trisomy of the sex chromosomes resulting in 47XXX, 47XXY, or 47XYY genotypes are generally healthy individuals who often have mild intellectual impairment, antisocial behavior XYY, and infertility.

Trisomy 18 leads to a particular syndrome, but is seldom survived past early infancy.

I believe there is one other Trisomy which would not be case-reportable if a baby were born alive with it, but which also leads to an early death.

All other trisomies are lethal in utero as best I can recall.

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Sue from El Paso

Experience is what you get when you didn't get what you wanted.

Jois
02-01-2000, 02:31 PM
Quote from above: ""Pääbo and King think instead that the most promising research avenue is to identify small sequence differences that subtly change the expression of genes that regulate the timing of development, such as those that code for transcription factors that might lengthen the growth period of the brain and, hence, allow more complex brain structure in human fetuses."

A chart in this biology book (Curtis & Barnes) compares Lemur, Chimpanzee and Human development:

Gestation: roughly the same
Infancy:
Lemur-9 months
Chimp-3-4 years
Human-4-5 years
Juvenile phase:
Lemur-1 year
Chimp-6 years
Human-12-13 years
Adult phase:
Lemur-20 years
Chimp-18 years
Human-15 plus years

My impression is that the genes might be alike or similar and same might be true of the protein that does the work. But it will be the timing, when things are turned on and off that will make most of the real differences between the primates.

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And it is nice out here on this limb.

Jois
02-01-2000, 02:36 PM
I forgot that I can't create indentations.

Here's another try:

Quote from above: ""Pääbo and King think instead that the most promising research avenue is to identify small sequence differences that subtly change the expression of genes that regulate the timing of development, such as those that code for transcription factors that might lengthen the growth period of the brain and, hence, allow more complex brain structure in human fetuses."

A chart in this biology book (Curtis & Barnes) compares Lemur, Chimpanzee and Human development:

Gestation: roughly the same
Infancy:
Lemur-9 months
Chimp-3-4 years
Human-4-5 years
Juvenile phase:
Lemur-1 year
Chimp-6 years
Human-12-13 years
Adult phase:
Lemur-20 years
Chimp-18 years
Human-15 plus years

My impression is that the genes might be alike or similar and same might be true of the protein that does the work. But it will be the timing, when things are turned on and off that will make most of the real differences between the primates.

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And it is nice out here on this limb.

02-02-2000, 12:54 AM
Also, there is a great deal more to making a functional protein then DNA -> mRNA -> polypeptide.

The same sequence of amino acids can be folded differently & behave very differently. Or some amino acids can be modified (post-translational processing) in the endoplasmic reticulum. Glucose molecules can be added to some (glycosylation). Metal ions can be used as a core to wrap the protein around - Mg++ & Mn++ are needed for many enzymes.

So even 100% DNA homology and 100% amino acid homology need not result in structural & functional identity.

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Sue from El Paso

Experience is what you get when you didn't get what you wanted.

Jois
02-02-2000, 01:37 AM
You've got it!

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Oh, I'm gonna keep using these #%@&* codes 'til I get 'em right.

NanoByte
02-02-2000, 05:32 AM
Jois:

So what happens to the human after only 15 yr as an adult? Does that refer to a human in the wild or something?

Ray (in his nth childhood)

Jois
02-02-2000, 11:15 PM
I wasn't sure about that either. The graph said, "Adult 15+" maybe to keep the graph from having human adulthood look like a smoke stack compared to the rest of the graph? Or just it's way of saying human longevity is variable - which would also be true of Lemurs and Chimps - makes me vote for the "smoke stack" idea.

It's a college biology text ('87 I'd guess) and this was just an aside - didn't even specify modern man or early Hss.



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Oh, I'm gonna keep using these #%@&* codes 'til I get 'em right.

Irishman
02-03-2000, 05:43 PM
Alphagene:
First of all chromosome number, like total DNA length has little to do with the "complexity" of an organism. Many amphibians have a longer genome than humans. IIRC, the genome of the lily is one of the largest known.


I'll back that up. From what I remember from by biology class, the two are completely unrelated. I vaguely recall some chart showing comparisons, but no numbers come to mind.

RobRoy:
Interesting also is the fact that variation between members of a species can be greater than that between the most closely related species, yet humans never produce chimps, etc.

Where are you getting that? I don't think that's true. I saw Nanobyte's post of this comment, but also Jimpy's reply. In fact, it seems pretty silly to think that way. If we were overlapping, then we would be able to interbreed. Also, some humans would have offspring that closely resembled chimps, and chimps would have offspring resembling humans. I know Robin Williams is a hairy guy, but he's not a chimp.

There are some species this may be true for. Species differentiation is a specialty in biology. With animals, the differentiation is typically that they won't mate and produce fertile offspring. However, there are some pairs of species that the reasons they won't mate has to due with behavioral/pheromonal triggers and mating rituals. If they don't share mating rituals/cues, then they won't interbreed, even if genetically they are compatible. Thus you have species that are genetically compatible but biologically incompatible through other reasons. This is not the case for humans and chimps. (Well, I don't know someone hasn't put this to the test.)

Jois:
The quote I gave you above had at least 3 references to groups who have have separately studied human to chimp or human to ape DNA, but this Tasmanian Devil Math Man is willing to say all of them put their shoes on the wrong feet?

It's okay if you or I get a little sloppy (Ray, wipe your feet outside on the mat) with our wording here but here's Jared Diamond, physiologist mentioned in the above article, listen to his wording: "A quarter-century of genetic studies has consistently found found that for any given region of the genome, humans and chimpanzees share at least 98.5% of their DNA..."

Maybe he is just saying only mathematicians know how to do math?

I don't see what you're saying. All the numbers above were reading 98 - 99 %. He said 98.5% - right between the two. Are you complaining about his choice of precision?

NanoByte
02-03-2000, 09:55 PM
Maybe Irishman can get a grant to study interbreeding between humans and chimps. Maybe some hairy "throwback" humans are actually half chimp. All this theory need some hard data.

Ray (How do you get leprechauns anyhow?)

Jois
02-04-2000, 01:40 AM
Irishman, Nanobyte first couple of posts were aimed at how mathematically correct were the methods used to get these numbers and he went to an article where a mathematician examined this question critically.

Jois
02-04-2000, 01:43 AM
Opps, sorry.

So, the question from your previous post goes directly to my saying - roughly - that several people have done several studies and so on.

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Oh, I'm gonna keep using these #%@&* codes 'til I get 'em right.