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Author Topic:   Nested Biological Hierarchies
RAZD
Member (Idle past 1488 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 76 of 87 (324121)
06-20-2006 9:17 PM
Reply to: Message 75 by kuresu
06-19-2006 11:36 PM


Re: color coded card analogy and biology? does it hold up?
Thanks, but it's more logic than math (that's just those funny numbers).
The next question (posed by ned thanks) is whether it represents actual biological patterns and processes.
In basic biological genetics at it's simplest level, we know that we inherit features from our parents. I can look at a portrait of one of my great-great grandfathers -- and he has the same hair patterns, nose, chin, eye color, etc that I do.
But that's only on the surface. The deeper level is at the molecular DNA level - the preservation of mutations in each family lineage ... replace that card with a 6 foot long string (about as long as your DNA strand is when stretched out btw), where you put the spot of the same color at the same location along the lengths of the string. We've all seen the pictures of DNA evidence that show dark bars on strips -- these are the locations of spots along the string for each individual, and they show different degrees of similarity depending on the relationships between the individuals. It can be used for paternity determination as well as criminal evidence because of the patterns of spots on the string being unique to the generation of the spots.
Nested Hierarchy patterns should be expected at even this fundamental level, because you inherit the basic package from parents who inherit their basic package from parents, etc.... But there is a problem here -- mixing of genetic material from two sources, essentially cross-branching two lines together. Individuals within a species population are always mixing it back up to some extent: I am also related to the same individual on the Mayflower from both my mothers and my fathers side of the family -- those branches have come back together.
This is the major difference between individuals within a species and the cards -- that genes are mixed between parents in the offspring generations. There is "cross-branching within every species by this mechanism, and this tends to average the diversity of the populations even with high levels of mutations introducing new patterns. Breeding within population groups blends the mutations across the population.
Where the card patterns come into play in biological evolution is when speciation separation occurs -- two species (populations with diverse mutations common to many but not all members) diverge from a common ancestor. Once this separation occurs there is no mechanism for the cross-branching blending to occur, no way to bring new mutations in population {A}{1} across the breeding barrier to population {A}{2} -- the cards have been separated into two groups and each group gets its own special marks.
Many of these special marks will be inconsequential (neutral mutations) to the species as it continues to change over time (evolve) but they will only be within that population at those places specific to each population.
There is no selection on neutral mutations (by definition, otherwise they wouldn't be neutral eh?), but they are still carried, and the markers they leave are in the same location, they have the same "color" and they have a unique form of mutation, inherited from the ancestor that first had it. So in addition to specific mutations that occur as a species adapts to its environment through mutation and selection of beneficial vs deleterious mutations, there will also be many mutations with no selection but which become part of the species mutations pattern, their genome.
The strings of colored letters that each species carries as their basic genome (that collection of DNA that represents the species) - taking into account the bath of variations (alleles) around the common theme - is how the nested hierarchies are determined from the genetics.
The expression of those colored letter strings into recognizable features within and between species - things as small as the number and kinds of teeth, or ribs, or vertebrae or the numbers of toes on a foot (even or odd), the way the bones articulate, etc. - is how those nested hierarchies are determined from 'traditional' biology taxonomy.
You could say one system is sorted by location on the string, the other by the 'color' of the expression of certain genes.
Evolution, or rather the theory of common ancestry part of evolution, predicts that both systems will result in the same nested hierarcy.
For ID though, there is no barrier to they type of cross-branching of mutations between individuals that you see within a species -- occurring between species, because the agent of change is not the mutation, or the organisms reproduction, or the species survival, but an intelligent interloper that either (a) interferes with the evolution pattern or (b) does no useful work worthy of scientific study in this field (so we may as well study evolution anyway).
So, each species division is a cut of the cards, the children inherit the colored spots of their ancestors, but each child species gets new spots of their own colors -- and not just one but hundreds. A child of {A}{1}{a} cannot have the same spots of {A}{1}{b} that are not shared by all {A}{1} children and vice versa.
Enjoy.

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This message is a reply to:
 Message 75 by kuresu, posted 06-19-2006 11:36 PM kuresu has replied

Replies to this message:
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NosyNed
Member
Posts: 9006
From: Canada
Joined: 04-04-2003


Message 77 of 87 (324137)
06-20-2006 10:18 PM
Reply to: Message 76 by RAZD
06-20-2006 9:17 PM


color coded cards and bones
The DNA is the most obvious fit to the cards.
I want to see some tie into the morphology of living animals and the bones of old ones. My guess is that the taxonomy process is much too complex to distill down into a post but perhaps someone can give a flavour.

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kuresu
Member (Idle past 2596 days)
Posts: 2544
From: boulder, colorado
Joined: 03-24-2006


Message 78 of 87 (324154)
06-20-2006 11:30 PM
Reply to: Message 76 by RAZD
06-20-2006 9:17 PM


Re: color coded card analogy and biology? does it hold up?
it's more logic than math
Of course, math is nothing but logic. Even those wierd logs (which I just got, and, scarily enough for me, I'm finding them fun. Wait, fun in math? Wow, I've changed).

All a man's knowledge comes from his experiences

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Hyroglyphx
Inactive Member


Message 79 of 87 (325229)
06-23-2006 9:04 AM
Reply to: Message 65 by kuresu
06-18-2006 11:49 AM


Re: The evolutionists argument of incredulity
I may be wrong in what fallacycop was trying to say, but if we were intelligently designed, why the heck would there be a non-functioning gene?
Well, I happen to believe that the non-coding DNA is not a complete waste of matter. I believe that we just know very little about psuedogenes, especially in light of recent discoverires involving junk DNA. More than a third and up to 98% of the human genome is described as being comprised of non-coding DNA. That's a huge percentage to simply dismiss it because we don't currently understand it. Part of the problem was that non-coding DNA was difficult to study because their operations didn't seem to perform any central function. But we've learned so much more about it since we've taken a more serious look into the possibilities.
In other words, there is a reason why psuedogenes exist. And i s a bit presumptuous for us to dismiss such a high volume of our DNA helix as mere 'junk' when it could very well mean that we just don't know much about it yet.

This message is a reply to:
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happy_atheist
Member (Idle past 4997 days)
Posts: 326
Joined: 08-21-2004


Message 80 of 87 (325331)
06-23-2006 12:24 PM
Reply to: Message 79 by Hyroglyphx
06-23-2006 9:04 AM


Re: The evolutionists argument of incredulity
In other words, there is a reason why psuedogenes exist. And i s a bit presumptuous for us to dismiss such a high volume of our DNA helix as mere 'junk' when it could very well mean that we just don't know much about it yet.
For genes that we don't know much about yet then I'd agree we shouldn't just lump them as pseudogenes and forget about them, but that argument doesn't work for genes that we DO know things about.
The example given was for the gene that regulates the production of vitamin C. Most mammals have a working copy of this gene. We have a broken copy of this gene. We can't survive without vitamin C. Why do we have a broken copy of the vitamin C gene? It makes no sense from a design point of view to knowingly put in a broken part.
If you argue that it was broken AFTER the design process, then you have to explain why our copy of the gene is broken in exactly the same place and in exactly the same way as other great apes such as Chimpanzees. There must be something that connects both us and the other great apes, but not Guinnea Pigs that have a broken vitamin C gene that is broken in a different way to ours.
Edited by happy_atheist, : Changed 'should' to 'shouldn't'

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Hyroglyphx
Inactive Member


Message 81 of 87 (327617)
06-29-2006 9:44 PM
Reply to: Message 65 by kuresu
06-18-2006 11:49 AM


Re: The evolutionists argument of incredulity
I may be wrong in what fallacycop was trying to say, but if we were intelligently designed, why the heck would there be a non-functioning gene?
That's a perfectly good question, but I can't help but noticing the level incredulity ascribed to it. By the same premise I could just as easily ask why natural selection did not choose to keep such a gene, when I think we could all agree that possessing the ability to synthesize our own vitamin C would be most beneficial. So what happened that we should lose the ability when its more than evident that vitamin C plays a significant role in our health? It would be one thing to lose a function simply because we don't need it anymore, such as the appendix, as some would suggest and yet still retain some atavistic traits reminiscent of a once fully functional gene. But this isn't the case because vitamin C is necessary in our diet.
Its like another question, similar to this, that has been posed concerning sex as well. What purpose did natural selection have in going from asexual procreation to a profoundly less efficient method that most organisms adhere to, sexual reproduction? Why did natural selection choose the weaker over the superior? Consider how difficult it must have been for nature designing the penis and vagina to coexist compatibly so magnificently, and yet clearly should have evolved at separate times which makes the liklihood of it evolving less and less likely. This doesn't even take into consideration the complexity of the sex organs themselves and going down all the way towards the microscopic contrivances. But that's another argument. My only purpose for mentioning it is that natural selection, it seems, does not always choose the most efficient way of changing. So again, what purpose does it serve to stll have the need for vitamin C only to lose the ability to synthesize your own for an arguably a less efficient method of having to seek it?
Aside from this, noticing the parallels of human and chimp similarity is a matter conjecture because there is not a uniformed method outside of the abstract. Its subjective because its so easy to say, "The mouse has eyes. We have eyes too. There, that proves it. We are definately related to mice." Or, "We have ears and so do Elephants. We are related." You might argue that we have so many similarites with chimps, but for everything that humans and their supposed closest ancestors share, there a millions more differences. Consider what it must have taken nature to produce such vast changes, and yet leave no discernable hard evidence of it ever happening. There are roughly 30 million single nucleotide changes, five million separate events of gene deletion or duplication that had to at some point have happened, as well as our chromosomal arrangement disimilarities. Single base pair substitutions can account for over half of the genetic disimilarities. That's a whole lot.
So, lets think about this for a minute. Enzymes that produce vitamin B12 are somehow oboslete for an inexplicable reason, even though having retained the function would have been concievably far more beneficial. As well, humans have several copies of the vitamin C synthetase genes. What I'm saying is, and the reason I brought up Junk DNA, is that we currently don't know what the function(s) is/are. Could it serve a function that we simply have yet to uncover? Why not? I think its a bit presumptuous to assume that there is no functionality in this particular gene or psuedogenes as well, especially when so much of our genome is comprised of them. The fact is that it remains to be determined what the function of the genes are. But, at this point we just don't know.

“Always be ready to give a defense to
everyone who asks you a reason for the
hope that is in you.”
-1st Peter 3:15

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Replies to this message:
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Coragyps
Member (Idle past 818 days)
Posts: 5553
From: Snyder, Texas, USA
Joined: 11-12-2002


Message 82 of 87 (327631)
06-29-2006 10:34 PM
Reply to: Message 81 by Hyroglyphx
06-29-2006 9:44 PM


Re: The evolutionists argument of incredulity
By the same premise I could just as easily ask why natural selection did not choose to keep such a gene, when I think we could all agree that possessing the ability to synthesize our own vitamin C would be most beneficial.
Based on the primate critters that all share that particular break in the GLO gene, it's real probable that the critter that we inherited the break from was a tree-dwelling monkey-ish sort of animal that ate a lot of fruit. The same animals that have the GLO pseudogene tend to have pretty good color vision, to see when fruit are getting ripe and full of vitamin C. And humans living close to the land didn't seem to have that much trouble with vitamin C deficiency - sailors used to get scurvy before they took fruit along to eat, but landlubbers typically get berries or other fruit now and again. (Though city-dwellers in the impoverished Third World may be in the same boat, so to speak, as the pre-Limey sailors were.)
Anyway, we humans got that broken gene from an ancestor that ate a lot of fruit, and for whom the lack of vitamin C synthesis was no handicap. We're kind of stuck with it, as there have been enough random mutations in it since the "break" that the chances of it regaining function through mutation are pretty durn slim.
noticing the parallels of human and chimp similarity is a matter conjecture
The screamingly obvious signs of our relatedness, again, are in the things we share that are "broken." We have a bunch of pseudogenes related to smell sensors in common with great apes - and they are functional genes in other primates. We have broken urate oxidase genes - same pattern. Humans and great apes start growing a vomeronasal organ and its "receiver", the accessory olfactory bulb of the brain as fetuses, but reabsorb the bulb and nearly lose the VNO by the end of infancy. Most other primates keep these bits as social/sexual sense organs.
And all this stuff fits into those nested hierarchies.....

This message is a reply to:
 Message 81 by Hyroglyphx, posted 06-29-2006 9:44 PM Hyroglyphx has replied

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Belfry
Member (Idle past 5169 days)
Posts: 177
From: Ocala, FL
Joined: 11-05-2005


Message 83 of 87 (327640)
06-29-2006 10:56 PM
Reply to: Message 81 by Hyroglyphx
06-29-2006 9:44 PM


Re: The evolutionists argument of incredulity
nemesis_juggernaut writes:
That's a perfectly good question, but I can't help but noticing the level incredulity ascribed to it. By the same premise I could just as easily ask why natural selection did not choose to keep such a gene,
(My bold.) A nitpick - be careful of anthropomorphic (theomorphic?) phrasing in reference to natural selection.
nemesis_juggernaut writes:
when I think we could all agree that possessing the ability to synthesize our own vitamin C would be most beneficial. So what happened that we should lose the ability when its more than evident that vitamin C plays a significant role in our health? It would be one thing to lose a function simply because we don't need it anymore, such as the appendix, as some would suggest and yet still retain some atavistic traits reminiscent of a once fully functional gene. But this isn't the case because vitamin C is necessary in our diet.
Not at all. If an organism's diet is saturated with vitamin C, then the ability to synthesize it becomes a neutral trait. Perhaps even slightly negative, if there is significant metabolic cost involved. Obviously, with our current lifestyle it would be beneficial to be able to manufacture our own. However, the ability was apparently lost before our lineage diverged from that of chimps, which bear the same genetic defect. Obviously, chimps are able to live on the high levels of ascorbic acid in their native diet, just as guinea pigs and many other animals are. As were our hunter-gatherer ancestors, for the most part. It's an abundant nutrient for those not living primarily on the meats and grains of an agricultural society.
Edit: Apparently I was much too slow, and Coragyps beat me to the Submit button by quite a margin.
Edited by Belfry, : No reason given.
Edited by Belfry, : No reason given.

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Hyroglyphx
Inactive Member


Message 84 of 87 (328275)
07-02-2006 12:59 PM
Reply to: Message 82 by Coragyps
06-29-2006 10:34 PM


Re: The evolutionists argument of incredulity
Based on the primate critters that all share that particular break in the GLO gene, it's real probable that the critter that we inherited the break from was a tree-dwelling monkey-ish sort of animal that ate a lot of fruit.
Your conjecture does not help us understand why natural selection would favor the weaker over the stronger. There are alot of tree-dwelling monkeys that can produce their own ascorbic acid who also eat vitamin C in the wild. They haven't lost the ability to synthesize their own. I presume you're presenting your case from the argument of toxicity, as in, if an animal already synthesizes their own ascorbic acid and also eat it out in the wild, they might recieve toxic levels. And so evolution weeds out the uneccessary gene instead of compelling the monkey to eat a particular fruit with vitamin C. But this doesn't make much sense because unlike most vitamins, one cannot overdose on vitamin C. The body simply passes the excess amounts through urine.
Anyway, we humans got that broken gene from an ancestor that ate a lot of fruit, and for whom the lack of vitamin C synthesis was no handicap. We're kind of stuck with it, as there have been enough random mutations in it since the "break" that the chances of it regaining function through mutation are pretty durn slim.
Pretty darn slim? You think that humans evolved from bacteria via mutations. If you believe that then you'll believe that anything is possible. Aside from this, the GLO gene apparently can make jumps in between the evolutionary tree.
Evidence Against Pseudogene Shared Mistakes | Answers in Genesis
Edited by nemesis_juggernaut, : typos

“Always be ready to give a defense to
everyone who asks you a reason for the
hope that is in you.”
-1st Peter 3:15

This message is a reply to:
 Message 82 by Coragyps, posted 06-29-2006 10:34 PM Coragyps has not replied

Replies to this message:
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Chiroptera
Inactive Member


Message 85 of 87 (328277)
07-02-2006 1:06 PM
Reply to: Message 84 by Hyroglyphx
07-02-2006 12:59 PM


Re: The evolutionists argument of incredulity
quote:
Your conjecture does not help us understand why natural selection would favor the weaker over the stronger.
It depends on what you mean by "weaker" and "stronger". If by "weaker" and "stronger" you refer to traits that you seem to think are preferable, then evolution doesn't care one whit about "weaker" or "stronger".
In the case of vitamin C production, if a creature lives in an environment where food full of vitamin C is plentiful, then an individual who cannot make vitamin C is no weaker than one who can.

"These monkeys are at once the ugliest and the most beautiful creatures on the planet./ And the monkeys don't want to be monkeys; they want to be something else./ But they're not."
-- Ernie Cline

This message is a reply to:
 Message 84 by Hyroglyphx, posted 07-02-2006 12:59 PM Hyroglyphx has not replied

  
lfen
Member (Idle past 4761 days)
Posts: 2189
From: Oregon
Joined: 06-24-2004


Message 86 of 87 (328295)
07-02-2006 3:04 PM
Reply to: Message 84 by Hyroglyphx
07-02-2006 12:59 PM


Re: The evolutionists argument of incredulity
I presume you're presenting your case from the argument of toxicity, as in, if an animal already synthesizes their own ascorbic acid and also eat it out in the wild, they might recieve toxic levels. And so evolution weeds out the uneccessary gene instead of compelling the monkey to eat a particular fruit with vitamin C.
Evolution is not an agent. The environment might be thought of in total as an agent but it's not singular. I don't think there is vit C toxicity occurring in that environment so it couldn't have a selective effect.
It was a genetic accident so to speak that didn't have an effect. There was more than enough vit C in the diet so there was no selection against the gene. Organisms that didn't possess working copies survived just as easily as those that did.
Why then did the descendants of these vit C'less individuals develop into homo and other primates? Does anyone have a theory beyond that was how it happened? No reason for it not to have happened though it could have happened differently as far as I can tell.
lfen

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Wounded King
Member (Idle past 116 days)
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 87 of 87 (328433)
07-03-2006 5:56 AM
Reply to: Message 84 by Hyroglyphx
07-02-2006 12:59 PM


Jumping (pseudo)genes
Aside from this, the GLO gene apparently can make jumps in between the evolutionary tree.
Evidence Against Pseudogene Shared Mistakes | Answers in Genesis
The evidence for this seems a bit limp. Certainly there are sites shared between the human and guinea pig sequences which aren't in rat but all that means is that the rat is different. Without more sequences showing that the Rat sequence represents the ancestral sequence I'm not sure how you can argue that this provides any evidence for the GLO pseudogene 'jumping'.
TTFN,
WK

This message is a reply to:
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