How does special creation/ID explain...

[Undertow]

It's a conundrum. Why did god make us with pseudogenes? They look like real genes, but the have mutations which render them useless. But why? There's no reason to make useless pseudogenes or if they do have any function at all, there's no reason to make defunct genes, which are conspicuously attributable to functional genes, perform the task. What say you? Why do we and the other primates have a pseudogene for the enzyme which synthesizes vitamin C when we actually need that enzyme or else, given a deficient diet, we get scurvy. Why are 40% of our olfactory system genes pseudgoenes?

http://www.ncbi.nlm.nih.gov/sites/entre ... stractPlus

http://www.ncbi.nlm.nih.gov/sites/entre ... stractPlus

[Undertow]

Might as well bung on something else -> Atavisms.

These things are interesting, they are thought to be characteristics kept in the genome stealthily and they pop up every now and then to recapitulate past evolution. Obviously the gist of evolutionary theory is that humans and the other primates evolved from other monkeys (in the larger classification of mammals) which had tails. Therefore evolution can explain and atavistic tail ->

http://www.ncbi.nlm.nih.gov/sites/entre ... stractPlus
http://www.ncbi.nlm.nih.gov/sites/entre ... stractPlus
http://www.ncbi.nlm.nih.gov/sites/entre ... stractPlus

The human atavistic tail is interesting in that it has formed nerves, blood vessels and sweat glands, etc. Added to this, a genetic allele for tail growth and regulation has been found in humans; it's analagous to the same kind of thing in mice.

http://www.ncbi.nlm.nih.gov/sites/entre ... stractPlus
http://www.ncbi.nlm.nih.gov/sites/entre ... stractPlus

Just for kicks, let's do another atavism, this time in whales. Now evolutionary theory states that whales evolved from land animals and interestingly, whale atavistic legs have been documented, the bones of these protrusions being very prominant.

http://digitallibrary.amnh.org/dspace/b ... /N0009.pdf
http://www.monkeymiadolphins.org/Pdf/Be ... 20Hall.pdf

Atavisms have a long history, though not always correct. Though now debunked, in the 1870's they were theorized to be linked with criminal behavior. Forget the name of the bloke who did this. Bet he isn't so happy now though . In regards to evolution, they are linked to many "redundant" appendages. Wings in wingless birds, hyoids in dogs, extra toes in horses, and even whales (though the sperm whale seems to favor this trait over other species of whales). Most of the whales found with this have the femur, tibia, and fibula. But some even have feet with complete digits (though these are more rare). COOLIO!

The question that arises is what benefit would species have in regaining primitive traits? Despite this, it fits with evolution. Evolution often has periods of progress marked with points in which it almost appears as if fossil remains show a reversal of evolution. We call these atavisms, but I am not sure it is anything more than a mutation.

Basically, atavisms are cool, but currently non-functional. But who knows what the future may bring. These aberrations may become vital means of survival??

I don't think it's a matter of benefit for the host organism - I think it's just a chance genetic anomoly, sort of like getting Down Syndrome. Obvioiusly Down Syndrome is a (genetic) disease and is a handicap, as would be atavistic legs for a supposed-to-be streamlined whale. It's an interesting thought that an atavism may be naturally selected for and yet again become predominant in a population yet I don't think this is the case for any particular atavism I've noticed thus far.

On a side note, where did you read about the rarer occurance of forming fully formed feet with digits on the ends of these atavistic legs? In the articles I provided? I must have missed it. Anyway direction to this anomoly in link form would be greatly appreciated if not in one of the articles I provided.

[alexiarose]

Might as well bung on something else -> Atavisms.

These things are interesting, they are thought to be characteristics kept in the genome stealthily and they pop up every now and then to recapitulate past evolution. Obviously the gist of evolutionary theory is that humans and the other primates evolved from other monkeys (in the larger classification of mammals) which had tails. Therefore evolution can explain and atavistic tail ->

http://www.ncbi.nlm.nih.gov/sites/entre ... stractPlus
http://www.ncbi.nlm.nih.gov/sites/entre ... stractPlus
http://www.ncbi.nlm.nih.gov/sites/entre ... stractPlus

The human atavistic tail is interesting in that it has formed nerves, blood vessels and sweat glands, etc. Added to this, a genetic allele for tail growth and regulation has been found in humans; it's analagous to the same kind of thing in mice.

http://www.ncbi.nlm.nih.gov/sites/entre ... stractPlus
http://www.ncbi.nlm.nih.gov/sites/entre ... stractPlus

Just for kicks, let's do another atavism, this time in whales. Now evolutionary theory states that whales evolved from land animals and interestingly, whale atavistic legs have been documented, the bones of these protrusions being very prominant.

http://digitallibrary.amnh.org/dspace/b ... /N0009.pdf
http://www.monkeymiadolphins.org/Pdf/Be ... 20Hall.pdf

Atavisms have a long history, though not always correct. Though now debunked, in the 1870's they were theorized to be linked with criminal behavior. Forget the name of the bloke who did this. Bet he isn't so happy now though . In regards to evolution, they are linked to many "redundant" appendages. Wings in wingless birds, hyoids in dogs, extra toes in horses, and even whales (though the sperm whale seems to favor this trait over other species of whales). Most of the whales found with this have the femur, tibia, and fibula. But some even have feet with complete digits (though these are more rare). COOLIO!

The question that arises is what benefit would species have in regaining primitive traits? Despite this, it fits with evolution. Evolution often has periods of progress marked with points in which it almost appears as if fossil remains show a reversal of evolution. We call these atavisms, but I am not sure it is anything more than a mutation.

Basically, atavisms are cool, but currently non-functional. But who knows what the future may bring. These aberrations may become vital means of survival??

I don't think it's a matter of benefit for the host organism - I think it's just a chance genetic anomoly, sort of like getting Down Syndrome. Obvioiusly Down Syndrome is a (genetic) disease and is a handicap, as would be atavistic legs for a supposed-to-be streamlined whale. It's an interesting thought that an atavism may be naturally selected for and yet again become predominant in a population yet I don't think this is the case for any particular atavism I've noticed thus far.

On a side note, where did you read about the rarer occurance of forming fully formed feet with digits on the ends of these atavistic legs? In the articles I provided? I must have missed it. Anyway direction to this anomoly in link form would be greatly appreciated if not in one of the articles I provided.

Sorry, meant to say occasionally in whales and rare forms in horses.
http://www.egyptsearch.com/forums/Forum ... 01947.html

Most of these examples are of whales with femurs, tibia, and fibulae; however, some even include feet with complete digits.

Many other famous examples of atavisms exist, including (1) rare formation of extra toes (2nd and 4th digits) in horses, similar to what is seen in the archaic horses Mesohippus and Merychippus,

[Undertow]

Ahk, thanks for that. I traced the source back to TalkOrigins. I might do a bit more research to satisfy myself.

[alexiarose]

Ahk, thanks for that. I traced the source back to TalkOrigins. I might do a bit more research to satisfy myself.

I have to. I keep forgetting I am not in class. I am used to people on my level, not above it. I am at the top of my class, but seriously lacking here.

That doesn't mean I am going to stop giving.....HUGS!!!!

[Confused]

It's a conundrum. Why did god make us with pseudogenes? They look like real genes, but the have mutations which render them useless. But why? There's no reason to make useless pseudogenes or if they do have any function at all, there's no reason to make defunct genes, which are conspicuously attributable to functional genes, perform the task. What say you? Why do we and the other primates have a pseudogene for the enzyme which synthesizes vitamin C when we actually need that enzyme or else, given a deficient diet, we get scurvy. Why are 40% of our olfactory system genes pseudgoenes?

http://www.ncbi.nlm.nih.gov/sites/entre ... stractPlus

http://www.ncbi.nlm.nih.gov/sites/entre ... stractPlus

Jumping in late here, but let me run something by you. These pseudogenes have essentially been denaturized proteins, hence making them useless. When I say denaturized, I am referring to essentially being mutated to render them useless. I have to wonder if the increasing entropy that occurs within us could be the culprit. We are referring mostly to biological systems with complex information molecules. Not just the basic 2nd law of thermodynamics where we don't really have to determine if energy is beneficial or destructive because it can only be added or taken away by an outside source. But in a biological system that reacts with such a great diversity, the energy become crucial. Recall the fried egg. If we add to much energy, it will denaturize the protein and destroy any chance that the egg would yield future life. But if we keep the energy at a very controlled level, the yolk and albumin are broken down by a complicated system of enzymes that will form molecules of energy the future chick can use to grow and hatch. So the energy here can either be constructive or destructive . To be constructive, it requires the right amount of energy to allow the enzymes to work.

These enzymatic systems essentially determine what biological organisms can or cannot do. Currently, there is no known mechanism that allows biological systems to direct external energy constructively to increase an organisms complexity. Random mutations and natural selection can slow the process of increasing entropy, not reverse it. There is no known enzymatic process that decreases entropy in a biological system.
Considering this, eventually, energy has a high chance of becoming destructive to a biological organism, ie. too much will denaturize the proteins making them essentially non-functioning pseudogenes.

Like I said, this is a stab in the dark, but I am curious what you might think.

[Undertow]

It's a conundrum. Why did god make us with pseudogenes? They look like real genes, but the have mutations which render them useless. But why? There's no reason to make useless pseudogenes or if they do have any function at all, there's no reason to make defunct genes, which are conspicuously attributable to functional genes, perform the task. What say you? Why do we and the other primates have a pseudogene for the enzyme which synthesizes vitamin C when we actually need that enzyme or else, given a deficient diet, we get scurvy. Why are 40% of our olfactory system genes pseudgoenes?

http://www.ncbi.nlm.nih.gov/sites/entre ... stractPlus

http://www.ncbi.nlm.nih.gov/sites/entre ... stractPlus

Jumping in late here, but let me run something by you. These pseudogenes have essentially been denaturized proteins, hence making them useless. When I say denaturized, I am referring to essentially being mutated to render them useless. I have to wonder if the increasing entropy that occurs within us could be the culprit. We are referring mostly to biological systems with complex information molecules. Not just the basic 2nd law of thermodynamics where we don't really have to determine if energy is beneficial or destructive because it can only be added or taken away by an outside source. But in a biological system that reacts with such a great diversity, the energy become crucial. Recall the fried egg. If we add to much energy, it will denaturize the protein and destroy any chance that the egg would yield future life. But if we keep the energy at a very controlled level, the yolk and albumin are broken down by a complicated system of enzymes that will form molecules of energy the future chick can use to grow and hatch. So the energy here can either be constructive or destructive . To be constructive, it requires the right amount of energy to allow the enzymes to work.

These enzymatic systems essentially determine what biological organisms can or cannot do. Currently, there is no known mechanism that allows biological systems to direct external energy constructively to increase an organisms complexity. Random mutations and natural selection can slow the process of increasing entropy, not reverse it. There is no known enzymatic process that decreases entropy in a biological system.
Considering this, eventually, energy has a high chance of becoming destructive to a biological organism, ie. too much will denaturize the proteins making them essentially non-functioning pseudogenes.

Like I said, this is a stab in the dark, but I am curious what you might think.

Confused, thanks for the input - I'm not sure I totally understand the significance of your post, which could partly be my fault, but I'll try to respond where I can.

First, I'm not so sure that thermodynamics plays a frontline role in the formation of pseudogenes - I'd say the main mechanisms of pseudogene formation are as follows:

1) Duplications of DNA segments - the duplicates potentially result in copies of genes yet only one copy of the gene is necessary - the copy will accumulate background mutations and become redundant.
2) Retrotransposition - the pseudogene in question will have resulted from it's mRNA copy being reverse transcribed back into the genome via an enzyme called reverse transciptase (how incredibly imaginative those scientists are, ey? ). These pseudogenes are obvious due to spliced introns (in us eukaryotes) and something called polyadenylation - a series of added Adenine (A) bases on the end of the gene. These retrotransposed genes can not be transcribed and translated in the regular fashion thereby rendering them useless.
3) Redundancy of the need for particular genes during evolution. If the gene is not needed, natural selection will not remove background mutations accumulating in them and they will become pseudogenes. Case in point is our human olfactory (smell) system - it's made of roughly 40% pseudogenes.

Second, I'm not so sure of the intricacies of thermodynamics on life processes or the nature of 'beneficial or destructive' energy but let me try and run this past you - as long as the sun keeps churning out photons, photosynthesis makes sugars, we animals and other heterotroughs (can't make our own foods - must consume other organisms) keep eating those sugars and our mitochondria keep participating in cellular respiration to form ATP, then I don't see where the problem lies. ATP is a very directable (I suppose you could say 'beneficial') form of energy due to the ability of phosphorylation - the specific activity to add a phosphate group to a molecule and release energy for specific molecular work (you may have heard the term "high energy phosphate" before - they certainly are that - the phosphate bond between the second and third phosphates in ATP holds a helpful punch of chemical energy).

On the fried egg, I suspect the proteins in it become denatured because of the excess of heat energy acting on them - in a proper cellular environment and allowing for excess heat to be radiated from an organism, this would not happen. With a specific energy yielding molecule such as ATP, there is some wasted energy as heat but the direction of chemical energy to drive cellular work is efficient enough for cellular life.

Thirdly, on the prospect of enzymes decreasing/increasing entropy in a biological system, I'm not sure this is the case (nor would this be the job of enzymes, I don't think). Enzymes, as I'm sure you're aware, will lower the activation energy needed for a reaction and when the reaction is endergonic, or requires an input of chemical energy, ATP is at the ready.

I think for the reduction of entropy or keeping it at bay to allow life to occur as it does, the increase of entropy in the sun must outweigh the decrease of entropy in life on earth. I'd say it's somewhat analagous to making a skyscraper - doing so obviously requires huge inputs of energy to make the steel girders, panes of glass, pipes and other materials, yet this decrease of entropy would be made up for by the increase of entropy during the expendature of energy to make the skyscraper's materials (i.e. making steel from iron ore and carbon in a huge vat would require the buring of huge amounts of fuels which often convert from a carbon solid or liquid into CO2 and H20 gas, thereby releasing stored chemical energy and increasing entropy).

In principle, I think that's the marker for how life can decrease entropy (or at least not increase it) - there must be a "checks and balances" type increase of entropy elsewhere in the system (in the sun, in this instance) so the system as a whole increases in entropy to comply with the 2nd law. Perhaps my thermodymaics are off - it's not my best subject.

Considering these things, I don't believe entropy must increase in life nor will it be the culprit of life's processes going bust, e.g. the formation of pseudogenes. I could be wrong, though.

[Confused]

It's a conundrum. Why did god make us with pseudogenes? They look like real genes, but the have mutations which render them useless. But why? There's no reason to make useless pseudogenes or if they do have any function at all, there's no reason to make defunct genes, which are conspicuously attributable to functional genes, perform the task. What say you? Why do we and the other primates have a pseudogene for the enzyme which synthesizes vitamin C when we actually need that enzyme or else, given a deficient diet, we get scurvy. Why are 40% of our olfactory system genes pseudgoenes?

http://www.ncbi.nlm.nih.gov/sites/entre ... stractPlus

http://www.ncbi.nlm.nih.gov/sites/entre ... stractPlus

Jumping in late here, but let me run something by you. These pseudogenes have essentially been denaturized proteins, hence making them useless. When I say denaturized, I am referring to essentially being mutated to render them useless. I have to wonder if the increasing entropy that occurs within us could be the culprit. We are referring mostly to biological systems with complex information molecules. Not just the basic 2nd law of thermodynamics where we don't really have to determine if energy is beneficial or destructive because it can only be added or taken away by an outside source. But in a biological system that reacts with such a great diversity, the energy become crucial. Recall the fried egg. If we add to much energy, it will denaturize the protein and destroy any chance that the egg would yield future life. But if we keep the energy at a very controlled level, the yolk and albumin are broken down by a complicated system of enzymes that will form molecules of energy the future chick can use to grow and hatch. So the energy here can either be constructive or destructive . To be constructive, it requires the right amount of energy to allow the enzymes to work.

These enzymatic systems essentially determine what biological organisms can or cannot do. Currently, there is no known mechanism that allows biological systems to direct external energy constructively to increase an organisms complexity. Random mutations and natural selection can slow the process of increasing entropy, not reverse it. There is no known enzymatic process that decreases entropy in a biological system.
Considering this, eventually, energy has a high chance of becoming destructive to a biological organism, ie. too much will denaturize the proteins making them essentially non-functioning pseudogenes.

Like I said, this is a stab in the dark, but I am curious what you might think.

Confused, thanks for the input - I'm not sure I totally understand the significance of your post, which could partly be my fault, but I'll try to respond where I can.

First, I'm not so sure that thermodynamics plays a frontline role in the formation of pseudogenes - I'd say the main mechanisms of pseudogene formation are as follows:

1) Duplications of DNA segments - the duplicates potentially result in copies of genes yet only one copy of the gene is necessary - the copy will accumulate background mutations and become redundant.
2) Retrotransposition - the pseudogene in question will have resulted from it's mRNA copy being reverse transcribed back into the genome via an enzyme called reverse transciptase (how incredibly imaginative those scientists are, ey? ). These pseudogenes are obvious due to spliced introns (in us eukaryotes) and something called polyadenylation - a series of added Adenine (A) bases on the end of the gene. These retrotransposed genes can not be transcribed and translated in the regular fashion thereby rendering them useless.
3) Redundancy of the need for particular genes during evolution. If the gene is not needed, natural selection will not remove background mutations accumulating in them and they will become pseudogenes. Case in point is our human olfactory (smell) system - it's made of roughly 40% pseudogenes.

Second, I'm not so sure of the intricacies of thermodynamics on life processes or the nature of 'beneficial or destructive' energy but let me try and run this past you - as long as the sun keeps churning out photons, photosynthesis makes sugars, we animals and other heterotroughs (can't make our own foods - must consume other organisms) keep eating those sugars and our mitochondria keep participating in cellular respiration to form ATP, then I don't see where the problem lies. ATP is a very directable (I suppose you could say 'beneficial') form of energy due to the ability of phosphorylation - the specific activity to add a phosphate group to a molecule and release energy for specific molecular work (you may have heard the term "high energy phosphate" before - they certainly are that - the phosphate bond between the second and third phosphates in ATP holds a helpful punch of chemical energy).

On the fried egg, I suspect the proteins in it become denatured because of the excess of heat energy acting on them - in a proper cellular environment and allowing for excess heat to be radiated from an organism, this would not happen. With a specific energy yielding molecule such as ATP, there is some wasted energy as heat but the direction of chemical energy to drive cellular work is efficient enough for cellular life.

Thirdly, on the prospect of enzymes decreasing/increasing entropy in a biological system, I'm not sure this is the case (nor would this be the job of enzymes, I don't think). Enzymes, as I'm sure you're aware, will lower the activation energy needed for a reaction and when the reaction is endergonic, or requires an input of chemical energy, ATP is at the ready.

I think for the reduction of entropy or keeping it at bay to allow life to occur as it does, the increase of entropy in the sun must outweigh the decrease of entropy in life on earth. I'd say it's somewhat analagous to making a skyscraper - doing so obviously requires huge inputs of energy to make the steel girders, panes of glass, pipes and other materials, yet this decrease of entropy would be made up for by the increase of entropy during the expendature of energy to make the skyscraper's materials (i.e. making steel from iron ore and carbon in a huge vat would require the buring of huge amounts of fuels which often convert from a carbon solid or liquid into CO2 and H20 gas, thereby releasing stored chemical energy and increasing entropy).

In principle, I think that's the marker for how life can decrease entropy (or at least not increase it) - there must be a "checks and balances" type increase of entropy elsewhere in the system (in the sun, in this instance) so the system as a whole increases in entropy to comply with the 2nd law. Perhaps my thermodymaics are off - it's not my best subject.

Considering these things, I don't believe entropy must increase in life nor will it be the culprit of life's processes going bust, e.g. the formation of pseudogenes. I could be wrong, though.

I am usually a bit scattered after 4am. My point was two-fold:
1) We currently have a few hypotheses as to the origin or degradation of pseudogenes. Reviewing some of my magazines, online articles, and my daughters genetics books, I have to wonder at the possible causes of the denaturizing of these proteins. Nothing really accounts for them. Perhaps they played a role in the past, perhaps they will play a role in the future. But most likely they are simply mutations. But what caused the mutations? Obviously, the mutations weren't deleterious, but benign. If they were active at some point, their role wasn't essential to life was it? Considering the effects of energy in the human body, my mind was drifting towards the same priciple as the fried egg. If energy wasn't utilized properly in the human body, excess amounts could in effect, destroy some of the enzymatic reaction required for cell life, thereby denaturizing the protein, rendering the gene inactive.
2) The human body does love its checks and balances. But it is anything but a well-balanced system. Usually, compensation occurs for one system at the expense of another. As it has been pointed out to me, the human body is an open system, gaining its energy from outside sources and releasing its energy back to outside sources. But again, this isn't effecient. Often, excess energy is the cause of body imbalances. ATP isn't effecient. The Kregs cycle isn't effecient. Aerobic vs Anaerobic fuel sources aren't any more effecient. It would seem to me that as energy has such fluctuations in the human body, it does quite a bit of damage. One can't see equilibrium even in the best of conditions. The point being, nothing in the human body can prevent or reverse entropy. It will continue to increase despite all the checks and balances. With every incremental increase, damage occurs.

The point I was trying to get across was that pseudogenes may not have been invented by God, but a byproduct of ID (which of course I reject so I guess this is really moot).

[Jose]

Considering this, eventually, energy has a high chance of becoming destructive to a biological organism, ie. too much will denaturize the proteins making them essentially non-functioning pseudogenes.

On the fried egg, I suspect the proteins in it become denatured because of the excess of heat energy acting on them - in a proper cellular environment and allowing for excess heat to be radiated from an organism, this would not happen. With a specific energy yielding molecule such as ATP, there is some wasted energy as heat but the direction of chemical energy to drive cellular work is efficient enough for cellular life.

Indeed, the proteins of a fried egg denature due to heat. Specifically, it's that the movement of the water molecules increases enough that they can no longer force the hydrophobic amino acids into the middle of the protein, so the proteins start to wobble and flop and unfold. They can then start to stick to each other, which makes the semi-solid glop we get when we cook eggs.

In cells, it's really hard to make this happen without killing the cell. But some proteins are more floppy than others, and may be targets for extra energy. In general, this happens when the temperature goes up (i.e. to get those water molecules twirling more). There's a cellular response that occurs when this happens--turning up the expression of a small set of genes--so it's easy to measure when cells are feeling stressed. In general, any temperature increase does it--but to get a "good" response, you need to get human cells up to 42C, well above a high fever. In a cute little experiment by Burr Atkinson and his Japanese postdoc, involving hot tubs, analysis of protein production in white blood cells, and rectal thermometers, it was found that you can't stay in a hot tub long enough to get your body up to a good "heat shock" temperature. But I digress.

The point is, denaturing proteins wholesale is hard to do. The heat-stress-induced proteins serve to protect cells from damage. They either hold onto the denatured proteins, and then fold them up again when the stress is over, or they tag them for degradation and the cell chews them up.

That's a bit of an aside, overall. The story is helpful in seeing that denatured protein doesn't relate to pseudogenes. There's no way to get an unfolded-protein "message" back to the gene, and in any event, the unfolded proteins are either repaired or degraded.

To get pseudogenes, you need to change the DNA directly. It's thought that it's either gene duplication, followed by mutation of one of the copies (which is OK if the other one works), or it's having a reverse-transcriptase (from a virus, perhaps) take a messenger RNA, copy it into DNA, and then have that DNA copy integrate into a chromosome. This puts a copy of the gene into the DNA, but without proper signals for expression. Eventually, the gene copy accumulates mutations. If it could be translated into protein, it would make a protein that doesn't fold up correctly--and would follow the same degradation fate as protein that's unfolded by heat stress.

My guess with vitamin C production is that a mutation occurred, knocking out the gene's function, but since everyone was eating plenty of fruits and leaves full of vitamin C, the mutation had no harmful effects. For whatever reason, the mutation eventually got fixed in the population. Once inactive, there was no longer selection on it for function, and additional mutations were able to accumulate--producing the current pseudogene.

Since we seem to have a pretty good handle on the mechanism of producing pseudogenes, wouldn't we have to conclude that god invented the mechanism, rather than the pseudogenes themselves? If he did insert them here and there in various genomes, he must have had a plan in mind, to make their locations and sequences fit nicely with the overall pattern that looks so much like evolution. Maybe he did...pretty tricky!

[Undertow]

Jose, thanks for the post, totally agreed.

[Undertow]

I think the creationist explanations for these phenomena are lacking... You're all still welcome to explain how creationism or a non genealogical life history explains these phenomena.

Anyway let's try and add something else - SINEs, or Short INterspersed Nuclear Elements. The best example here is the 'Alu' SINE, which has amplified through primate genomes, including our own, to roughly 1 million copies occupying 10% of our genome. They amplify through a mechanism called retrotransposition and are deemed under the broad category of genetic elements called 'retrotransposons' or retroposons. Now I think I explained this a bit on the pseudogenes point but I'll reiterate here for clarity - retroposition occurs by a copy-paste mechanism whereby a genetic segment, such as an Alu, is transcribed into mRNA and then reverse transcribed by an enzyme called reverse transcriptase into the genome. Through this mechanism the Alu family of retroposons has amplified thoughout our evolutionary history. Now these Alu elements in particular are considered to be homoplasy free, meaning the chance of two of any given Alu inserting into the same genomic loci (location) twice is very slim. So, finding many Alu elements shared between human and chimp loci would obviously evidence a genealogical relationship, yet how does creationism or ID explain the miniscule chance of many Alu elements inserted into identical loci between humans and chimps?

Alus are excellent molecular markers for a variety of reasons. They aid in tracing the complex pattern of duplication and rearrangements that occurred during the evolution of primate genome. Unlike other mutations, Alu sequences are rarely lost completely once retroposed, have a defined ancestral state and are free from homoplasy since independent and identical insertions are highly unlikely. Because of these characteristics, Alus are literally molecular fossils. Polymorphic Alu loci are especially useful in studies of human genetic diversity and in pedigree and forensic analysis.

General reading: [1]

Journal reading:

The [alpha globin pseudogenes] genes of both human and chimpanzee are flanked by the same Alu family member. The structure and position of this repeat have not been altered since the divergence of human and chimpanzee, and it is at least as well conserved as its immediate flanking sequence. Comparing human and chimpanzee, the 300 bp Alu repeat has accumulated only two base substitutions and one length mutation; the adjacent 300 bp flanking region has accumulated five base substitutions and twelve length mutations.

Here we compare the sequences of seven pairs of chimpanzee and human Alu repeats. In each case, with the exception of minor sequence differences, the identical Alu repeat is located at identical sites in the human and chimpanzee genomes. The Alu repeats diverge at the rate expected for nonselected sequences. Sequence conversion has not replaced any of these 14 Alu family members since the divergence between chimpanzee and human.

Phylogenetic analysis of Alu Ye5 elements and elements from several other subfamilies reveals high levels of support for monophyly of Hominidae, tribe Hominini and subtribe Hominina. Here we present the strongest evidence reported to date for a sister relationship between humans and chimpanzees while clearly distinguishing the chimpanzee and human lineages.

At eight Alu Ye5 loci and two previously identified Alu Yi and Yd loci (18, 45), amplification of filled sites was obtained in human, bonobo, and common chimpanzee.

The utility of SINE insertions, and mobile elements in general, for phylogenetic analysis continues to be bolstered by studies such as this one. Here, we present the first application of SINEs to fully elucidate the phylogeny of the hominid lineage and present the strongest evidence to date for phylogenetic relationships among the hominid lineages. Of the 133 Alu insertion loci, 95 were unambiguously informative for determining the relative divergence of each of the major lineages.

The Alu Ye lineage appears to have started amplifying relatively early in primate evolution and continued propagating at a low level as many of its members are found in a variety of hominoid (humans, greater and lesser ape) genomes.

For the Ye subfamilies, 120 of the 153 elements identified in the draft human genomic sequence were amplified by PCR. Examination of the orthologous regions of the various species genomes displayed a series of different PCR patterns indicative of the time of retroposition of each of the elements into the primate genomes. Results from a series of these experiments showed a gradient of Ye Alu repeats beginning with some elements that are recent in origin and unique to the human genome (e.g. Ye5AH110) and ending with elements that are found within all ape genomes (e.g. Ye5AH148). The distribution of all the Ye elements in various primate genomes is summarized in Additional File 2. [See the word document file]

Repetitive elements, particularly SINEs (short interspersed elements) and LINEs (long interspersed elements), provide excellent markers for phylogenetic analysis: their mode of evolution is predominantly homoplasy-free, since they do not typically insert in the same locus of two unrelated lineages, and unidirectional, since they are not precisely excised from a locus with the flanking sequences preserved (Shedlock and Okada 2000 ). Indeed, the use of SINEs and LINEs to elucidate phylogeny has a rich history. SINEs and LINEs have been used to show that hippopotamuses are the closest living relative of whales (Shimamura et al. 1997 ; Nikaido et al. 1999 ), to determine phylogenetic relationships among cichlid fish (Takahashi et al. 2001a ,b ; Terai et al. 2003 ), and to elucidate the phylogeny of eight Primate species, providing the strongest evidence yet that chimps are the closest living relative of humans (Salem et al. 2003 ). In each one of these studies, the presence or absence of a repetitive element at a specific locus in a given species was determined experimentally by PCR analysis, using flanking sequences as primers.