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EVIDENCE FOR EVOLUTION FROM THE GENES FUNCTIONING IN SIGNALING MECHANISMS
HOMOLOGIES ARE PREDICTED BY THE EVOLUTIONARY MODEL
The following images depict three different receptors: an FSH receptor on an ovary whose response to FSH is required for gamete formation, a dopamine receptor whose response to dopamine is required for the functioning of the brain, and an olfactory receptor which detects odors.
What do these receptors have to have in common? Technically, nothing. FSH is a peptide, dopamine is a modified amino acid, and odorants can have a broad diversity of chemical structures.
In the same way, what do the cell membrane receptors for potassium, sodium, and calcium have to have in common? Nothing.
What similarities are expected between the proteins which determine cystic fibrosis and multidrug resistance in human cancer cells? What similarities are expected between these two human proteins and eye pigment transporters in fruit flies or metabolite transporters in bacteria? None, necessarily.
When comparing cell membrane proteins within one organism or between organisms, there is no pattern of similarities in cell membrane proteins which would be expected if evolution had not occurred. The molecular evidence does not support this model. Analysis of the cell membrane proteins used in a single organism and those of different organisms identifies homologous groups of genes predicted in the evolutionary model.
1) HOMOLOGIES IN GENE FAMILIES
The first set of drawing in the preceding section depicted FSH, dopamine, and olfactory receptors. All of these receptors are members of the same gene family which has produced thousands of new receptors from modified duplicates of ancestral ones. This gene family, the G-protein coupled receptor (GPCR) superfamily, is the largest gene family in vertebrate genomes, including that of humans. Not only has variation of the extracellular regions resulted in receptors which can react to a diversity of signaling molecules produced inside a multicellular organism (most polypeptide hormones, neurotransmitters, growth factors, extracellular calcium etc.), but also with a diversity of stimuli from the environment. G protein coupled receptors include the receptors that humans use to detect taste, smell, and even light.
As a result, there are GPCR gene family members
which perform entirely different functions. For example, GnRH receptor mutations cause hypogonadism
and different alleles of the MC1R receptor result in red hair and also
blond/light brown hair. Variations
in this receptor are also associated with the inability to tan and the
increased risk of melanoma. Some
GPCRs are receptors for local hormones (such as histamine and bradykinin
receptors) while some chemokine receptors are coreceptors for HIV. (CCR2 is a receptor for MCP1, the monocyte chemoattractant
protein. One allele of this receptor
offers resistance from HIV. CCR5
is a coreceptor for HIV. Different
alleles affect the progression of AIDS and some alleles offer resistance
to HIV. CXCR4 is a coreceptor for
HIV and is involved in atherosclerosis.
One allele causes a rapid progression of AIDS. The chemokine receptors CXCR4 and CCR5 serve
as coreceptors for HIV and SIV viruses (
Other GPCRs function as the receptors for neurotransmitters and can have quite profound effects on human neural function and personality. There are a number of dopamine receptors (DRD1 through DRD5). DRD2 alleles have been linked to schizophrenia, recurrent major depression, and adolescent emotional disorders. The A1 allele of DRD2 is more common in those addicted to alcohol, cigarettes, opiates, and other substances and is associated with high novelty seeking and high harm avoidance (Berman, 2002). The Ser311Cys allele of DRD2 is more common in those with persecution delusional disorder (Morimoto, 2002). DRD4 receptors are expressed in the limbic system and affect cognition, emotions, and anger. Different alleles of DRD4 are associated with scores on personality tests related to novelty seeking (high scores with novelty seeking are correlated with impulsive and exploratory behaviors; low scores are correlated with being stoic, loyal, and frugal)(OMIM).
Taste receptors are G protein coupled receptors. The T1Rs family of receptors is involved in the perception of sweet tastes. Taste receptors TAS1R1 and TAS1R2 respond to a diversity of sweet compounds (sucrose, monosaccharides, artificial sweeteners, and the amino acids tryptophan and glycine) (Pin, 2003).
Olfactory receptors are the largest gene family in multicellular organisms and thus the largest gene family of the G-protein coupled receptors superfamily. It is estimated that there are hundreds of these genes in the human genome (some estimate from 500 to 1000) and that olfactory receptors are capable of detecting millions of different compounds (Fuchs, 2001).
The rhodopsin group is one of the largest family of genes within the G protein coupled receptor superfamily (which is the largest gene family in eukaryotes). Members of this family have been modified to perceive biogenic amines (adrenaline, dopamine, histamine, and serotonin), short peptides, proteins (LH, FSH), nucleosides, nucleotides, lipids, eicosanoids, and light (Fredriksson, 2003).
GPCRs are not the only gene family which function on cell membranes. ABC transporters and helicases are superfamilies of proteins which are found in all groups of organisms, including bacteria, plants, and vertebrates. Homologous regions suggest that both are modified versions of the same ancestral genes. While most ABC transporters function is transport, some ABC transporters do not perform any transport and are involved in DNA repair (such as MutS, Rad50, and bacterial UvrA). ABC transporters are also homologous to the protein RecA which mediates recombination. The many human genes in these families include the genes whose mutations cause cystic fibrosis, the multidrug transporters which must be considered in cancer treatment, and the TAP proteins which are required for the recognition of “self” by the immune cells
The many kinds of ion channels are homologous members of the same gene family including sodium, potassium, and calcium channels. SCN1A mutations cause generalized epilepsy, myoclonic epilepsy, and febrile seizures. KCNA7 is expressed in the heart and mutations may be a factor in heart blocks. The sodium potassium ion exchange pumps which allow for the generation of electrical messages in neurons are homologous to a number of calcium channels.
2) HOMOLOGIES IN DISTANTLY RELATED ORGANISMS
There is no expectation that homologs of human genes would exist in other organisms if they were not evolutionarily related. There are arguably many ways to convert a signal at the cell membrane to a cytoplasmic signal and non-humans would not be expected to possess similar cellular processes if they were completely unrelated to humans. For example, given that the GPCRs are involved in the functioning of the human brain, the human senses, and the perception of human hormones, there is no reason to assume their homologs exist in more primitive organisms, especially unicellular ones. However, evidence indicates that this gene family is an ancient family which transduces signals in organisms as primitive as bacteria. For example, the light-detecting bacteriorhodopsin is homologous to GPCRs of higher organisms although exon shuffling has changed the order of the transmembrane regions (Pardo, 1992; Bartus, 2003).
G protein coupled receptors (GPCRs) are the receptors for most of these signals, and they mediate the signals of the nervous system which result in muscle contraction, hormone secretion, sensory awareness, emotions, memory, and personality.
GPCRs compose the largest gene family in eukaryotes (Bartus, 2003). Unicellular yeast respond to mating pheromones through G-protein coupled receptors, reminiscent of homone-receptor interactions of animals (Blumer, 1998; Poggeler, 2001). Gene duplication had produced many of the subfamilies of the G proteins and protein tyrosine kinases before the lineages leading to modern sponges separated from those leading to higher animals (Suga, 1999). Cnidarians possess a GPCR for biogenic amines homologous to mammalian receptors for NE and E. Cnidarians also seem to possess GPCRs which are homologous to dopamine and serotonin receptors (Bouchard, 2004). GPCRs represent more than 5% of the genome of the nematode C.elegans (with more than 1000 genes) and 1% of the genome of Drosophila (with 160 genes; (Rouquier, 2000; Zozulya, 2001; Takeda, 2002; Halpern, 2003; Chyb, 2004).
Higher eukaryotes share the same components of G-protein signaling pathways including ligands, GPCRs, effector pathways, heterotrimeric G proteins, and regulator proteins (although the latter group has not yet been demonstrated in plants). The basic pattern of this form of signal transduction had evolved by the separation of eukaryotic lineages (Sierra, 2002).
The human retina depicted below uses molecules of rhodopsin to detect light and allow for vision. How did this sense evolve? Opsins are G protein coupled receptors which are known in organisms as primitive as bacteria. The ancestors of vertebrates possessed a number of opsins expressed in neural tissue and other tissues which were involved in a number of responses to light other than vision. The vertebrate eye evolved from neural tissue which expressed opsins. A duplication in the red opsin gene in the ancestor of Old World monkeys and apes allowed for the trichromatic color vision of higher primates including humans
Not only do other organisms have homologs of human genes, humans have homologs of those genes found in other organisms, even if humans don’t use these genes. It was estimated that 48% of the olfactory receptor genes (388/802) in the human genome are functional (Nimura, 2003). Only about 27% of those in Old World monkeys and virtually none of those in New World monkeys are pseudogenes (Rouquier, 2000; Zozulya, 2001). Because of the large number of olfactory receptor genes whose mutations have rendered them functionless pseudogenes, higher primates have lost much of the acuity that more primitive primates and most mammals possess in their ability to detect odors.
A second example of GPCR pseudogenes in the human genome which are homologous to functional genes in other organisms are the vomeronasal organ receptors. Humans, like most land vertebrates, possess two completely distinct anatomical senses of smell although one of the two, the vomeronasal organ, appears to be non-functional. While the vomeronasal organ in New World monkeys seems to be functional, its function may be less adaptive than is the case in most mammals. TOnce TRP2 became a pseudogene, there would no longer have been a selective pressure to maintain functional VNO receptors. Statistically, the small number of VNO receptor genes which still have open reading frames in humans falls into the expected range of the number which would remain after about 35 million years of mutation. Of the 5 remaining V1R genes in humans, V1RL5 and V1RL3 seem to be in the process of pseudogenization, given the high frequency of mutations which exist in current human populations. No V2R genes exist as open reading frames in humans. Humans also have at least one V3R gene which is expressed in the apical portion of the VNO. (Zhang, 2003; Giorgi, 2000; Rodriguez; Kouros-Mehr, 2001 ; Ryba, 1997; Lane, 2001).
Other cell membrane gene families evolved long before humans. In humans, ABC transporters have a number of functions and their variants can cause cystic fibrosis and multidrug resistance in cancer cells. In bacteria, ABC transporters can be used in osmoregulation, transport of bicarbonate, nitrite, nitrate, maltose, trehalose, sugars, ions, peptides, cellobiose, fructose, sulfur, glucose, molybdate, anions, arsenite, heme, manganese, phosphate, and carnitine. ABC transporters compose 1-2% of the genes in some bacterial genomes such as E. coli (where they are the largest gene family in the genome), Bacillus subtilis, and archaea. (Horlacher, 1998; Liu, 1998; van der Heide, 1999).
In order for humans to conduct electrical messages in their nervous and muscular systems, they require voltage regulated ion channels. Voltage regulated ion channels probably exist in all living organisms (Anderson, 2001). The many kinds of ion channels are homologous. The structure of the ancestral ion channel seems to have been a small protein with two transmembrane regions on either side of a pore-forming region. This is the structure of the protein in many prokaryotic channels and eukaryotic inward rectifier channels. Before the split between prokaryotes and eukaryotes, four additional transmembrane regions were added to an ancestral channel, producing a protein with a pore-forming region and 6 transmembrane regions. Some prokaryotic channels and most eukaryotic channels possess this structure. Some channels resulted from a fusion of a 6 transmembrane segment channel and a 2 transmembrane segment channel (Anderson, 2001). Most potassium channels are formed by the interaction of four separate subunits composed of 6 transmembrane regions. All sodium and calcium channels are formed by a single protein which is formed by four tandem regions composed of 6 transmembrane regions (Anderson, 2001).
C) THE GENE CLADOGRAM AND “IRREDUCIBLE COMPLEXITY”
One of the main arguments in “Intelligent Design” is that of “irreducible complexity.” Advocates of Intelligent Design have argued that molecular systems in living organisms involve multiple interacting genes and that such complex pathways could not have evolved gradually. Analysis of the distribution of cell membrane proteins strongly refutes this. As the following gene cladogram illustrates, the components of molecular pathways do not appear all at once in complex pathways. Instead, it is apparent that throughout evolution organisms incorporated cell membrane proteins which their ancestors possessed into new roles which were elaborated over time. The complex molecular systems found in humans are not irreducibly complex in that, while their multiple interacting parts may be required for human life, no such system is a requirement for life in general. Early cells and early animals did not require the ability to respond to the variety of hormones, neurotransmitters, and environmental signals found in humans. They did not possess excitable cells capable of conducting electricity. A much simpler set of molecular mechanisms were sufficient for these earlier organisms.
Some of these organisms evolved new cell membrane proteins and new molecular systems through the duplication and modification of existing genes, the shuffling of protein domains, mutation, etc. At first these novelties would not have been essential for life, but rather supplementary systems which gave their bearers an advantage over other organisms. The descendants of these organisms evolved in ways so that these molecular mechanisms were required to support greater molecular complexity.
THE GENE CLADOGRAM
Many of the genes which humans require to be human evolved long before humans. The distribution of these genes among modern organisms supports that modern groups of organisms can be organized into clades which share a common ancestry. The same clades of organisms which are supported through the analysis of signaling molecules are supported by the analysis of other genes, anatomical features, embryological development, and the fossil record. The organization of modern organism into a nested hierarchy of clades is predicted by the evolutionary model but not alternative models.
--GPCRs (Fredriksson, 2003a; Josefsson, 1999).
--GPCRs opsin for light detection (Pardo, 1992; Bartus, 2003)
--Voltage regulated ion channels probably exist in all living organisms (Anderson, 2001).
--potassium channel (Jiang, 2002a and 2002b).
--ABC transporters (Horlacher, 1998; Liu, 1998; van der Heide, 1999).
--gene duplications the largest gene family in eukaryotes (Bartus, 2003
--yeast respond to mating pheromones through G-protein coupled receptors, reminiscent of homone-receptor interactions of animals (Blumer, 1998; Poggeler, 2001).
-- Plants are known to possess members of families A, B, and F (Josefsson, 1999) family C is known in slime molds and sponges (Pin, 2003).
--G-protein signaling pathways had evolved by the separation of eukaryotic lineages (Sierra, 2002).
--almost all human ABC transporters have homologs in yeast (Decottignies, 1997).
--The P-gp (MDR1) family subfamily of ABC transporters seems to be specific to eukaryotes and include MDR1-like proteins which are responsible for multiple drug resistance and other subfamily members which pump bile salts and phosphatidyl choline (Dassa, 2001).
--While eukaryotic sodium channels are large proteins, composed of four homologous domains of a potassium-channel like region, a simpler sodium channel is known in bacteria. It has a single domain, similar to the smaller potassium channels (Catterall, 2001).
--Calcium pumps originally existed on the cell membrane but were added to the ER in the evolution of eukaryotes. The ER pumps are homologous to those of the plasma membrane (Sorrentino, 2000).
--Virtuallly all protists use calcium to depolarize the cells (with the exception of the heliozoan Actinocoryne contractilis which uses sodium). Sodium dependent action potentials are typical of animals since the simplest animals which possessed a nervous system, the cnidarians (Paulsen, 2000).
--duplications lineages leading to modern sponges separated from those leading to higher animals (Suga, 1999).
--Sponges have a metatropic glutamate/GABA-like receptor of the GPCRs (Muller, 2001).
--type II rhodopsins (Spudich, 2000).
--Multiple potassium channels are typical of animals, even cnidarians (Anderson, 2001).
--Sodium α subunit (which is primarily responsible for the depolarization during an action potential) exist in a diversity of invertebrates, including cnidarians, whose sodium channels are similar to those in mammals (Anderson, 2001; Plummer, 1999).
--Voltage regulated calcium channels are known in cnidarians (Zoccola, 1999).
--Its homolog in C. elegans (ced-7) is a protein which functions in adhesion in dying cells and the cells engulfing them. This suggests that the mechanism of engulfing cells after apoptosis is conserved from nematodes through mammals.
--The two subfamilies of ICRCs diverged before the evolution of nematodes (there is some evidence of their presence in plants); both nemaotodes and flies possess one inositol triphosphate receptor and the ryanodine receptor (Sorrentino, 2000).
--cannibinoid receptors (Onaivi, 2002).
--Members of the STRP, OTRP, and LTRP channels are known in both C.elegans and mammals (Harteneck, 2000).
--The ancestral condition for vertebrates seems to have been 3 retinal opsins (rhodoposin, a color opsin with maximum absorption <500 nm, and a color opsin with maximum absorption >500 nm) in addition to extraretinal opsins. (Nathans, 1999).
--The homologue of the chemokine receptor Cxcr4 in zebrafish functions in development for the migration of germ cells (Knaut, 2003).
Of the class II OLFACTORYgenes, several subfamilies of one family have expanded considerably in mammals (Glusman, 2000)
--3 opiod receptors (Darlison, 1997).
--one group has undergone expansion in primates (Fuchs, 2001).
--VNO reduced importance (Linman, 2003; Liman, 1999).
--While 60-70% of the olfactory receptor genes are pseudogenes in humans, only about 27% of those in Old World monkeys and virtually none of those in New World monkeys are pseudogenes. (Rouquier, 2000; Zozulya, 2001).
--TRP2 a pseudogene causing loss of function of VNO (Zhang, 2003; Giorgi, 2000; Rodriguez; Kouros-Mehr, 2001 ; Ryba, 1997; Lane, 2001).
--The gene COX8H became an inactivated pseudogene in Old World monkeys, apes, and humans (Goldberg, 2003).
--duplication of long/middle opsin produced green cone pigment (Nathans, 1986a; 1986b).
--duplication of X linked opsin gene produces red and green opsin genes (Deeb, 1994)
--7 amino acid residues in red opsin and 9 in green opsin unique to higher apes compared to Old World monkeys (Deeb, 1994; gibbons not in analysis)
ABCC13 protein contains only 6 exons of the 28 which are present in the gene due to a frameshift mutation which prevents the other exons from being translated. The complete protein is expressed in Old World monkeys while a shared 11 base pair deletion (which results in the frameshift) exists in humans, chimps, and gorillas. Although the gene is expressed in the colon, bone marrow, salivary gland, and fetal liver the truncated transcript cannot function as a transporter. The gene is thought to be in the process of becoming a pseudogene (Annilo, 2004).