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Wednesday, 19 June 2013

Genetic Evidence for Human Evolution - Shared Genomic 'Errors' (B)


The evidence for human evolution: Shared genetic errors (B)

In part 2 we looked at the basic concepts behind the evidence for common descent as shown by shared 'genetic errors' such as pseudogenes, retrotransposons and endogenous retroviruses. A few examples will follow, in order to highlight why the evidence for common descent just from this branch of science is regarded as overwhelming.

Shared pseudogenes

The enzyme cytochrome P450 C21 is of critical importance in the biosynthesis of  steroid hormones. Humans have both a working copy of the CYP21 gene (which has eight exons)0 C21, as well as a pseudogene, which is damaged in three main ways:
  • An eight base pair deletion in exon 3 of the gene
  • A one base pair substitution at codon 318 of exon 8
  • A single nucleotide insertion in exon 7
Kawaguchi et al analysed the DNA of humans, orangutans, chimpanzees and gorillas to clarify how and when the defects in the CYP21 pseudogene occurred:
The primary purpose of this study has been to determine the evolutionary origins of the three defects characterizing the human CYP21P gene. The study shows that the 8-bp deletion in exon 3 is present in the chimpanzee but not in the gorilla or orangutan genes, whereas the T insertion in exon 7 and the substitution generating the stop codon in exon 8 are restricted to human genes. [1]
In other words, the 8 base pair deletion occurred in a common ancestor of humans and chimpanzees, while the substitution and insertion occurred after the human-chumpanzee speciation event:

Our results are consistent with this scenario: the 8-bp deletion apparently occurred after the gorilla lineage split off but before the chimpanzee and human lineages separated from each other. We can thus date the occurrence of the 8-bp deletion rather precisely within a relatively short period of some 6 Myr ago. The deletion was followed, in the human lineage, by the two other defective mutations. [2]
Again, recall our analogy of multiple examination papers with the same wrong errors and the same mistakes in the wrong answers, down to the same spelling errors. No one would seriously advance multiple independent errors as a valid explanation. Rather, they'd conclude that copying had occurred. The same applies here. When we have identical errors in the CYP21 pseudogene of chimpanzees and humans, it stretches credibility to assume that:
  • Purely by chance, chimpanzees and humans both have a CYP21 pseudogene which arose via a duplication event
  • Purely by chance, they both acquired the same eight base pair deletion
Common descent, with the duplication event occurring in a species ancestral to human and chimpanzee which was then passed down to chimpanzee and human lineages is the only credible explanation. (Special creationists explanations as expected are absent from the mainstream scientific literature.)

Other examples of shared pseudogenes follow:

1. The GBA gene, which codes for the enzyme glucocerebrosidase has a pseudogene present not only in humans, but in chimpanzees and gorillas. Human, chimpanzees and gorillas share the same 55 base pair deletion. [3]

2. The RT6 gene normally codes for a protein which is found on the surface membrane of T lymphocytes (a class of white blood cell). In both humans and chimpanzees it is a pseudogene, which means this protein is not expressed. Haag et al have examined the human and chimpanzee RT6 pseudogene:
We have now cloned and sequenced the homologues of the RT6 genes from humans of distinct ethnic backgrounds and of the chimpanzee. Surprisingly, in each case, three premature in-frame stop codons preclude expression of the single copy RT6 gene as a cell surface protein. Otherwise, the RT6 genes of human and chimpanzee exhibit high structural conservation to their rodent counterparts. RNA expression analyses indicate that the RT6 gene is not transcriptionally active in human T cells or any other human tissue analyzed so far. To our knowledge, RT6 represents the first mammalian membrane protein identified that has been lost universally in the human and chimpanzee species due to gene inactivation. [4]
Again, here is an example of humans and chimpanzees having the same pseudogene with the same crippling mutation, which makes sense if humans and chimpanzees shared a common ancestor in which this mutation took place and from whom the two lines inherited the pseudogene. From a special creationist point of view, this is inexplicable.

3. Humans and apes are unable to synthesise the enzyme urate oxidase, as the gene which normally would code for it is a pseudogene. In humans, chimpanzees, this is due to the same mutation. In gibbons, which are also unable to synthesise urate oxidase, this is due to a separate mutation event:
Two nonsense mutations at codon positions 33 and 187 and an aberrant splice site were found in the human gene. These three deleterious mutations were also identified in the chimpanzee. The nonsense mutation at codon 33 was observed in the orangutan urate oxidase gene. None of the three mutations was present in the gibbon; in contrast, a 13-bp deletion was identified that disrupted the gibbon urate oxidase reading frame. These results suggest that the loss of urate oxidase during the evolution of hominoids could be caused by two independent events after the divergence of the gibbon lineage; the nonsense mutation at codon position 33 resulted in the loss of urate oxidase activity in the human, chimpanzee, and orangutan, whereas the 13-bp deletion was responsible for the urate oxidase deficiency in the gibbon. [5]
4. Humans have thirteen genes which code for the oxygen-carrying molecule haemoglobin. Four of them in adults are functional, while five are active only in the foetal stage and are inactivated around birth. The remaining four are pseudogenes. The genes occur in two clusters, the alpha cluster (three pseudogenes and four genes) and the beta cluster (one pseudogene and five genes).

The single pseudogene in the beta cluster - the ψβ pseudogene - is considerably degraded, with around 30% of the gene sequence mutated when compared with the functional β haemoglobin gene. Given the known rate of mutation, this means the ψβ pseudogene must have been disabled a long time ago. Therefore, common descent would predict we'd see it not only in humans and the great apes, but in more distantly related primates, and that is exactly what we see. The ψβ pseudogene is seen in humans, apes, baboons and new world monkeys. Furthermore, when we examine the ψβ pseudogene in humans, chimpanzees and gorillas, we see the same crippling mutations:
These three pseudogenes each share the same substitutions in the initiator codon (ATG → GTA), a substitution in codon 15 which generates a termination signal TGG → TGA, nucleotide deletion in codon 20 and the resulting frame shift which yields many termination signals in exons 2 and 3. [6]
One of the pseudogenes in the alpha cluster, the ψζ pseudogene is almost identical with the working ζ foetal haemoglobin gene. It is another example of a duplicated pseudogene, one which was inactivated only a relatively short time ago [7]. When we look at the genome of the chimpanzee, regarded as the closest living relative of humans, we see two ζ haemoglobin genes, confirming that the conversion of the duplicated ζ gene to a pseudogene took place after the human-chimp speciation event, relatively recently.



Source: Fairbanks D.J. "Relics of Eden: The Powerful Evidence of Evolution in Human DNA" (2007, Prometheus Books)
5. Finally, humans, apes and monkeys, unlike most other animals, are unable to synthesise their own vitamin C. As one would have guessed by now, this is because one of the enzymes involved in the biosynthesis of vitamin C,   L-gulonolactone oxidase is not synthesised as GULO, the gene that codes for the enzyme, is a pseudogene in humans, apes and monkeys. Furthermore, it is crippled in exactly the same way [8], consistent with the gene being converted to a pseudogene in the common ancestor of humans, apes and monkeys.

Furthermore, when we examine the GULO pseudogene in these primates, we find random mutations, which is what one would expect in a section of DNA that is selectively neutral. Common descent would predict that primates that share a recent common ancestor would differ by fewer random mutations than those that share a remote common ancestor. This is exactly what we see. Furthermore, when we plot this data in tree form, we get an evolutionary family tree consistent with the standard one obtained from morphological data.


Source: http://pandasthumb.org/archives/2008/05/23/images/GULO_PHYLIP_Tree_Common_names.png

This consonance between morphological and molecular phylogenetic trees is exactly what common descent would predict, and utterly impossible to honestly reconcile with common design, unless God was deliberately creating life with errors in order to fake common descent.
This barely touches the surface of the vast array of pseudogene evidence demonstrating human-ape common ancestry. As molecular biologist Daniel Fairbanks notes:
With a few notable exceptions, chimpanzees and humans have the same pseudogenes in the same places, and they are, on average, about 98 percent similar. [9]
Needless to say, the odds of these two species purely by chance having the same genes convert to pseudogenes with exactly the same genetic mutation causing the pseudogenisation of these genes is so remote as to be impossible. Common design fails to explain this evidence:
  • It fails to explain why, if a creator did not intend for humans and apes to have these genes in the first place, were they created with broken versions of genes that in other animals are functional.
  • It fails to explain why these broken genes were created in closely related animals with the same crippling mutation.
  • It fails to explain why these broken genes were also created with random mutations places in exactly the right way to allow scientists to construct evolutionary family trees that are consonant with the standard evolutionary family trees. Such consonance is exactly what one would expect if common descent was true. Special creation is simply unable to honestly account for this evidence. 
It is worth noting that even the intelligent design apologist Michael Behe fully accepts the weight of evidence in favour of common descent from the pseudogene data.
"Both humans and chimps have a broken copy of a gene that in other mammals helps make vitamin C ... It's hard to imagine how there could be stronger evidence for common ancestry of chimps and humans." [10]
"More compelling evidence for the shared ancestry of humans and other primates comes from...a broken hemoglobin gene." [11]
The evidence for common descent just from pseudogenes is clear, and unarguable. It is however not the only source of evidence for common descent from shared genetic 'errors'.

Shared retrotransposons

Retrotransposons are mobile genetic elements that copy and paste themselves randomly throughout the genome. Essentially, they are genetic parasites. More importantly, their presence is evidence of a prior insertion event in the genome - any argument that they were specially created can be dismissed, if only because of the considerable evidence [12-15] linking retrotransposons with genetic disease.

As the presence of retrotransposons in the genome is evidence of prior copying and pasting of that genetic element, if we see the same retrotransposon in exactly the same place in the genome of two related species, then we have two options:
  • Purely by chance, the same retrotransposon inserted itself into exactly the same place in human and ape genomes
  • The retrotransposon was first inserted in the genome of the common ancestor of human and ape, and then inherited by the descendant species.
The odds of independent identical retrotransposon insertion at identical places in human and ape genomes is remote. If we have an example where seven retrotransposons are found in exactly the same places in human and chimpanzee genomes, then the chances are so remote as to be impossible. This is exactly what we have found. In the alpha haemoglobin cluster of humans and chimpanzees. Researchers have found that "[i]n each case, with the exception of minor sequence differences, the identical Alu repeat is located at identical sites in the human and chimpanzee genomes." [16]

In fact, by looking for the presence of retrotransposons in primate genomic data, we have been able to construct a reliable evolutionary family tree that is consistent with the accepted tree based on morphological data.

Source: Gene (2007) 390:39-51

The use of the unique pattern of retrotransposon data has real-world applications in allowing researchers to identify - for example - what sort of primates a carnivore eats based on the genetic material detected in its faeces. It also allows accurate identification of products seized in the illegal wildlife trade. [18] It is also worth noting that this approach can be used to identify humans. [19] Special creationists who accept the result of a paternity test should, to be consistent, accept this technique when it confirms common descent of humans and apes.

Shared endogenous retroviral elements

The evidence for common descent from retrotransposons and pseudogenes is overwhelming, so looking at what endogenous retroviral elements have to say may appear overkill. However, the ERV data is perhaps the most compelling of all. While pseudogenes and retrotransposons are 'indigenous' to the species in question for want of a better term, ERV data is unarguably alien, presence of an ancient retroviral infection that became integrated into the germ line of the animal, and passed down the generations. Therefore, the presence of identical retroviral elements at the same position in human and ape genomes strongly suggests infection and integration of the retroviral element in a species ancestral to human and ape.
John Coffin, an acknowledged expert in virology  notes that:
Because the site of integration in the genome, which comprises some three billion base pairs in humans, is essentially random, the presence of an ancient provirus at exactly the same position in different, but related, species cannot occur by chance, but must be a consequence of integration into the DNA of a common ancestor of all the species that contain it. It evolution of retroviruses follows, therefore, that we can infer what viruses were present millions of years ago by examining the distribution of endogenous proviruses in modern species. [20]
Johnson, in a paper coauthored with Welkin Johnson [21] showed that ERV elements can be used to construct primate evolutionary family trees. This hinges on the principle that ERVs, once integrated into the germ line will be inherited, and therefore of use as markers of inheritance. They used human endogenous retroviruses (HERVs) and found that these HERVs are:
the result of integration events that took place between 5 and 50 million years ago, as indicated by the distribution of specific proviruses at the same integration sites (or loci) among related species. The evolution of primates has been the subject of intense study for well over a century, providing a well established phylogenetic consensus with which to compare and evaluate the performance of ERVs as phylogenetic markers. [22]
The idea behind this is fairly simple. An ERV element should not be under positive selection as it is of no use to the organism, and will eventually accumulate random mutations. The longer the time between the divergence of the two lines leading to the modern speies, the more mutations will accumulate in these ERV elements. From this data, an evolutionary family tree can be constructed.
ERV elements differ from pseudogenes and retrotransposons in that they have three sources of information that allow evolutionary family trees to be constructed:
  • The distribution of ERVs among related species
  • Accumulated mutations in ERVs,  allowing an estimate of genetic distance
  • Sequence divergence between the LTRs at each end of the ERV, which is a source of information unique to endogenous retroviruses.
The odds of this distribution of ERV elements occuring by chance is remote. The vertebrate genome is huge, and retroviral integration is random, making the odds of identical ERV integration at the same place in multiple genomes unlikely:
Therefore, an ERV locus shared by two or more species is descended from a single integration event and is proof that the species share a common ancestor into whose germ line the original integration took place. Furthermore, integrated proviruses are extremely stable: there is no mechanism for removing proviruses precisely from the genome, without leaving behind a solo LTR or deleting chromosomal DNA. The distribution of an ERV among related species also reflects the age of the provirus: older loci are found among widely divergent species, whereas younger proviruses are limited to more closely related species. [23]
The second point has been addressed previously, and need not be covered again. The final point is one unique to ERVs. At each end of the ERV is a sequence known as a LTR, or Long Terminal Repeat. The mechanics of reverse transcription mean that both LTRs will be identical when the ERV integrates into the genome. Johnson and Coffin note:
Furthermore, both clusters are predicted to have similar branching patterns as determined by the phylogenetic history of the host species, with similar branch lengths. Thus, each tree displays two estimates of host phylogeny, both of which are derived from the evolution of an initially identical sequence. As we shall see, deviation of actual trees from this prediction provides a powerful means of testing the assumptions and detecting events other than neutral accumulation of mutations in the evolutionary history of a species. [24]
Johnson and Coffin looked at the distribution of ERVs in the primate genetic material analused, and found:
Three of the loci, HERV-KC4, HERV-KHML6.17, and RTVL-Ia, were detectable in the genomes of OWMs and hominoids, but not New World monkeys, and therefore integrated into the germ line of a common ancestor of the Old World lineages. HERV-K18, RTVL-Ha, and RTVL-Hb were found exclusively in humans, gorillas, chimpanzees, and bonobos, and thus are consistent with a gorilla/chimpanzee/human clade. None of the loci was detected in New World monkeys. [25]
This  is perfectly explained by common descent. To reiterate an “ERV locus shared by two or more species is descended from a single integration event and is proof that the species share a common ancestor into whose germ line the original integration took place.” Johnson and Coffin found many loci shared by these primate species, some shared only by humans, chimps, bonobos and gorillas, some shared only by old world monkeys and hominoids (humans and great apes). This data is consistent with an evolutionary origin of these species, but impossible to explain by special creation.
Most of the ERVs analysed produced phylogenetic trees consistent with expectation. Their conclusions:
The HERVs analyzed above include six unlinked loci, representing five unrelated HERV sequence families. Except where noted, these sequences gave trees that were consistent with the well established phylogeny of the old world primates, including OWMs, apes, and humans… Phylogenetic analysis using HERV LTR sequences gives rise to trees with a predictable topology, on which is superimposed the phylogeny of the host taxa, and allows ready detection of conversion events. [26]
Other studies show that humans and primates share ERVs in a way consistent with common descent.  Barbulescu et al showed that many human ERVs of the HERV-K class (present in humans, apes and old world monkeys) are unique to humans:
Two proviruses, HERV-K105 and HERV-K110/HERV-K18 were detected in both humans and apes. HERV-K110 was present in humans, chimpanzees, bonobos and gorillas but not in the orangutan. Thus, this provirus formed after orangutans diverged from the lineage leading to gorillas, chimpanzees, bonobos and humans, but before the latter species separated from each other. HERV-K105 was detected in humans, chimpanzees and bonobos, but not in gorillas or the orang-utan. The preintegration site, however, could not be detected in gorillas or orang-utans using several different primers based on the human sequences that flank this provirus. It is therefore unclear from this analysis whether this provirus formed after gorillas diverged from the human–chimpanzee–bonobo lineage, or if it formed earlier but was subsequently deleted in one or more lineages leading to modern apes. It is clear that at least one full-length HERV-K provirus in the human genome today has persisted since before humans, chimpanzees, bonobos and gorillas separated during evolution, while at least eight formed after humans diverged from the extant apes. [27]
Belshaw et al, looking at the long-term reinfection of the human genome by ERVs note that:
Within humans, the most recently active ERVs are members of the HERV-K (HML2) family. This family first integrated into the genome of the common ancestor of humans and Old World monkeys at least 30 million years ago, and it contains >12 elements that have integrated since the divergence of humans and chimpanzees, as well as at least two that are polymorphic among humans…This recent activity makes this family ideal for distinguishing between the alternative mechanisms of proliferation. [28]
The pattern of HERV-K elements, shown below, demonstrates just how powerful the ERV evidence is in demonstrating human-ape common ancestry, as well as confirming the standard evolutionary history of primates.  Again, ERVs are remnants of ancient viral infection. They are not native to humans or primates, but bear witness to ancient retroviral infection. The odds of multiple identical HERV elements integrating into primate and human DNA in exactly the right places to simulate common descent are so low as to be effectively zero.

Approximate integration times of HERV-K elements. Arrows indicate the lineage in which a particular LTR was first detected, and numbers refer to the cluster as identified in Fig. 1 Time estimates for divergence of the different primate lineages were taken from Bailey et al. From Patrik Medstrand and Dixie L. Mager Human-Specific Integrations of the HERV-K Endogenous Retrovirus Family J Virol. 1998 December; 72(12): 9782–9787. 

Conclusion

The existence of multiple shared genetic 'errors' such as broken genes, mobile genetic parasites and ancient retroviral infection in human and ape DNA is without doubt the most emphatic confirmation of human-ape common ancestry that could ever hope to obtain. This is not common design - these element are almost always without function, and are evidence of ancient genetic 'errors' that have been passed down to descendant species. The only credible, intellectually honest position a special creationist can take after reviewing this evidence is to accept the fact of common descent.
This article first appeared at my Facebook page here

References

1. Karaguchi H, O'hUign C, Klein J "Evolutionary Origin of Mutations in the Primate Cytochrome P450c2l Gene" Am. J. Hum. Genet. (1992) 50:766-780

2. ibid, p 777.

3. Wafaei J.R., and Choi F.Y., "Glucocerebrosidase Recombinant Allele: Molecular Evolution of the Glucocerebrosidase Gene and Pseudogene in Primates" Blood Cells, Molecules, and Diseases 35 (2005) 35: 277-85.

4.  Haag F, Koch-Nolte F, Kiihl M, et al. Premature stop codons inactivate the RT6 genes of the human and chimpanzee species. J Mol Biol  (1994) 243:537-546

5. Xiangwei Wu, Donna M. Muzny, Cheng Chi Lee, C. Thomas Caskey "Two independent mutational events in the loss of urate oxidase during hominoid evolution" Journal of Molecular Evolution (1992) 34:78-84
6. L.-Y.Edward Chang, Jerry L. Slightom  "Isolation and nucleotide sequence analysis of the β-type globin pseudogene from human, gorilla and chimpanzee" Journal of Molecular Biology (1984) 180:767:783

7.  W. C. Wong et al., "Comparison of Human and Chimpanzee Zeta 1 Globin Genes" Journal of Molecular Evolution (1985) 22: 309-15

8. Ohta Y, Nishikimi M. "Random nucleotide substitutions in primate nonfunctional gene for L-gulonogamma-lactone oxidase, the missing enzyme in L-ascorbic acid biosynthesis"  Biochim Biophys Acta (1999) 1472:408-11.
9. Fairbanks D.J. "Relics of Eden: The Powerful Evidence of Evolution in Human DNA" (2007, Prometheus Books) p 54

10. Behe M "The Edge of Evolution. The Search for the Limits of Darwinism" (2007, Free Press) p 71-72

11. ibid., p 71

12. Ostertag E.M. et al "SVA Elements Are Nonautonomous Retrotransposons that Cause Disease in Humans" Am J Hum Genet (2003) 73:1444-1451

13. Callinan, P. and Batzer, M.A. (2006) Retrotransposable elements and human disease. In Genome and Disease. Genome Dynamics (Vol. 1) (Volff, J., ed.), pp. 104–115, Karger

14. Crow, Mary K. "Long interspersed nuclear elements (LINE-1): potential triggers of systemic autoimmune disease." Autoimmunity 43.1 (2009): 7-16.

15. Schneider, Anna M., et al. "Roles of retrotransposons in benign and malignant hematologic disease." Cellscience 6.2 (2009): 121.

16. Sawada I. et al "Evolution of alu family repeats since the divergence of human and chimpanzee" Journal of Molecular Evolution (1985) 22:316-322

17. Scott W. Herke S.W. et al  "A SINE-based dichotomous key for primate identification" Gene (2007) 390:39-51


18. ibid, p 43

19. Novick G.E. et al. "Polymorphic human specific Alu insertions as markers for human identification." Electrophoresis (1995) 16: 1596-1601.

20. Coffin JM “Evolution of Retroviruses: Fossils in our DNAProceedings of the American Philosophical Society (2004) 148:264-280

21. Johnson WE Coffin JM Constructing primate phylogenies from ancient retrovirus sequences Proc. Natl. Acad. Sci USA (1999) 96:10254-10260

22. ibid p 10254

23. ibid p 10255

24. Johnson WE Coffin JM op cit p 10255-10256

25. ibid p 10256

26. ibid p 10259

27. Barbulescu M et al “Many human endogenous retrovirus K (HERV-K) proviruses are unique to humans” Current Biology (1999) 9:861-868

28. Belshaw R et al “Long-term reinfection of the human genome by endogenous retroviruses” PNAS (2004) 101:14;4894-4899