The article below appeared in the
April 2011 Journal of Creation,
Volume 25, Issue 1
The PDF is free to download
here.
Shared mutations in the human and chimpanzee β-globin pseudogenes is not evidence for a common ancestor
by Bryan Anderson
Evolutionists have often postulated that there are ‘shared mutations’
in pseudogenes (supposedly defective genes) from different baramins
(biblical kinds) and that this is
conclusive evidence that the different baramins share a common ancestor.
Consequently, this postulation appears to falsify biblical creation in
favor of evolution. This argument is so
convincing because a similar argument is used in other non-biological
fields to prove a common source for two pieces of information. For
example, two similar written articles can be compared
to identify plagiarism, by searching for unusual spelling errors that
appear in both articles. If unusual spelling errors are identified, this
is compelling evidence that one of the authors
has copied the other’s article, or that both of the authors have copied
another author’s article.
Evolutionists have suggested that the β-globin pseudogenes in humans
and chimpanzees contain shared mutations and they have used this idea to
conclude humans and chimpanzees share a
common ancestor.
1 Despite the recent discoveries that some pseudogenes actually have a
function,
2 the apparent β-globin pseudogenes and their so-called shared mutations are still being used as evidence for a common
ancestor for humans and chimpanzees in the current literature.
3 This conclusion is incompatible with biblical creation since the Bible
says that humans and the ancestors of chimpanzees were created separately.
Human and chimpanzee β-globin gene clusters
Globin genes code for the predominate proteins in red blood
cells—hemoglobin. It binds and transports oxygen from the lungs to cells
throughout the body. Hemoglobin is needed because
oxygen dissolves poorly in the blood plasma. Humans carry nine globin
genes, which are all slightly different to each other. Five of these
genes are clustered together in a region of DNA called
the ‘β-globin gene cluster’, which is located on chromosome 11 in humans
(figure 1). These genes are not all switched on at the same time but in
stages, corresponding to their
position on the chromosome and the different stages of human
development.
The β-globin pseudogene in humans is located in the β-globin gene
cluster, between the γ-A and the δ-globin genes (figure 1). There are
two copies of the γ-globin
genes, called γ-A and -G. The β-globin pseudogene shows higher
similarity to the γ-globin gene, but is called the β-globin pseudogene
because it was originally identified
by comparing it to the β-globin gene of rabbits.
4 Chimpanzees have the same globin genes in the same order, including the
β-globin pseudogene.
Apparent genetic defects in the β-globin pseudogenes
Evolutionists hypothesized several point mutations and deletions in
the β-globin pseudogenes of humans and chimpanzees and these differences
render these regions incapable of being
translated (figure 1). The start codon (a codon is a sequence of three
adjacent nucleotides constituting the genetic code) of the human
β-globin pseudogene has two apparent point
mutations which prevents the protein-synthesizing machinery (ribosome)
identifying it as a gene. A point mutation has been suggested in humans
at codon 15 that signals the ribosome to
prematurely terminate synthesis of the protein (premature stop codon).
At codons 20 and 145 in humans it has been suggested that there are
deletions of 1 bp. The first deletion messes up the
code of the gene, resulting in six stop codons in the exons downstream,
and the second scrambles a correct stop codon at the end of the
pseudogene. These same hypothesized defects are found
at the same position on the chimpanzee chromosome. In addition to the
theoretical predictions, scientists have not detected any evidence using
wet laboratory techniques that these pseudogenes
in humans or chimpanzees are translated.
4
Figure 1. The organization of the
β-globin gene cluster in humans and an expanded view of the β-globin
pseudogene, showing the ‘defects’.
The first (horizontal) track displays the position on the chromosome (in
bp). The second track is a diagrammatic illustration of the
organization of β-globin gene cluster. Arrows indicate
the direction of the genes. The bottom bar is an expanded view of the
β-globin pseudogene. The white boxes are introns.
Interesting findings about the β-globin pseudogenes
There are three interesting findings about the β-globin pseudogenes
from humans and chimpanzees. Firstly, when the pseudogenes from human
and chimpanzee are aligned and analyzed for
differences they are almost identical.
1 The high level of
similarity is not only seen in the exons of these pseudogenes, but also
in the regions immediately upstream of the first
exons (promoters and 5’ untranslated regions), between (introns), and
immediately downstream of third exons (3’ untranslated regions). These
regions have only 31 bp that are
different. Secondly, there are putative promoters located upstream of
these pseudogenes that are almost identical, with only 1 bp of the 15 bp
TATA- and CAAT-like boxes that is different in
humans and chimpanzees.
1 The TATA- and CAAT-like boxes of the
human β-globin pseudogene are located at nucleotides -25 and -81,
respectively. The transcription initiation site
is numbered as the +1 position and nucleotides upstream are numbered
with negative integers. The human β-globin pseudogene TATA-like box has
the sequence of TAAAAA and the CAAT-like box
has the sequence GGTCAATAG. Normally, TATA and CAAT boxes are centered
at nucleotides -25 and -80, respectively, with the consensus TATAAA and
GGCCAATCT. Therefore, the TATA- and CAAT-like boxes
of the human β-globin pseudogene are located at the correct positions
and are only 1 and 3 bp, respectively, from the consensus sequence.
Finally, the predicted intron junctions of the
pseudogenes obey the ‘GU/AG RNA splicing rule’
1 (‘RNA splicing’ is the modification of an RNA transcript, in which the transcript is cut at the intron
junctions; the introns are then removed and the exons are spliced together).
Evolutionists have shown little interest in these findings about the
β-globin pseudogenes. This is because they have assumed that these
pseudogenes are just more nonfunctional junk
DNA. Evolutionists believe the DNA of more complex organisms, such as
primates, must consist of mainly junk,
5
so finding pseudogenes
within the β-globin gene clusters is unsurprising to them. In addition
to this, scientists may have detected that two exons of the β-globin
pseudogene in humans are transcribed into
non-coding RNA (ncRNA).
6-8
However, this possible finding has been largely ignored by the
scientific community, again because of the assumption that this region
is a pseudogene. Some evolutionists prematurely dismiss this finding as
merely noise in their wet laboratory results. They
assume that many of the RNA transcripts detected in humans, primates and
the other more complex organisms are because of the limitations of the
current techniques and equipment used. Therefore,
they have concluded these regions are not transcribed to RNA.
9
Discussion
The fact that these β-globin pseudogenes in humans and chimpanzees
are almost identical suggests that they either (1) have not been copied
in each organism from generation to generation
for the past five million years, (2) the entire regions, including the
promoters, 5’ untranslated regions, introns and 3’ untranslated regions
are functionally constrained and must
remain almost identical, or (3) they have been transferred from
chimpanzees to humans or vice versa, recently. The first suggestion is
consistent with the Creation hypothesis. The second is
unlikely, because Sanford has shown that natural selection cannot
maintain the integrity of human DNA for so long.
10
The third
suggestion is also unlikely because there is no evidence in nature that
large amounts of genetic material can be transferred between humans and
chimpanzees. Consequently, the fact that high
rates of mutations are not seen and that these regions are almost
identical suggests they are young. Hence, this reduction in time for the
existence of human and chimpanzee organisms makes it
highly improbable they evolved from a common ancestor.
Based on the above evidence and our present understanding of
genetics, the best hypothesis for these regions is that they function to
remove the γ-globin RNA transcripts. As stated
earlier in this article, subsets of globin genes are switched on and off
according to the order on the chromosome, and their order correlates to
the different stages of development. At the
birth of a human infant, the γ-globin genes are significantly
down-regulated and the β-globin gene is significantly up-regulated, with
normal adult levels reached for each gene by
the end of the first year of the infant’s life. The ncRNA transcripts
from these pseudogenes may bind with ncRNA transcripts partners that are
mirror images to the pseudogene transcripts,
these transcripts are known as ‘antisense transcripts’. The pair of
transcripts is then cut up, a process known as ‘dicing’, and the RNA
fragments are used to direct
degradation machinery to the γ-RNA transcripts. This process is known as
‘RNA induced RNA silencing’. Thus cellular levels of the γ-RNA
transcripts are decreased.
Although, the γ-globin genes may have their own antisense transcripts, a
third antisense transcript would amplify the process of γ-globin RNA
transcript removal.
This hypothesis is supported by the following facts. That in humans and chimpanzees;
- Since TATA- and CAAT-like boxes have been identified upstream of these regions, these regions may be transcriptionally active;
- the predicted intron junctions obey the
GU/AG rule, therefore, suggesting that splicing would occur if these
regions were transcribed;
- all three exons have at least one stop codon;
- these regions are similar to the γ-globin genes; and
- these regions are located between the γ-A and the β-globin genes.
In addition to this, transcripts may have been detected for the
second and third exons, in humans. Finally, scientists have identified a
pseudogene in mice that codes for an antisense
transcript. Once this antisense transcript is bound to its cognate
transcript, it is diced and then used to induce silencing.
11 Although
this phenomenon in mice is somewhat different, it does add support for the above hypothesis.
Thus, evolutionists have somewhat prematurely concluded that these
regions in humans and chimpanzees are genuine pseudogenes (i.e. former
genes deactivated by mutations) and that there are
shared mutations in these regions. Whatever the reason for these
pseudogenes, there is a lack of evidence in these regions to suggest
that humans and chimpanzees have a common ancestor.
Related Articles
Further Reading
References
- Chang, L.Y. and Slightom, J.L., Isolation and
nucleotide sequence analysis of the β-type globin pseudogene from
human, gorilla and chimpanzee, J. Mol.
Biol. 180:767–784, 1984. Return to text.
- Sasidharan, R. and Gerstein, M., Genomics: protein fossils live on as RNA, Nature 453:729–731, 2008. Return to
text.
- Miller, K.R., Only a Theory: Evolution and the Battle for America’s Soul, Penguin, New York, 2009. Return to text.
- Fritsch, E.F., Lawn, R.M. and Maniatis, T., Molecular cloning and characterization of the human β-like globin gene cluster, Cell 19:959–972, 1980. Return to text.
- ReMine, W.J., The Neutral Theory of Evolution; in: The Biotic Message: Evolution versus Message Theory, Saint Paul Science, Minnesota, MN, pp. 248–250, 1993. Return to text.
- Harrington, J J., Sherf, B., Rundlett, S. et al., Creation of genome-wide protein expression libraries using random activation of gene expression, Nat. Biotechnol. 19:440–445, 2001. Return to text.
- Kent, W.J., BLAT—the BLAST-like alignment tool, Genome Res. 12:56–64, 2002. Return to text.
- Hillier, L., Clark, N., Dubuque, T. et al., Unpublished work, Stanford University, Stanford, CA, 1995–1996. Return to text.
- Wang, J., Zhang, J., Zheng, H. et al., Mouse transcriptome: neutral evolution of ‘noncoding’ complementary DNAs, Nature 431:1–2, 2004. Return to text.
- Sanford, J.C., Genetic Entropy and the Mystery of the Genome, FMS Publications, Waterloo, NY, 2008. Return to text.
- Tam, O.H., Aravin, A.A., Stein, P. et al., Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes, Nature 453:534–538, 2008. Return to text.
between developmental
biology and our knowledge of the history of life, the theory of
intelligent design, and the interaction of science and theology. Paul
lectures frequently at colleges and universities throughout the United
States and Europe, has spoken on American and Italian national public
radio, and written for popular publications as varied as the Oslo Dagbladet and the Christian Research Journal.
since 1998. His Ph.D. was in plant breeding and plant genetics. While a professor at Cornell, John has trained graduate students and conducted genetic research at the New York State Agricultural Experiment Station in Geneva, NY. During this time, John bred new crop varieties using conventional breeding and then became heavily involved in the newly-emerging field of plant genetic engineering. John has published over 80 scientific publications and has been granted over 30 patents. His most significant scientific contributions involve three inventions, the biolistic ("gene gun") process, pathogen-derived resistance, and genetic immunization. A large fraction of the transgenic crops (in terms of numbers and acreage) grown in the world today were genetically engineered using the gene gun technology developed by John and his collaborators. John also started two biotech enterprises derived from his research, Biolistics, Inc., and Sanford Scientific, Inc. John still holds a position at Cornell (Courtesy Associate Professor), but has largely retired from Cornell and has started a small non-profit organization, Feed My Sheep Foundation.
A scientific convert to six-day creation, his groundbreaking new book Genetic Entropy and the Mystery of the Genome (http://creation.com/store_redirect.php?sku=10-3-506) demonstrates why human DNA is inexorably deteriorating at an alarming rate, thus cannot be millions of years old.
