Chromosome 2, evidence for common ancestry ?

Chromosome 2, evidence for common ancestry ? 


https://reasonandscience.catsboard.com/t1707-chromosome-2-evidence-for-common-ancestry

chromosomal fusions happen to be fairly common - even within the same species.  In fact, there are humans alive today that have chromosomal fusions - and surprise surprise, they're still human! - morphologically and functionally indistinguishable from other modern humans.  Another example can be found with horses.  Hybrids of the wild horse have 33 pairs while the domesticated horse has 32 chromosomal pairs. Also, domestic dogs and wolves of the genus canis have 78 chromosomes while foxes have a varied number from 38-78 chromosomes. Yet another example is the house mouse Mus Musculis, which has 40 chromosomes, while a population of mice form the Italian Alps was found to have only 22 chromosomes 1

Doubts about the cause of fusion 2
It is clear that chromosome fusion occurred. Yet, there is reason to challenge the evolutionary explanation. When chromosomes break, “sticky ends” result, which readily combine with other chromosomes that have also broken apart. Yet, while it is not unusual for chromosomes to fuse, they will almost never fuse with intact chromosomes because of telomeres. These structures, in addition to providing stability, are designed to prevent chromosomes from undergoing fusion with chromosome fragments.
For human chromosome 2 to arise, it would have required either telomere-telomere fusion (a highly unlikely event) or fusion of an intact chromosome at its telomere with a sticky end generated when another chromosome fractured near its telomere. This type of fusion can happen, but it is a rare occurrence. Fusion would also need to occur in one of the gametes (sperm and egg cells), thereby changing the number of chromosomes. When the sperm fertilizes the egg, if the chromosome numbers do not match, fertilization almost always results in either: (1) a nonviable zygote or embryo; (2) a viable offspring that suffers from a diseased state; or (3) a viable offspring that is infertile. Though possible, it is extremely rare for the offspring to be viable and fertile.

Evidence of genetic engineering
The highly unlikely nature of these events could be taken as evidence for the Creator’s role in engineering or designing the fusion. The Bible’s description of animal and human creation suggests a large degree of genetic similarity (which would include similarity of chromosomes) is to be expected between humans, hominids, and chimpanzees (and the other apes). We propose that the apparent fusion of two chimp chromosomes to produce human chromosome 2 offers a hint as to how the Creator worked. Perhaps God used a preexisting template that He reshaped to create the physical makeup of the hominids and human beings. And perhaps part of the reshaping activity involved fusing together two chromosomes to make human chromosome 2. After all, genetic engineers—who are made in God’s image—are capable of altering organisms by manipulating genetic material. Might not the Creator do the same? Could not God be thought of as a divine genetic engineer? If valid, we predict that in the future geneticists will find that the fused chromosome has functional importance.

1. http://www.detectingdesign.com/pseudogenes.html#Fusion
2. Who was Adam? : a creation model approach to the origin of man / Fazale Rana ; with Hugh Ross. -- Second expanded edition. page 251

The Key Human-Ape Differences 1


  
Pseudogenes are also being found to have similar functionality as miRNAs.  "Transcripts of processed pseudogenes can contain regions with significant antisense homology, which may suggest a regulatory role for transcribed pseudogenes through an RNAi-like mechanism" (see Link ).  Two recent studies have demonstrated that such transcribed pseudogenes can regulate transcription of homologous protein-coding genes. Transcription of a pseudogene in Lymnea stagnalis, that is homologous to the nitric oxide synthase gene, decreases the expression levels for the gene through formation of a RNA duplex; this is thought to arise via a reverse-complement sequence found at the 5′ end of the pseudogene transcript (Link). In a second example, transcription of the makorin1-p1 TPΨg in mouse was required for the stability of the mRNA from a homologous gene makorin1. This regulation was deduced to arise from an element in the 5′ areas of both the gene and the pseudogene (Link).  More recently, Weil et al. discovered that the murine FGFR-3 pseudogene is transcribed in fetal tissues in an antisense direction. This prompted the following consideration:
 

 As the regions of exact identity between FGFR-3 and its pseudogene can be up to 60 nt long, it may be envisioned that FGFR-3 transcripts could play a regulatory role in FGFR-3 expression. If these antisense transcripts could hybridize to sense FGFR-3 transcripts inside the cells, this may lead to either rapid degradation or inhibition of translation. (Link)


 As Yao et. al., predict, "Further studies on transcribed pseudogenes will add to our understanding of their potential roles as non-coding RNA genes or other new types of functional elements." (Link)  It seems like many transcribed pseudogenes may act as giant miRNAs to regulate the function of protein-coding genes and other genetic elements.
 
Other interesting differences include the fact that over 6% of the genes between humans and apes are unique to either humans or ape - i.e., they are not shared.  
 

 "Our results imply that humans and chimpanzees differ by at least 6% (1,418 of 22,000 genes) in their complement of genes, which stands in stark contrast to the oft-cited 1.5% difference between orthologous nucleotide sequences. This genomic “revolving door” of gene gain and loss represents a large number of genetic differences separating humans from our closest relatives." ^55sup>


         And, if one thinks a 6% difference is impressive, what about a difference of more than 30 percent?  Impossible?  Think again.  A study published by Nature in early 2010 shows just such a difference between the Y-chromosomes of humans and apes.  The Y-chromosome for chimps had never been completely sequenced and mapped directly before this study was performed.  It showed many striking differences between human and chimp chromosome structure, gene content, and even qualitatively unique genes between the two species.  As far as looking at specific genes, the chimp and human Y-chromosomes seem to have a dramatic difference in gene content of up to 53 percent. In other words, the chimp is lacking approximately half of the genes found on a human Y-chromosome. Because genes occur in families or similarity categories, the researchers also sought to determine if there was any difference in actual gene categories. They found a shocking 33 percent difference. The human Y-chromosome contains a third more gene categories, entirely different classes of genes, compared to chimps.⁵⁸
       Under evolutionary assumptions of long and gradual genetic changes, the Y-chromosome structures, layouts, genes, and other sequences should be much the same in both species, given only six million years or so since chimpanzees and humans supposedly diverged from a common ancestor. Instead, the differences between the Y-chromosomes are marked. R. Scott Hawley, a genetics researcher at the Stowers Institute in Kansas City, though not involved in the research, told the Associated Press, "That result is astounding." ⁵⁹
        Because virtually every structural aspect of the human and chimp Y-chromosomes is different, it is hard to arrive at an overall similarity estimate between the two. The researchers did postulate an overall 70 percent similarity, which did not take into account size differences or structural arrangement differences. This was done by concluding that only 70 percent of the chimp sequence could be aligned with the human sequence - not taking into account differences within the alignments.
        In other words, 70 percent was a conservative estimate, especially when considering that 50 percent of the human genes were missing from the chimp, and that the regions that did have some similarity were located in completely different patterns. When all aspects of non-similarity (sequence categories, genes, gene families, and gene position) are taken into account, it is safe to say that the overall similarity is actually much lower than 70 percent. In fact, this difference is so striking that the authors of the Nature article described the discrepancy with the standard evolutionary model in a rather intriguing way: 
 
Indeed, at 6 million years of separation, the difference in MSY gene content in chimpanzee and human is more comparable to the difference in autosomal gene content in chicken and human, at 310 million years of separation.


        Given the standard evolutionary model of origins, it is indeed rather stunning to consider that the human Y-chromosome looks just as different from a chimp as the other human chromosomes do from a chicken. How is this explained within the evolutionary mindset?  Obviously, the believer in mainstream evolutionary models is now forced to invent more just-so stories of major chromosomal rearrangements and rapid generation of many new genes, along with vast amounts of regulatory DNA, within very short spans of evolutionary time.
        However, since each respective Y-chromosome appears fully integrated and interdependently stable with its host organism, the most logical inference from the Y-chromosome data, without any prior commitment to the evolutionary story of origins, is that humans and chimpanzees were each specially created as distinct creatures, or evolved over a far far greater period of time...



Additional research carried out by scientists at the University of Oxford and the University of Chicago found that hotspot regions that determine the locations for genetic recombination during cellular meiosis in sexual reproduction showed "no overlap between humans and chimpanzees."⁶²  This was an "extraordinarily unexpected finding"⁶² given the other similarities between humans and chimps.  Professor McVean explains:
 
"Genetic recombination has been likened to shuffling a deck of cards, which ensures that children are given a different genetic 'hand' than their parents. We know that in many cases recombination occurs where a particular thirteen letter sequence is present -- this is like a run of hearts from ace to king determining where we cut the deck of cards. Because humans and chimpanzees are genetically very similar, we might explain that you can only 'cut the cards' at the same point -- in fact, we find that this is not true." ⁶²

http://www.detectingdesign.com/pseudogenes.html

Chromosome Fusion? It’s Getting Harder and Harder to Believe.

People have 23 pairs of chromosomes, for a total of 46 chromosomes. Most apes have 24 pairs of chromosomes, for a total of 48 chromosomes. One very popular piece of genetic evidence for the idea that humans and apes have a common ancestor is that human chromosome 2 looks like two chimpanzee chromosomes that have been stitched together. As the evolutionary story goes, the common ancestor between apes and humans had 24 pairs of chromosomes, and it initially passed them to those animals that began evolving into apes and humans. The apes kept that number of chromosomes, but after the human lineage split off from the chimpanzee lineage, something happened to fuse two of the chromosomes, leading to only 23 pairs of chromosomes in humans. As Dr. Francis Collins puts it:1

The fusion that occurred as we evolved from the apes has left its DNA imprint here. It is very difficult to understand this observation without postulating a common ancestor.

This idea has been around for a long time, but I never put much stock in it. Why? Because even if human chromosome 2 is the result of two independent chromosomes being fused together (an example of which is shown in the illustration above), I don’t see why this can only be understood in the context of evolution. After all, we know that chromosome fusion events happen in human beings today.2 Thus, if human chromosome 2 really is the result of a fusion of two chromosomes, it could have happened early in the history of human beings. It need not have happened to some hypothetical evolutionary ancestor. Any event that restricted the human population to those who arose from the people who originally experienced the chromosomal fusion would then fix that chromosome in the population. A worldwide Flood in which a single family was saved would be one example of such an event.
Regardless of whether or not human chromosome 2 is evidence of common ancestry, it’s getting hard to understand how it could even be the result of two chromosomes fusing.

Dr. Jeffrey P. Tomkins, a former director of the Clemson University Genomics Institute, recently published a paper in which he analyzed the genetic content of the site at which this fusion was supposed to have taken place. He found something really interesting, but to understand why it is interesting, you need to understand something about the structure of genes. In the DNA of eukaryotes (all organisms whose cells have a nucleus), genes are composed of two regions: exons and introns. When the information in a gene is copied so the cell can use it to make a protein, both the introns and the exons are copied. Before the copy is used to make the protein, however, the introns are removed, as shown in this figure:


In other words, the exons are the parts of the gene that contain the information the cell needs to make a specific protein. The introns are “spacers” that separate these chunks of information. Why is a gene constructed this way? Because each exon is a module of information, and the modules can be put together in many different ways. As a result, many different proteins can be made from a single gene. This process is calledalternative splicing, and it vastly increases the amount of information that DNA can store. Indeed, there is a specific human gene that can be used to make 576 different proteins thanks to the way its introns and exons are arranged.3 In the fruit fly, there is a specific gene that can be used to make 38,016 different proteins!4 This is just one of the many features of DNA that shows it is the result of incredible design.
So here’s where Dr. Tomkins’s research gets interesting: He finds that the place on chromosome 2 where the two chromosomes are supposed to have fused is right in the intron of a gene!5 The gene is charmingly named DDX11L2, and it is known to be used in several different cells, including those performing tasks related to the nervous system, muscle system, immune system, and reproductive system.
It’s really hard to understand how two chromosomes could fuse at the intron of a functional gene, but that’s not the end of the story. The fusion site also contains an important sequence of DNA called a transcription factor binding site. This is a sequence to which a molecule can attach so as to regulate how often the gene is used. So not only is the fusion site right in the middle of a functional gene, it is actually found in a region that helps to regulate how that gene is expressed. That makes it even more difficult to understand how a fusion event could have taken place there.
Is this conclusive evidence against the idea that our second chromosome is the result of two independent chromosomes being fused together? Not really. After all, the spot that Dr. Tomkins studied does bear a remarkable resemblance to the kinds of sequences found when two chromosomes fuse together. Thus, if it is not the result of chromosome fusion, we need to understand why that region of the chromosome has a sequence characteristic of such things. Also, it is well known that the human chromosome 2 has two centromeres, and typical chromosomes have only one. As the illustration at the top of this article shows, a fusion event would explain why this chromosome has two centromeres. At the same time, however, there is a known genetic process in which a chromosome can form a second centromere.6 It is certainly not a common event, but it does happen.
Dr. Tomkins’s research has definitely made it harder to believe that human chromosome 2 is the result of a fusion event, but there still needs to be a lot more research done on the issue. Nevertheless, even if it turns out that geneticists can explain how a chromosome fusion event happened in the middle of a functional gene at one of its transcription binding sites, it still offers no evidence for common ancestry. It only shows that at some point in the past, two chromosomes fused. There is no reason to think it was more likely to have happened in some hypothetical evolutionary ancestor than it was to have happened as a part of human history.

REFERENCES

1. Francis Collins, The Language of God: A Scientist Presents Evidence for Belief, Free Press 2006, p. 138
2. Iain D O’Neill, “Homozygosity for constitutional chromosomal rearrangements: a systematic review with reference to origin, ascertainment and phenotype,” Journal of Human Genetics 55:559-564, 2010
3. Douglas L. Black, “Splicing in the Inner Ear: a Familiar Tune, but What Are the Instruments?,” Neuron 20:165–168, 1998.
4. Guilherme Neves, Jacob Zucker, Mark Daly, and Andrew Chess, “Stochastic yet biased expression of multiple Dscam splice variants by individual cells,” Nature Genetics 36(3):240-246, 2004.
5. Jeffrey P. Tomkins, “Alleged Human Chromosome 2 ‘Fusion Site’ Encodes an Active DNA Binding Domain Inside a Complex and Highly Expressed Gene—Negating Fusion,”Answers Research Journal 6:367-375, 2013 (available online)
6. Warburton PE, “Chromosomal dynamics of human neocentromere formation,”Chromosome Research 12(6):617-26, 2004

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