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Filling the sequence gaps

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"And since (the DNA) is so old, it's full of holes! That's where our geneticists take over!"
Mr DNA(src)
Filling the sequence gaps
Filling dna gaps2

Main article
Recreating dinosaurs

Related articles
Extracting the DNA and proteins
Decoding the DNA sequence
Filling the sequence gaps
Cloning and growing embryo's
Parenting dinosaurs
Modify dinosaurs
Creating a Lost World

The DNA that was obtained in the previous steps were probably fragments of only 500 base pairs long. Even after the reassembling of the fragments the code could still contain gaps if not all the DNA was conserved. The following task would be to build from these fragments a complete set of chromosomes.

In Jurassic Park media the DNA of other species is used to fill these gaps.

Species of the sample Edit

See Identify the species of the sample for a complete discussion.

Not all dinosaur species had the same DNA. For example, Theropod genomes (DNA per cell) were half the size of Ornithischian dinosaurs. Therefore, the species of the DNA sample has to be known before the gaps can be filled.

Gaps Edit

In the fossilization process, molecules are altered. DNA in amber or bones cannot survive completely without gaps for tens or hundreds of millions of years. The novel attempts to address this problem by mentioning that Hammond and InGen have purchased virtually the world's entire stock of amber, in the quest for the maximum number of possible samples of blood from ancient mosquitoes. Even after the reassembling of the fragments the code would still contain gaps.

To successfully clone a dinosaur DNA has to be correct (it has to contain every chromosome) and should contain no sequence gaps.

Jurassic Park media Edit

The Jurassic Park novel and Jurassic Park film did address this issue. In the book Henry Wu filled the gaps in the DNA by inserting the DNA from either bird, lizard, or frog DNA. In the movie, only frog DNA is used. The use of frog genes was a plot device, to allow some females to change sex and breed. Henry Wu's method is criticised by Laura Sorkin, who regards it as an unethical shortcut. Additionally, in the Jurassic World tie-in website, the hybridized frog genes were used as a retroactive explanation for why the dinosaurs of Jurassic Park do not have feathers, as it was only discovered in the real world that dinosaurs had feathers after the release of the original novel and movie.

Similarity in DNA Edit

In the novel Michael Crichton writes

DNA in living creatures was exactly the same. DNA was an incredibly ancient
substance. The DNA was so old that its evolution had essentially finished more
than 2 billion years ago. There had been little new since that time. Just a few
recent combinations of the old genes.
When you compared the DNA of man and the DNA of a lowly bacterium, you found that
only about 10 percent of the strands were different. This innate conservatism of
DNA emboldened Wu to use whatever DNA he wished.[1]

Crichton is right to some extent. Genes code for proteins. A protein like Glycogen synthase converts glucose (sugar) into glycogen. Whether this protein is inside a yeast or a human, its function is the same. As a consequence, its structure and the DNA it encodes are (mostly) the same. Furthermore, the differences in gene sequence that do exist have no functional consequence most of the time.

The eyes absent (short eya) gene encodes a protein that is ential for eye development in fruit flies. In vertebrates a similar protein (an ortholog) is infolved with eye formation. The sequence of the mouse and fly version of the gene only have a 49% similarity. In 1997 Dr Bonini and her team investigated the effect of differences in these orthologs. In fruit flies the eya gene was mutated in such that it was unable to function. Then they inserted the mouse version of the gene into the fly. The flies that got the mouse gene developed fully functioning compound eyes.[2]

In The Lost World novel the scientists haven't found the dinosaur version of the Glycogen synthase kinase 3 gene. Therefore they used a mammalian version of this gene. Because many embryos died in the cloning process a scientist "CC" proposed to use a frog ortholog of the gene.[3]

However, in order to fill gaps effectively knowledge of the genome of many creatures is required.

The issue of the sequence gaps is discussed in The Humpty-Dumpty problem chapter of The Science Of Jurassic Park And The Lost World. The writers conclude:

If you were trying to do this at all, your best bet would be to look at bird  
genomes, because birds are thought to be the nearest living relatives of 
dinosaurs. But even birds aren't that close to dinosaurs. ... Nevertheless, 
there's a common history that can perhaps be exploited; you don't really have any 
other option but to look at bird genomes.[4]

DeSalle and Lindley use a lot of prejudicial language to convince the reader of the difficulty with the Jurassic Park scenario. It turns out that the writers were wrong about a lot of things. They claimed that "birds aren't that close to dinosaurs", whereas the current consensus is that birds are dinosaurs (see Bird#Evolution_and_taxonomy).

Dino chromo900

10 ancestral bird chromosomes.

DeSalle and Lindley also claim that "you don't really have any other option but to look at bird genomes". As discussed in the Dinosaur DNA article, the genomes of extant Archosauromorphs (birds, crocodiles, and turtles) share many genetic features. Chicken chromosomes 1, 2, 3, 4q, 5 and Z (see figure) are almost identical to chromosomes found in Ratites and turtles.[5] If (at least theropod) dinosaur DNA missed parts of these chromosomes, it would be safe to complete them using bird DNA. Future research might identify other chromosome regions that are shared among archosaurs.

Not only entire chromosomes but also genes can be reconstructed using DNA of extant species. In 2002 Dr. Chang and his team compared the Rhodopsin gene (a protein involved in light perception) of 30 bird and Crocodilia genes. By this comparison they were able to estimate the Rhodopsin sequence of their common ancestor that lived probably 240 million years ago.[6]

Costs and time Edit

In the mid 90s, when the Jurassic Park films were made and critics wrote their responses, not one bird or reptile species was fully sequenced. Scientists at universities and research centres from the United States, the United Kingdom, Japan, France, Germany and Spain had been working from 1990 until 2003 to sequence the human genome. The project had cost roughly $3 billion (publicly funded).

In that situation DeSalle and Lindley wrote:

You then need to sequence completely the genomes of several such birds - as many 
species as possible. Bear in mind that this would be a task at least as expensive 
and time-consuming as the Human Genome Project. It will take all your powers of 
persuasion to get Hammond to underwrite this particular part of 
the enterprise.[7]
Cost per genome

Sequencing costs for a human sized genome. By the NHGRI Genome Sequencing Program.

As explained in the article DNA sequencing-article, the costs for whole genome sequencing have dropped dramatically in modern times. In 2012 the cost to sequence a human sized genome (twice as large as birds) was close to $1000.

The following reptiles and birds the genomes are fully sequenced:

References Edit

  1. Jurassic Park (novel), Chapter Tim, page 208 (Novel bundle).
  2. Bonini N.M., Bui Q.T., Gray-Board G.L., Warrick J.M. (1997). The Drosophila eyes absent gene directs ectopic eye formation in a pathway conserved between flies and vertebrates, Development, Volume 124, page 4819-4826. Link
  3. The Lost World (novel), Laboratory chapter, page 548.
  4. DeSalle R. & Lindley D. (1997). The Science Of Jurassic Park And The Lost World Or, How To Build A Dinosaur, page 75.
  5. Griffin D.K., Robertson L.B.W., Tempest H.G., Skinner B.M. (2007), The evolution of the avian genome as revealed by comparative molecular cytogenetics, Cytogenetics, 117, 64-77.
  6. Chang and team (2002). Recreating a Functional Ancestral Archosaur Visual Pigment, Mol. Biol. Evol., Volume 19(9), page 1483–1489.
  7. DeSalle R. & Lindley D. (1997). The Science Of Jurassic Park And The Lost World Or, How To Build A Dinosaur, page 75, 76.

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