Biological issues in Jurassic Park

&nbsp Jurassic Park, a book by Michael Crichton, with a film version directed by Steven Spielberg, revolves around the resurrection of dinosaurs via genetic engineering. Scientists and enthusiasts have brought up a number of issues with facts and feasibility. Some of the speculative or inaccurate features attributed to the dinosaurs of Jurassic Park have become embedded in popular culture, most popular among them being the idea of Tyrannosaurus only seeing motion; giant, feather-less, intelligent velociraptors, and dwarf, frilled, poison-spitting Dilophosaurus. In general, the novel is more accurate than the film, with Spielberg adding some features to the dinosaurs (like the frill on the dilophosaurs).

Velociraptor
The raptors in the novel, following through to the film raptors, were larger than the species going by the name because during the writing of the novel, a previously discovered dinosaur named Deinonychus (closely related to Velociraptor, but larger) was interpreted as a Velociraptor species by some scientists, notably Gregory S. Paul. In the novel, Deinonychus is mentioned, but the character Alan Grant then says that scientists have reclassified it as a species of Velociraptor. Crichton wrote his novel based on the idea of a human sized raptor, but after the publication, when the film was already in production, the idea of Deinonychus being a Velociraptor species was dropped by the scientific community. The film makers had the size of the film's Velociraptor increased for dramatic reasons, and changed the shape of the snout. However, during filming, paleontologists came across a larger dromaeosaurid species named Utahraptor and the larger raptors remained, even though Utahraptor was substantially larger (21 feet long) than the film's raptors. At the start of the film, a Velociraptor skeleton is uncovered in Montana; no examples of the dinosaur have been uncovered in the United States (although both Deinonychus and Utahraptor are American dinosaurs). The fossil skeleton is similarly inaccurately large. The high intelligence of the film's velociraptors are considered somewhat unlikely by scientists, given the relative size of their brains and comparisons with modern animals. It is now known that Velociraptor had feathers. Neither the film nor the novel dinosaurs had feathers; however, both were created before the discovery of feathered dinosaurs closely related to Velociraptor (e.g. Microraptor). In Jurassic Park III, the raptors were remodelled and small feathers on the males' heads were included, while still looking similar to the original design. As with other bipedal dinosaurs in the films, the hands of Velociraptor are depicted with the palms able to rotate, but this would have been anatomically impossible for the real animals, as their forearm bones (ulna and radius) could not rotate in this way. Their palms should have been relatively fixed facing each other, like a person about to clap.

Dilophosaurus
The film's Dilophosaurus stands about 1.2 meters (4 ft) tall, while its real-life counterparts measured on the order of 6 meters (20 ft) long and 1.4 meters (4.5 ft) tall at the hips. According to a "Making-of" book, this was a deliberate deviation from accuracy for stylistic purposes, and to differentiate it from the velociraptors. It also has a frill like the Australian frill-necked lizard, which is not considered accurate by paleontologists. The novel's version is full-sized and lacks the frill. Both depictions of the dinosaur eject a potent, blinding venom in both their bite and their spit, like a spitting cobra, and use it to hunt; the novel acknowledges the fact that this is not suggested by fossil evidence.

Tyrannosaurus
The film theorizes that the Tyrannosaurus rex would be unable to see someone if he stayed still; however, evidence has shown T. rex to have had high visual acuity and binocular vision. Some argue that it would still be able to smell them regardless. In the novel, it is mentioned that the reason the dinosaurs can not see someone standing still, is due to the frog DNA in their genome, and it is shown that other dinosaurs, such as the island's Maiasaura, have this problem as well. This is not mentioned in the film, and instead it is shown as if the inability to see without movement was an actual trait of Tyrannosaurus. In the sequel novel, The Lost World, it is suggested that the Tyrannosaurus can in fact see inanimate objects, and was actually not hungry, but merely "playing" in the first encounter. A character who specifically attempted this technique dies when the T. rex sees him there and kills him; the character Ian Malcolm mentions that he was listening to "the wrong scientists." Tyrannosaurus is also shown as being able to keep (sprinting) pace with a jeep traveling at considerable speed; however, it is debated within the palaeontological community whether a T. rex could even achieve this speed in real life, much less maintain it for as long a period of time as the film depicts. Anatomically, its short forelimbs would have been unable to cushion an impact if it were to fall; meaning that accidents at such speeds could have been fatal. Also, biomechanical studies by Dr John Hutchinson of the Royal Veterinary College have shown that in order to run at this speed in a crouched position, Tyrannosaurus would have needed over 43% of its muscle mass in each leg. That would mean 86% of its muscle mass would be in its legs, leaving little room for anything else in its body: a physical impossibility. Dr Hutchinson’s work also suggests that an upper speed limit for Tyrannosaurus would, actually, only fall in the 10–25 mph range. Animators at Industrial Light & Magic were forced to use optical illusions in order to make the computer-generated Tyrannosaurus appear to convincingly keep pace with the vehicle.

Brachiosaurus
The Brachiosaurus in the film is shown to be chewing its food with a side to side motion of its lower jaw. In reality, it could not feed like this. Brachiosaurid skulls and jaws were limited to up and down motions, and their teeth were specialized for shearing and cropping plant material. Other sauropods, such as diplodocoids, could move their jaws backward and forward, but were probably using this motion to strip branches, not to chew plants. Instead of processing food in the mouth, sauropods probably relied on taking in as much food as possible and processing it farther down the digestive tract, either through gastroliths (rocks swallowed and used for grinding in a gizzard-like organ; note however that this hypothesis, while common in the popular literature, is now considered unlikely in sauropods), or simply by digestion through fermentation by microorganisms. One of the most well known scenes of the movie shows a brachiosaur rearing into a bipedal stance. However, a biomechanical analysis of sauropod rearing abilities shows that Brachiosaurus is probably the sauropod least able to rear. It has a center of mass placed further forward than any other sauropod, which means that a bipedal or tripodal pose would be highly unstable.

Pteranodon
Like the Cearadactylus in the novel, the Pteranodon in Jurassic Park III is interpreted as aggressive and able to pick a teenager up with its feet (a similar scene was planned for the climax of The Lost World: Jurassic Park, but omitted after palaeontological advisers on the production declared that this would not have been possible). Both pterosaur genera were thought to have eaten fish, and were incapable of grasping with their feet. However, in the novelization it states that they were able to carry things with their feet due to them being genetically engineered. Also, although the name Pteranodon means 'winged without teeth' or 'winged toothless', the Pteranodon in Jurassic Park 3 have small sharp teeth in their bills.

Procompsognathus and Compsognathus
The Procompsognathus are given several attributes in the novels that cannot be determined from the fossil evidence to date. They are presented as living and hunting in large groups; as scavengers and coprophagists (eaters of feces), useful in keeping the park clean of sauropod excrement; and as secreting a venom described as similar to that of a cobra, although more primitive. In the films, they are dropped in favour of Compsognathus. In reality, Procompsognathus is known from a single partial skeleton from the Late Triassic of Germany, with a partial skull that may belong to it or, more likely, an early relative of modern crocodilians. Because only one individual is known, there is no direct evidence that it lived in groups; however, related animals such as Coelophysis and Megapnosaurus have been found in groups of numerous individuals, such as at Ghost Ranch. As there are no uncontroversial remains of the head of Procomposognathus, its diet cannot be inferred from the form of its teeth and jaws; other coelophysoids are seen as carnivores with skull adaptations that may have been advantageous when handling small prey. There is no evidence that the bite of Procompsognathus was venomous. A venomous bite has been proposed for a possible theropod from the Late Cretaceous of Baja California, known from a single tooth with grooving similar to that found on the teeth of venomous snakes and lizards. A venomous bite has also been proposed for the Lower Cretaceous Chinese dromaeosaurid Sinornithosaurus, based on its long grooved teeth similar to those of rear-fanged snakes, as well as a possible venom-gland cavity in the bone of the upper jaw.

Spinosaurus
The Spinosaurus in Jurassic Park III appeared to be larger and more heavily built than its real-world counterpart. Also, its teeth were very straight, conical and crocodilian in reality, but they are hooked and serrated in the film. Spinosaurus also had only one crest on its head, not two.

Biotechnological background
The popularity of the novel and movie have sparked actual debate in the laymen and scientific community, as to the plausibility of actually recreating dinosaurs. In the novel/movie the dinosaur DNA is extracted from fossilized mosquitoes, and this small amount is then amplified by polymerase chain reaction (PCR). This has been done before, for example with a Cretaceous weevil in Cano et al. (1993) (no dinosaur DNA was found). There are some problems with this approach: Furthermore, in the fossilization process, molecules are altered. Nevertheless, amber is the best preservative, because organic material is preserved. But DNA 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. However (see below) the admixture of different strains of dinosaur genetic material makes the acquisition of viable genetic material haphazard at best, coupled with the CpG Methylation (see above). That said, the use of multiple Cray X-MP supercomputers whose sole task is pattern recognition is doubtless a shrewd guess as to the size of the task and the scale of resources needed to perform the feat. Tens of thousands of DNA base pairs were recently sequenced from 40,000-year-old skeletal remains of cave bears without using PCR, establishing that, in principle, large-scale genomic sequencing of fossilized remains is possible.. Of course, the remains used in this study are orders of magnitude younger than anything from the dinosaur era, and the technique might not extend to those creatures. In the book the gaps in the DNA are filled by hybridizing the DNA with either bird, lizard, or frog DNA. In the movie, only frog DNA is used. This is extremely difficult, as one would need to know which dinosaur genes are homologous with frog genes. The use of frog genes was a plot device, to allow some females to change sex and breed (although natural sex change is also possible in other vertebrates, such as fish). The dinosaurs were genetically altered so they could not produce lysine, forcing them to depend on lysine supplements provided by the park's veterinary staff. Most vertebrates cannot produce lysine by default, which makes it an essential amino acid for them. The movie states that all dinosaurs are female because all vertebrate embryos are inherently female, requiring an extra hormone at the right phase to make them male. This is not technically true. Vertebrate embryos are undifferentiated, possessing organs that can grow into either male or female reproductive systems. In mammals, at a certain developmental stage the Y chromosome triggers a flood of testosterone, causing the fetus to develop into a male. If, for some reason this doesn't happen, the fetus will develop as an XY female (See Swyer syndrome). Birds and reptiles (and presumably, dinosaurs) don't use Y chromosomes in this way. In fact, they seem to use an opposite system with females possessing a W chromosome and a Z chromosome and males possessing two Z chromosomes. In the scenario presented in Jurassic Park, it seems likely that all the dinosaurs in the park would have been functional males or sterile males possessing an extra chromosome (See Hermaphrodite). The next step would be bringing the DNA strands to expression. For that, one would need to inject the dinosaur DNA into the nucleus of a fertilized egg cell of a close relative of dinosaurs (birds or crocodiles, not frogs). This technique is based on reproductive cloning, which was used to clone Dolly. In the movie, ostrich and emu eggs are used for this purpose. However, the development of an embryo is regulated by hormones in the egg/uterus and the environment. These (bird or crocodilian) hormones need to have the same effect as their original dinosaurian counterparts. For that, they have to be able to recognize particular pieces of dinosaur DNA, a currently impossible task. New research in plastics, however, has allowed for the creation of synthetic eggs such as those that were used in the book. In the book, Henry Wu claims that egg yolk is nothing but a growth medium that can be created in a laboratory. However, if it were this simple, an embryo could just be put into such a medium and left to grow (a scene in the third movie seems to show that some embryos were placed in tanks and that the scientists achieved some success because the embryos did grow big enough to be visible. Extra hormones are needed from the original parent specimen, however, or constructed precisely from using the genome in order for the embryo to flourish.
 * The DNA featured in the movie comes from a Dominican amber mine, though this mine is never stated to be the sole source. The novel indicates sources are global as Hammond's widespread purchasing and stockpiling of amber comes under scrutiny. Dominican amber is 10 million years to 30 million years old, whereas dinosaurs died out 65 million years ago.
 * None of the dinosaurs featured in the movie are known to have existed in the Dominican Republic 65 million years ago (though, again, whether that mine is the only source for DNA is unknown).
 * The mosquito had to have had just one species of dinosaur as its food source to avoid a mix-up. Since some species of mosquito have a female lifespan of only a few days and tend to lay eggs following each feeding, this is semi-plausible, though in that case dozens of mosquitoes of different species would have to be found in order to recreate as many kinds of dinosaurs.
 * The scene featuring a close-up of the mosquito clearly shows fuzzy antennae, meaning the particular insect is male. Only female mosquitoes, however, suck blood.
 * It is unknown which dinosaur the sample contains. It would be impossible to tell which species it is, because the DNA sequences would fit somewhere between that of birds and crocodiles. The book does address this, stating that they "just grow it and find out", to mathematician and chaos theorist Ian Malcolm's annoyance.
 * The dinosaur DNA has to be correct (it has to contain every chromosome) and should contain no sequence gaps. The book and movie did address this issue, however, and had the scientists use frog DNA (and also bird and lizard DNA in the novel) to compensate for the gaps in the dinosaur DNA.
 * The DNA is mixed with mosquito, bacterial, and viral DNA. Although PCR is very specific, it is sensitive to contamination, and if the wrong primers are used, it will also amplify the other DNA.
 * Because DNA is broken down by nucleases in the mosquito gut, the mosquito would have to be preserved immediately after feeding; this would be problematic for the park's scientists, although it would explain the lack of mass contamination in the individual samples.
 * The processes of CpG methylation and cytosine deaminization must also be considered. A common regulatory device in eukaryotic DNA is the process of CpG methylation, where cytosine immediately preceding a guanine on the same strand is methylated. This acts as a molecular flag to control gene expression. Over time cytosine deamination can occur, in which a cytosine amine group is hydrolysed (replaced with a carbonyl oxygen). An unmethylated cytosine will read as uracil in any technique that relies on Watson-Crick base pairing. If the cytosine has been methylated then the product of deamination will be thymine, which again will be read as thymine. This issue can be addressed in a number of ways. If the DNA sample taken contains more than one copy of the DNA, a mixed signal of thymine and cytosine will suggest the occurrence of cytosine deamination. If the entire sample has suffered cytosine deamination at that point in the sequence, CpG tend to be found in "islands" rich in CpG, so TpG-rich islands or TpG/CpG rich islands would suggest cytosine deamination.