User:Jurassic Park Treasury

In the book Challenging Nature: The Clash of Science and Spirituality at the New Frontiers of Life, Lee Silver predicted that it would one day be possible to create facismiles of dinosaurs (recreating true non-avian dinosaurs is almost certainly impossible due to the half-life of DNA), as illustrated in this extract:

"...evolutionary developmental geneticists believe that comparisons of DNA in birds and reptiles -on either side of the evolutionary line leading to dinosaurs- could provide some, although not complete, insight into the extinct genome of dinosaurs. Genetic, developmental, and evolutionary understanding and data could be combined with molecular understanding to allow rational design of a dinosaur on a computer. Starting with a virtual chicken genome, virtual genetic changes could be implemented to increase overall adult size, eliminate feathers and restore scales, turn wings back into elongated front and back legs, and mold the virtual animal into a reasonable facsimile of a particular dinosaur, such as a giant long-necked Apatosaurus, a triceratops, or even a Tyrannosaurus rex. The designed electronic genome would be converted into organic DNA with nano-DNA writing machines that automatically link up thousands of smaller DNA fragments into whole chromosomes. The genome would then be inserted into a chicken egg devoid of its own DNA -in an advanced version of the process that created Dolly- and presto, dinosaur facsimiles (Please note that it is not possible to clone animals that lay hard-shelled eggs, but there is another way to bring them to term)" (Page 312, 313, emphasis is mine)

My userpage will show what we currently understand about the genetics, development and evolution of dinosaurs. Work in progress.

Understanding of dinosaurs
This is a work in progress.

Genetic

 * 584 megabases (about 584,000,000 base pairs) of the genome of the last common ancestor of crocodilians and birds have been inferred, as well as the common ancestor of living birds. These may provide a glimpse at the genomes of early dinosaurs and those related to birds. Deduced dinosaur-like genes could then be inserted into cell cultures to see if they are functional.
 * The chicken karyotype has been found to be the one most similar to that of the ancestral dinosaur.
 * The average genome size of a theropod dinosaur was around 1.78 billion base pairs, similar to birds, while the average genome size of an ornithischian was around 2.49 billion base pairs, similar to crocodilians and monitor lizards.
 * The average genome size of a sauropod was 2.02 billion base pairs, in between the averages of birds and reptiles.

Developmental

 * Around 23 mutations in mice have been linked to shortened or fused tails in mice, resembling the fossil record's transition from bird-like theropods to birds. Understanding how the tail was lost in birds may provide clues as to how to reverse this change by creating birds with long, dinosaur-like tails, one of the main aims of the Chickenosaurus project.
 * Arhat Abzhanov has created chicken embryos with snouts resembling those of alligator embryos, though it is illegal to hatch these eggs. He achieved this by controlling the expression of two genes, one coding for the protein WNT and the other coding for the protein FGF8. The palate of the embryo also changed into a more dinosaur-like state. The genetic cause of this evolutionary change remains to be investigated.
 * Rudimentary teeth can develop in chicken embryos. However, the mutation that does this also causes other, more severe deformities, meaning that the chickens never hatch (though the same result can be achieved non-lethally in wild type chickens using a viral vector, the teeth are later reabsorbed into the beak). Also, birds have lost their genes for enamel, meaning that scientists will have to borrow genes from other animals to make teeth for the Chickenosaurus.
 * Studies of paralyzed bird embryos have found that the embryos retain a dinosaur-like metatarsal. It is currently unknown what genes are responsible for the development of this feature, however.

Molecular

 * Proteins have been sequenced from Tyrannosaurus rex  and Brachylophosaurus  . While some have suggested that these findings were the result of contamination from bacteria, amphibians or even ostriches, both of the Brachylophosaurus collagen sequences and the collagen type |, alpha | sequence from T. rex are unique, with no 100% match to any modern organism so far (though a type || collagen sequence is completely identical to amphibians in BLAST with one Brachylophosaurus peptide also being identical to mouse, indicating that contamination was present in the samples). A study in 2011 revealed possible mechanisms of protein survival and found that the proteins were likely endogenous. Proteins are coded by DNA, and looking at protein code and give an incomplete glimpse of the DNA code, though the third nucleotide in the amino acid codons are usually ambiguous. DNA in the dinosaur facismiles could be altered to produce the dinosaur amino acid code, though these would likely have no effect on phenotype.
 * A study published in 2011 found evidence of endogenous collagen in a Prognathodon fossil, suggesting that protein can indeed survive as far back as the Cretaceous.
 * In 2002, scientists managed to deduce an ancestral archosaur visual pigment, known as rhodopsin, that was functional when transfected into monkey cells. They found that the ancestral pigments had a slightly redshifted spectrum, and that early archosaurs may have been nocturnal.

Woolly mammoth

 * Genes for mammoth hemoglobin were spliced with hemoglobin genes in Asian elephants to create a chimeric sequence. By splicing the mammoth hemoglobin into bacteria, it was found that mutations in mammoth hemoglobin allowed the hemoglobin to function at low temperatures, unlike most other hemoglobins which have difficulty functioning in cold temperatures.
 * Two whole genomes from two woolly mammoth specimens have been sequenced. Comparisons of mammoth DNA with Asian elephant DNA could reveal regions of mammoth DNA that confer notable mammoth traits surrounding cold tolerance, such as the hemoglobin mentioned above, long hair and subcutaneous fat, which could then be spliced into elephant cells whose nuclei can be used to clone a hybrid.

An amateur's take at deducing dinosaur genetics
Deducing dinosaur genetics is not hard. One can have a go at it, though not very professionally, with some simple understanding of genetics, bioinformatics and evolution. For example, one could easily deduce that as primitive archosaurs, such as turtles, have a Z chromosome, and birds, descendants of non-avian dinosaurs, have a Z chromosome, the ancestral dinosaurs and theropods had a Z chromosome as well. The same logic could be used to deduce features such as codons.

Dinosaur mitochondria
The sizes of mitochondrial genomes of the following archosaurs are below:


 * American rhea: 16,714 base pairs.


 * African softshell turtle: 16,590 base pairs.


 * Nile crocodile: 16,830 base pairs.


 * Chicken: 16,785 base pairs.


 * Green sea turtle: 16,497 base pairs.


 * American alligator: 16,646 base pairs.


 * Giant moa: 17,040 base pairs.

It is likely that the mitochondrial genomes of ancestral dinosaurs and theropods were around 16,000 to 17,000 base pairs long. The order of mitochondrial genes in turtles and birds are very similar, with only two genes out of order between them. Both have an H-S-L region, while crocodiles have an S-H-L region. The H-S-L region must have been present in dinosaurs. All three groups of archosaurs have 15 mitochondrial genes.

Translating protein sequences into DNA
Use this tool to translate protein into DNA. Do not put the long XXXXXXXXXXXXXX sequences into it, as they are gaps.

You may notice that some of the nucleotides are not the usual A, T, G or C letters that are found in most genetic code. This is because the DNA code is deduced from amino acid code. For example, lysine is coded by both AAA and AAG. The translator will not know which one is correct. Therefore it will give AAR. R can mean either A or G, while N could be any of the four bases. Below is a complete table.
 * A = adenine
 * C = cytosine
 * G = guanine
 * T = thymine
 * R = G A (purine)
 * Y = T C (pyrimidine)
 * K = G T (keto)
 * M = A C (amino)
 * S = G C (strong bonds)
 * W = A T (weak bonds)
 * B = G T C (all but A)
 * D = G A T (all but C)
 * H = A C T (all but G)
 * V = G C A (all but T)
 * N = A G C T (any)

Important information
I will get to reading all this, someday.
 * Archosaur genome: Materials and methods.
 * Ancestral reconstruction.