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How many dinosaur genes are in a chicken genome?

How many dinosaur genes are in a chicken genome?


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I read recently that we can "work back" to a dinosaur by selectively turning off certain genes in chickens, and we were able to create a chicken with a snout instead of a beak.

How many dinosaur genes are still hanging around in a chicken genome? I understand there is a lot of overlap for vertebrates, but shouldn't these genes have shuffled out over time?

Otherwise, couldn't we work back to worm or even earlier life forms? Is the whole history of a creature's evolution contained in its genome?

Edit This was a news story about a month ago. Here's excerpts from the BBC's write-up: "Chicken grows face of dinosaur: A chicken embryo with a dinosaur-like snout instead of a beak has been developed by scientists"

To understand how one changed into another, a team has been tampering with the molecular processes that make up a beak in chickens.

By doing so, they have managed to create a chicken embryo with a dinosaur-like snout and palate, similar to that of small feathered dinosaurs like Velociraptor. The results are published in the journal Evolution.

Link to Evolution paper included.

Also this piece from about a year ago: "Paleontologist Jack Horner is hard at work trying to turn a chicken into a dinosaur"

In 2009, the world's most famous paleontologist made a bold claim. In “How to Build a Dinosaur,” Jack Horner proposed re-creating a small dinosaur by reactivating ancient DNA found in its descendants, chickens.

The toothy snout is already here. At his lab at Harvard Medical School, Matthew Harris has made chicken embryos that express ancient genes for the growth of conical, crocodile-like teeth.


Be careful when reading media as they tend to exaggerate. That Abzhanov paper is interesting; it will be better when it's published and the figures released. He does a lot of evo-devo work surrounding beak development. What they did in this paper was to inhibit in chick embryos two signalling pathways (which are actually conserved amongst all animals, not just birds and reptiles) so that their expression domain more closely matched that of extant reptiles (which lack medial activation, as opposed birds). They found that doing so results in premaxillary and palatine bones which resemble ancestral archosaurs. While incredibly interesting, this is a far cry from creating living chickens with dinosaur snouts.

To somewhat answer your question, chickens do not contain all of the genes that dinosaurs once had. They will have both gained and lost information. There will be much conservation in the same way that there is conservation between all organisms. For example, the Wnt pathway studied in this paper is conserved across all animals, from chickens to humans to placazoans to, presumably, dinosaurs. It's impossible to say how much has changed since we do not have any whole dinosaur genomes, but it's also important to note that it's not only which genes an organism has but also when and where they are expressed and how they interact.


Scientists have traced what dinosaur DNA could have looked like

Researchers have figured out how the genome of a dinosaur might have looked by studying turtles and birds.

A team based at Kent University's School of Biosciences analysed the genomes of modern-day species, including a chicken, a zebra finch and a budgerigar.

A genome is full the set of genetic material inside a cell, and it contains all the information needed to build and maintain an organism, whether it is a fish, plant, human or dinosaur.

By comparing the chromosomes of turtles and birds (the living descendants of dinosaurs), the team worked out the likely genome of a common ancestor of those animals. It lived 260 million years ago (about 20 million years before dinosaurs first emerged).

They then traced how chromosomes changed over evolutionary time from the common ancestor of turtles and birds to the present day.

The results suggest that, had scientists had the opportunity to make a chromosome preparation from a theropod dinosaur like a T.rex, it might have looked very similar to that of a modern-day ostrich, duck or chicken.

Prof Paul Barrett, a Museum dinosaur expert, contributed to the study.

He says, 'Using these advanced genomic techniques we can reconstruct a plan for how the dinosaur genome was organised, shedding further, more detailed light on the biology of these amazing animals.

'Although this won’t allow us to resurrect a Diplodocus, or any other extinct dinosaur, it does show how many features that used to be considered unique to birds appeared much earlier in time, in their theropod ancestors, including at the genome level.'

An illustration of Hypsilophodon by the artist Neave Parker, created in the 1960s. Parker's reconstructions were initially believed to be accurate. But as our scientific knowledge of the biology, morphology and behaviour of these dinosaurs has increased, their perceived appearance has changed.


'Dino-chickens' reveal how the beak was born

Chicken embryos have been altered so that the birds grow dinosaur-like snouts.

Biologists have created chicken embryos with dinosaur-like faces by tinkering with the molecules that build the birds' beaks.

The research, details of which are published today in Evolution 1 , does not aim to engineer flocks of hybrid ‘dino-chickens’ or to resurrect dinosaurs, says Bhart-Anjan Bhullar, a palaeontologist now at the University of Chicago in Illinois, who co-led the work. “We’re never going back to the actual dino-chicken or whatever it is.” Rather, he says, the team wants to determine how snouts might have turned into beaks as dinosaurs evolved into birds more than 150 million years ago.

The transition from dinosaur to bird was messy — no specific anatomical features distinguished the first birds from their meat-eating dinosaur ancestors. But in the early stages of bird evolution, the twin bones that formed the snout in dinosaurs and reptiles — called the premaxilla — grew longer and joined together to produce what is now the beak. “Instead of two little bones on the sides of snout, like all other vertebrates, it was fused into a single structure,” Bhullar says.

Facial reconstruction

To better understand how these bones might have become fused, a team led by Bhullar and Arhat Abzhanov, an evolutionary biologist at Harvard University in Cambridge, Massachusetts, analysed the embryonic development of beaks in chickens and emus, and of snouts in alligators, lizards and turtles. They reasoned that reptile and dinosaur snouts develop from premaxilla in a similar way, and that the developmental pathways that form the snout were altered in the course of bird evolution.

The team found that two proteins known to orchestrate the development of the face, FGF and Wnt, were expressed differently in bird and reptile embryos. In reptiles, the proteins were active in two small areas in the part of the embryo that turns into the face. In birds, by contrast, both proteins were expressed in a large band across the same region in the embryo. Bhullar sees the result as tentative evidence that altered FGF and Wnt activity contributed to the evolution of the beak.

To test this idea, the team added biochemicals to block the activity of both proteins in dozens of developing chicken eggs. The researchers did not actually hatch the eggs, says Bhullar, because they did not write that step into their approved research protocol. Instead, they discerned differences in the faces of ready-to-hatch chicks, which looked subtly different from chicks without their proteins inhibited. The altered chicks still had a flap of skin over their would-be beaks, so the difference is not obvious, says Bhullar. “Looking at these animals externally, you would still think it’s a beak. But if you saw the skeleton, you’d just be very confused," he says. "I would not say we gave birds snouts.”

In some embryos, the premaxillae were partly fused, whereas in others the two bones were distinct and much shorter some of the altered embryos did not look all that different from those of regular chickens. The team created digital models of their skulls with a computed tomography scanner and found that some of these more closely resembled the bones of early birds such as Archaeopteryx and dinosaurs such as Velociraptor, than unmodified chickens.

“Very cool,” says Clifford Tabin, a developmental biologist at Harvard Medical School in Boston, Massachusetts. He thinks that Bhullar’s team makes a strong case that altered expression of FGF and Wnt shaped the bird's beak. Identifying the genetic changes responsible, however, will prove much more difficult. They could lie in the genes coding for FGF and Wnt, or to genes in related biochemical pathways, or in ‘regulatory’ DNA that influences gene expression. If these changes could be identified, it might be possible to modify chicken genomes to include them (and, conversely, to make reptiles more bird-like through genome editing).

Jack Horner, a palaeontologist at Montana State University in Bozeman, hopes to take a genetic approach to imbuing chickens with dinosaur-like tails. In a paper published last year 2 , his team identified mutations potentially involved in the disappearance of the tail in modern birds. But applying these insights to engineering ‘dino-chickens’ has proved difficult, he says. “We’re having a little more trouble with the tail. There are so many components.” Other anatomical features could be altered by tinkering with development proteins, Horner adds. “It gives us a lot of opportunities to think about making new kinds of animals.”

Bhullar says that he admires Horner’s vision, but he is more interested in replaying evolution to reveal how it creates new forms. His lab plans to study the expansion of the mammalian skull and the unusual lower limbs of crocodiles by resurrecting ancient anatomy. “I think it will open as big a window as you could possibly get into the deep past without having a time machine,” he says.


Gene content of the chicken genome

The genome sequence of an organism encodes both ncRNAs and proteins. Extensive analysis of the genome sequences of human 1 , mouse 2 and rat 3 has provided our current best assessment of mammalian gene content and has illuminated much about the evolution of genes. The chicken genome provides new perspectives on both the structure and content of mammalian genes, as well as yielding insight into avian gene content and evolution of ncRNA genes.

Non-coding RNA genes

A total of 571 ncRNA genes, from over 20 distinct gene families, were identified within the chicken genome assembly (Table 2) using bioinformatic approaches 33,34 (see Methods). Predicted ncRNA pseudogenes are greatly reduced in number relative to their human ncRNA counterparts. The chicken ncRNA predictions therefore represent a set that is mainly functional. If ncRNA genes maintain their placement with respect to neighbouring genes, chicken ncRNA gene locations could be used to identify which mammalian copies are likely to be functional and which are probable pseudogenes. However, few chicken and human ncRNA genes are paired in regions of conserved synteny (Table 2), relative to the high level of shared gene order observed for protein-coding genes (see below). Those classes of ncRNAs that are most often syntenic are microRNAs (miRNAs) and small nucleolar RNAs (snoRNAs), which are often found in the introns of protein-coding genes (or, rarely, of specialized ‘host’ genes 35 ). Most ncRNA genes thus seem to have been translocated to distant genomic sites during vertebrate evolution, without accumulating large numbers of pseudogenes, as would be expected were this process to occur via retrotransposition. This is also in contrast to duplication of genes via unequal crossing over, which results in tandem copies. These insights will require considerably more analysis for a definitive resolution, but it seems that these ncRNAs may not use the same duplication and/or translocation mechanisms as protein-coding genes.

Development of a protein-coding gene set

An evidence-based system (Ensembl 36 ) and two comparative gene prediction methods (Twinscan 37 and SGP-2 (ref. 38)) together predicted a common set of 106,749 protein-coding exons, with 85,929 additional exons predicted by one or two methods (Supplementary Table S3). Particular attention was paid to the identification of selenoproteins, which are usually mispredicted in annotated genomes because of their usage of the TGA codon, usually a stop codon, to code for the amino acid selenocysteine (see Methods). Of the human genes predicted using chicken as the “informant”, only 311 genes predicted by SGP-2 are absent from previously identified sets (namely, Vega 40 , Ensembl 41 , RefSeq 42 , MGC 43 and H-Invitational 44 ) and have homologous chicken predictions that possess orthologous intron positions. These data, and those of another study (E. Eyras et al., unpublished data), suggest that most of the protein-coding genes conserved among vertebrates are represented in existing complementary DNA sets.

We tested the sensitivity and specificity of the chicken gene predictions. Sensitivity was assessed by comparing predicted exons to those of chicken cDNAs 32 representing long open reading frame (ORF)-containing protein-coding genes (Table 3). All three methods correctly predicted about 80% of cDNA-based exons with >80% coverage. An independent SAGE-based analysis (ref. 166, and M. B. Wahl et al., unpublished data) provided a similar, although marginally lower, estimate. Specificity was assessed by testing random exon pairs from the prediction sets using polymerase chain reaction with reverse transcription (RT–PCR) (E. Eyras et al., unpublished data, and ref. 44). Briefly, Ensembl predictions have a false positive rate of ∼ 4%. When an exon pair is predicted by any two of the three methods (predominantly joint Twinscan plus SGP-2 exons) ∼ 50% are confirmed, suggesting that some genes are missing from the Ensembl set, but we cannot reliably distinguish these from a similarly large number of Twinscan plus SGP-2 false positives. Using our estimates of specificity and sensitivity, we predict a total of between 20,000 and 23,000 protein-coding genes in chicken, with 80–90% of these found in the present Ensembl set (see Methods). This estimate overlaps the lower bounds in the corresponding ranges for mammalian genomes determined by similar calculations (for example, see refs 2, 3, 45).

Evolutionary conservation of gene components

Alignments of chicken and human orthologous protein-coding genes demonstrate the expected pattern of sequence conservation, with highest identity in protein-coding exons and minimal identity in introns (Fig. 2). These alignments allowed us to examine sequence conservation at different sites within genes.

The reference structure was taken from human or mouse, and only those with cDNA-based definitions of the structure were used. The central figure shows an idealized gene structure, with the grey exons representing coding sequence and white boxes representing 3′ and 5′ untranslated regions.

Alignments of coding regions often did not extend to the previously annotated human protein start codons. Rather, we observed a fourfold increase in the frequency of methionine at the first position of the alignment (Fig. 3), suggesting that these internal ATG codons could be the true start sites for at least some of ∼ 2,000 human genes. For these proteins, the overall distribution of amino acids upstream of the end of the alignment in human was markedly different from that downstream and was more consistent with a codon distribution derived from non-coding nucleotide sequence. Using this comparative signal and other features, such as the Kozak sequence 46 , we can potentially improve the annotation of mammalian protein-coding start sites.

Alanine is shown as an example of non-methionine amino acids: many amino acids show significant changes before compared with after the alignment.

Sequence conservation around mammalian splice sites can be predicted by divergence at unselected (non-consensus) base pairs at the neutral rate, coupled with purifying selection on sites matching the splice site consensus 47 . Given the high level of neutral site divergence that has occurred between mammalian and chicken orthologous sequences (see neutral evolutionary rate, below), one would expect that orthologous mammalian–chicken splice sites should show a level of conservation no different from that of any unrelated pair of splice sites. However, in contrast to analogous comparisons within the mammalian lineage, there is a detectable signal in orthologous splice site comparisons beyond the consensus derived from comparing non-orthologous splice sites (Supplementary Fig. S1). This suggests that either some subtle classes of splice site sequences are conserved beyond the generic consensus that can only be observed at the bird–mammal evolutionary distance, or that there is a significant but weak conservation in mammalian introns that is not detectable in mammalian–bird alignments 48 .

To explore the role of conserved non-coding sequence segments that are probably regulators of protein-coding genes, we examined the frequency of non-coding alignments of at least 100 base pairs (bp) in, respectively, the 5′ flanking region, 5′ untranslated region (UTR), at least one intron, 3′ UTR, or 3′ flanking region (see Methods) within human–chicken orthologue pairs in relation to gene function (as determined by gene ontology (GO) category, Table 4). Some GO categories (for example, development and transcriptional regulation) showed enrichment for conservation in all five regions, suggesting that conserved regulatory signals exist within all of these locations. However, other categories showed more specific patterns. As one example, introns of ion channel genes are particularly enriched for conserved sequences, in agreement with reports that such introns contain RNA-editing targets 49,50 .

Pseudogenes and retroposed copies in the chicken genome

Only 51 duplicates of protein-coding genes probably formed by retroposition (that is, exhibiting loss of introns) 51 were identified in the chicken genome, in contrast to the more than 15,000 cases observed in mammalian genomes 3,52 . In mammals, the ancient LINE1 (L1) transposable element is responsible for the origin of most if not all retroposed (pseudo) genes 53 . Although birds host their own LINE-like elements (chicken repeat 1 (CR1) see below) 54 , the reverse transcriptase encoded by these elements is unlikely to copy polyadenylated mRNAs 55 , probably explaining the paucity of processed pseudogenes in chicken. Within the set of 51 (Supplementary Table S4), 36 clearly represent pseudogenes, because their former coding regions are disabled by alterations (including frameshifts and premature stop codons) that preclude protein function. Among the remaining 15 elements, eight show strong evidence for selective constraint (Supplementary Table S4) and therefore may represent functional retroposed genes. We found no clear bias towards either particular gene families or chromosomal locations for the retrocopies (Supplementary Table S4).


Scientists analyzed the composition of dinosaur DNA — and it’s really similar to birds’

While bones and other fossils can be preserved for millions and millions of years, the same can’t be said about DNA. Despite what Jurassic Park might have you believe, DNA can hardly last one million years — and since dinosaurs went extinct some 66 million years ago, finding intact dinosaur DNA is not really a realistic expectation.

However, by starting from currently living species and using some creative maths, researchers were able to figure out what it probably looked like.

They started from modern-day turtles and birds — the first being one of the closest living relatives of the dinosaurs, and the latter being, well, dinosaurs — yes, birds are technically dinosaurs. Working backward from these modern species, Prof. Darren Griffin and colleagues at the University of Kent used mathematical techniques to identify the possible genetic characteristics of the earliest dinosaurs.

According to their calculations, the DNA of dinosaurs has remained quite stable through the ages and was very similar to the DNA shared by birds today. Essentially, dinosaur DNA, much like bird DNA, is organized into “chunks” called chromosomes. Birds have 80 chromosomes, which, relatively speaking, is a lot — for comparison, humans have 46, and frogs have around 20.

Birds are one of the most varied animal groups, and it’s partly owed to their large chromosome number. If dinosaurs shared the same feature, it could help explain why they also exhibit such a great variety — from horned vegetarian “tank” to small bipedal predator to true giants. But throughout all this variation, the overall structure of the DNA seemed to have remained stable over the years.

“Our results suggest that most elements of a typical ‘avian-like’ karyotype (40 chromosome pairs, including 30 microchromosomes) were in place before the divergence of turtles from birds

255 million years,” the researchers write in the study. “This genome organisation therefore predates the emergence of early dinosaurs and pterosaurs and the evolution of flight.”

“This genomic structure therefore appears highly stable yet contributes to a large degree of phenotypic diversity.”

Griffin says that dinosaurs found a recipe for success — they found what worked from them, built a stable genetic basis, and from there, spurred a great deal of variation. But unfortunately for them, this wasn’t enough to help them survive the dramatic meteorite event 66 million years ago, which wiped the dinosaurs (and many other creatures) out of existence.


The Institute for Creation Research

In his recent book How to Build a Dinosaur, evolutionary paleontologist Jack Horner suggested that birds could be genetically engineered backward to take the form of their supposed dinosaur ancestors. 1 He argued that birds arose through the selection of beneficial dinosaur mutants, and if those specific mutations could be identified and reversed in a new generation, then the resulting bird-like creature would hatch and grow into something resembling a dinosaur.

One paleontologist is attempting to do just that. Hans Larsson, Chair in Macro Evolution at McGill University in Montreal, is taking the first steps toward engineering a chicken with a dinosaur tail. He told international news agency AFP that this will be a &ldquodemonstration of evolution.&rdquo 2

But would it really? Larsson apparently is targeting a particular developmental gene that helps specify the length of the tail. If he succeeds in engineering (by purposeful design) a viable chicken with a long tail, will that be heralded as evidence of evolution? And if so, would such an achievement actually demonstrate evolution?

Larsson had previously asked, &ldquoWhy can&rsquot we take all the genetics, just change it around a little bit, and produce a Tyrannosaurus Rex, or something that looks like one?&rdquo 3 The answer is that it would not be so easy, because more than &ldquoa little bit&rdquo needs to change, a fact that Larsson and his colleagues will most likely discover during their research.

A long-tailed chicken would not truly demonstrate evolution. This &ldquoreverse-transitional&rdquo form would be less fit than its peers, having to drag around a uselessly long tail. Also, any successful changes would have been engineered by design, so they could not demonstrate something that happened through purely natural forces. Third, a long-tailed chicken would resemble a dinosaur only superficially, like attaching a long aluminum tube onto the back of a car to make it more like an airplane. Such a contraption would be much more difficult to drive and would be no closer to being able to fly.

Evolutionists have pointed out a few of the many critical differences between birds and the theropod dinosaurs from which they supposedly evolved. 4 One researcher examined the different breathing apparatuses required by each kind.

Recently, conventional wisdom has held that birds are direct descendants of theropod dinosaurs. However, the apparently steadfast maintenance of hepatic-piston diaphragmatic lung ventilation in theropods throughout the Mesozoic poses fundamental problems for such a relationship. The earliest stages in the derivation of the avian abdominal air sac system from a diaphragm-ventilating ancestor would have necessitated selection for a diaphragmatic hernia in taxa transitional between theropods and birds. Such a debilitating condition would have immediately compromised the entire pulmonary ventilatory apparatus and seems unlikely to have been of any selective advantage. 5

In other words, the dinosaur breathing system operated like a bellows, with a muscle (the diaphragm) expanding and contracting to move air in and out. To transition it to the flow-through ventilation system used by birds would require a change to this muscle that would have immediately killed the newly-mutated form. If an animal cannot breathe, it cannot evolve.

To overcome the differences between dinosaur and bird would require re-engineering the entire chicken genome&mdashnot only adding new genes and new gene cassettes, and removing certain others, but also adding and removing specific genetic and epigenetic 6 control and regulation systems to specify what, when, how often, how much, and where those cassettes should be used during an embryo&rsquos development.

Larsson, starting with the assumption of evolution, predicted that simply by &ldquoflipping certain genetic levers during a chicken embryo's development, he can reproduce the dinosaur anatomy.&rdquo 2 In contrast, starting with the biblical assertion that each creature was made to reproduce after its own kind, 7 the amount and precision of genetic and cellular alterations that would have to be bioengineered to transform a chicken into a legitimately dinosaurian creature are so vast that no natural process could achieve it.

Rather than demonstrate evolution, these attempts to transform chickens will certainly demonstrate the precise and intricate design of this created kind.

  1. Horner, J. and J. Gorman. 2009. How to Build a Dinosaur: Extinction Doesn&rsquot Have to Be Forever. New York: Dutton. . AFP. Posted on breitbart.com August 25, 2009, accessed August 29, 2009.
  2. Brennan, Z. Jurassic Park comes true: How scientists are bringing dinosaurs back to life with the help of the humble chicken. Daily Mail. Posted on dailymail.co.uk June 13, 2008, accessed September 8, 2009.
  3. See references in Thomas, B. Do New Dinosaur Finger Bones Solve a Bird Wing Problem?ICR News. Posted on icr.org July 9, 2009, accessed September 8, 2009.
  4. Ruben, J.A. et al. 1997. Lung Structure and Ventilation in Theropod Dinosaurs and Early Birds. Science. 278 (5341): 1269.
  5. Epigenetics is a new field in biology, discussed briefly in Thomas, B. Epigenetics: More Information than Evolution Can Handle. ICR News. Posted on icr.org. January 30, 2009, accessed September 8, 2009.
  6. Genesis 1:20-21, 24-25.

* Mr. Thomas is Science Writer at the Institute for Creation Research.


RESULTS AND DISCUSSION

BAC Fingerprinting

We fingerprinted a total of 66,048 clones from the three complementary BAC libraries (Lee et al. 2003 Table 1 ) on 1032 autoradiographs using the DNA-sequencing gel-based restriction fingerprinting method (Zhang and Wing 1997 Tao and Zhang 1998 Chang et al. 2001 Tao et al. 2001 Zhang and Wu 2001). Of these fingerprints, 7969 clones (12.0%) were deleted during fingerprint editing due to failures in standard DNA markers, insert-empty clones, or failed fingerprinting. In addition, 988 clones (1.5%) were ignored by the FPC V6.0 program (http://www.genome.clemson.edu/fpc/faq.html Soderlund et al. 2000) during contig assembly, because they contained four or fewer bands in the range of from 58 to 773 bp, providing insufficient information to be included in the contig assembly. Thus, a total of 57,091 clone fingerprints were used for contig assembly. These clones contain 𢏇.9-fold representation for the autosomes and 4.0-fold for each sex chromosome of the chicken genome. Studies (Zhang and Wing 1997 Chang et al. 2001 Tao et al. 2001 Xu et al. 2003) have demonstrated this redundancy to be sufficient for construction of a high-coverage physical map. The clones from the BamHI library, the EcoRI library, and the HindIII library had an average of 33.2, 35.2, and 38.0 bands per clone, respectively, in the range of from 58 to 773 bp ( Table 1 ).

Table 1.

The Source BACs Fingerprinted for the Chicken Physical Map


This study was conducted during Raman Akinyanju Lawal PhD programme, supported by the University of Nottingham Vice Chancellor’s Scholarship (International) award. Financial supports for sampling and/or genome sequencing were obtained from the University of Nottingham, Biotechnology and Biological Sciences Research Council (BBSRC), the UK Department for International Development (DFID) and the Scottish Government (CIDLID programme, BB/H009396/1, BB/H009159/1 and BB/H009051/1), BMGF Grant Agreement OPP1127286, the National Plan for Science, Technology and Innovation (MAARIFAH), King Abdulaziz City for Science and Technology, Kingdom of Saudi Arabia. Olivier Hanotte poultry research programme is supported by the CGIAR - Livestock CRP and the Centre for Tropical Livestock Genetics and Health (CTLGH).

Paul M. Hocking is deceased.

Affiliations

Cells, Organisms and Molecular Genetics, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK

Raman Akinyanju Lawal & Olivier Hanotte

Present Address: The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA

Present Address: Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3FL, UK

Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK

Open University of Diversity - Mouth Foundation, Hasselt, Belgium

Technology and Service B.V., Hendrix Genetics, P.O. Box 114, 5830 AC, Boxmeer, The Netherlands

Department of Animal Science, Faculty of Agriculture, University of Peradeniya, Peradeniya, Sri Lanka

Genetics and Biotechnology, Animal Science Department, Agriculture Faculty, Mutah University, Karak, Jordan

Department of Animal Production, King Saud University, Riyadh, Saudi Arabia

Small Ruminant Genomics, International Centre for Agricultural Research in the Dry Areas (ICARDA), P.O. Box 5689, ILRI-Ethiopia Campus, Addis Ababa, Ethiopia

Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China

Dong-Dong Wu & Ya-Ping Zhang

State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China

Dong-Dong Wu & Ya-Ping Zhang

The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK

Paul M. Hocking & Jacqueline Smith

Centre for Tropical Livestock Genetics and Health, The Roslin Institute, Edinburgh, EH25 9RG, UK

David Wragg & Olivier Hanotte

LiveGene, International Livestock Research Institute (ILRI), P. O. 5689, Addis Ababa, Ethiopia


Paleontologist Jack Horner is hard at work trying to turn a chicken into a dinosaur


Matthew Carrano of the Smithsonian’s National Museum of Natural History, left, with paleontologist Jack Horner, who wants to use DNA from chickens to recreate a small dinosaur. (Nikki Khan/The Washington Post)

In 2009, the world’s most famous paleontologist made a bold claim. In “How to Build a Dinosaur,” Jack Horner proposed re-creating a small dinosaur by reactivating ancient DNA found in its descendants, chickens. His 2011 TED talk on the subject went viral. And then for the past four years, the public heard nothing.

While the Internet moved on to other viral videos and ideas, Horner and his team have been working on the “chickenosaurus” and moving ahead the science of evolutionary development. The project has already resulted in some of the first research into the embryonic development of tails.

The idea that birds are descended from dinosaurs is no longer questioned within the mainstream scientific community. Paleontologists have long studied the changes in bone structure of dinosaurs and birds over time. Meanwhile, molecular biologists have studied the composition of modern bird genes. By merging these scientists’ work, Horner, who is curator of paleontology at the Museum of the Rockies in Bozeman, Mont., hopes to answer questions about evolution.

Horner’s premise can be viewed from the launchpad of the late Michael Crichton’s novel and film “Jurassic Park,” a story that involved obtaining dinosaur DNA from undigested blood in mosquitoes preserved in amber. The idea of finding dinosaur DNA this way was taken seriously by many people, and the possibility was explored by scientists.

Jack Horner knows the “Jurassic Park” theory very well, having served not only as the inspiration for one of the main characters but also as a technical adviser for the film. But 24 years after the novel was published, we have yet to find any DNA in mosquitoes from the time of the dinosaurs.

Paleontologist Jack Horner thinks some genetic engineering can lead to the creation of what he calls a “chickenosaurus.” (Image by Phil Wilson)

DNA degrades under even ideal storage conditions. Cool, sterile conditions can extend its useful life to as long as perhaps a few million years, and dinosaurs disappeared about 65 million years ago. No matter how perfect a mosquito we find in a blob of amber, we cannot make a dinosaur out of that mosquito’s last blood meal.

There is only one way that DNA has been proved to survive millions of years relatively intact: by replicating itself during that time. This is exactly what happened as birds evolved from dinosaurs.

Chickens may not seem like the most obvious modern bird to convert into a dinosaur. Ostriches are the most primitive surviving species of bird. Sandhill cranes have been largely unchanged for about 10 million years. The chicks of a bird called a hoatzin have dinosaur-like claws on their fingertips that they use to climb trees before they are fledged. But ostriches, sandhill cranes and hoatzins would each be challenging to work with in a laboratory. Chickens have the advantage of being highly domesticated and easy to care for at low cost.

Working with chickens also allows scientists to benefit from decades of work that has already been done on their genome and anatomy. A massive amount of research has already been conducted on the domestic chicken due to its economic importance. Poultry science is a large field with long-established journals and entire departments at respected universities.

A genome does not evolve in a tidy fashion. Old genes are not always discarded when they fall out of use. For example, there may be a whole host of genes that direct the growth and movement of a dinosaur’s arm and fingers. If another gene evolved to fuse some of those bones into a wing during embryonic development, many of those arm-and-finger genes would be pushed to the sidelines. But the potential for a dinosaur arm could still be there. If you can identify the newer gene that causes bone fusion and disrupt its expression, those sidelined genes may suddenly start producing arms.

Horner posits that three primary engineering tasks will lead him from a conventional chicken to something resembling a miniature velociraptor (a small predator that became famous in “Jurassic Park”): creation of a long tail the development of a toothed, beakless head and the fashioning of arms with fingers and claws instead of wings.

The toothy snout is already here. At his lab at Harvard Medical School, Matthew Harris has made chicken embryos that express ancient genes for the growth of conical, crocodile-like teeth.

The project is considered more than an effort to make a living toy in fact, it has the potential to affect medical research.

“We were asking, ‘What are the genetic means by which nominal features come about?’ ” Harris said.

“After 70 million years, the organism still maintains the latent mechanisms of making the beginning stages of these teeth. If that is the case, what other sort of latent potential still exists in other animals or ourselves? How does that equate to ideas about repair or medicine?”

Horner’s team will build on Harris’s work, but it will have to combine that with transgenic work, which means taking a gene from one organism and inserting it into the genome of another.

“We can do the teeth already, but birds have lost the enamel gene,” Horner said. “To make real teeth, we are going to have to do some transgenics. We are going to have to add the enamel back. This isn’t actually a very big deal to get done.”

“The hands are probably the easiest to deal with,” Horner said. Indeed, an X-ray of a chicken’s wing reveals the same bones found in the arm of a small dinosaur. All of the parts are already there.

To date, the biggest challenge in making the chickenosaurus has been the tail. Modern birds don’t have a tail beneath their feathers. Instead, they have a complicated appendage called a pygostyle, with short, fused vertebrae and connected muscles that allow them to control and fan out their tail feathers.

Turning a pygostyle back into a long tail requires learning how the pygostyle evolved in the first place. This was a question that nobody had been able to answer until recently. Horner and colleagues recently published a paper that reveals 23 different mutations that can result in fused, shortened tails among mice. In effect, they sought to mimic the history of the fossil record in a laboratory.

Bird embryos still grow dinosaur-like tails before absorbing the structure through a process known as resorbtion. Learning how to cause tail resorbtion in gecko embryos may help scientists prevent tail resorbtion in birds.

“Using genetic markers, we’ve identified what genes turn on to make certain parts and what is resorbing that particular part,” Horner said. “We are looking for what kinds of genes actually take out whole segments of tail. Our next step really is now to get ourselves a colony of [geckos] and then see if we can take some of these pathways and actually see if we can knock out the tail. . . . We’re pretty sure that the tail genes we’ve discovered in mice will work here.”

Harris is skeptical about the idea of making a chickenosaurus.

“Just because you can do an experiment doesn’t mean that you should do an experiment. What is the scientific question that is being asked? Jack is asking a question: ‘Can you remake something that was once lost?’ It is the wrong question to ask. What are you going to learn if you could do it? Technically, you are going to have a messed-up chicken. It’s not a dinosaur. It’s never going to be a dinosaur. It’s just going to be a really awful monstrosity. What we should ask is: Knowing the history of birds, what are the interesting parts of their biology that can tell us something about the dinosaurs?”

Horner disagrees about the appropriateness of making a chickenosaurus.

“I think we could achieve a suite of changes in one embryo so that the resulting animal could hatch and live out a normal life span, eating, moving and functioning without difficulty,” he said.

Horner and Harris agree that the research involved in designing a chickenosaurus could pay scientific and medical dividends. Research into factors that influence embryonic tail growth could lead to new treatments for spinal disorders. Understanding more about the mesenchyme tissue (cells that develop into circulatory, lymphatic and connective tissue) of chicken embryos that direct the growth of teeth may eventually have applications in treatment of human sarcomas, which are cancers of mesenchymal cells.

As all small dinosaurs did, the chickenosaurus would have feathers. “Jurassic Park” got that wrong, though the creator of the film’s special effects is making it up to Horner. George Lucas has funded most of the cost of the chickenosaurus project thus far, and the final price tag is expected to be relatively low.

“I’d be really surprised if we don’t have them in 10 years,” Horner said. “If we’re lucky, we’ll have them in five years. [We wouldn’t need] more than $5 million. If we did have $5 million, then we would have three different labs working on it.”

For less than the cost of the special effects for any of the “Jurassic Park” films, Jack Horner just might succeed in making a living dinosaur.



Comments:

  1. Dojind

    How could it not be better!

  2. Henwas

    Eh, hold me seven!

  3. Aonghas

    It's a pity that I can't speak now - I'm forced to go away. I will be set free - I will definitely speak my mind.



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