WinAce

Can the methods of textual criticism (specifically, comparison between extant related species) give us startling insights into the content of the original ancestral genomes?

And, if we can reconstruct the ancestral state of a genome, would it be feasible to splice it together and create a clone of the common ancestor between various species without having the original DNA preserved?

Alix Nenuphar

Dashed clever people, these Americans. If we're not careful, they might end up dominating the world...

Since I know very little about this field, I thought my logical five centimes would be useful, and I need a break from baiting Nelson Alonso.

The difficulty with implementing some of the same methodology used in textual reconstruction, is that generally different copies of the text are available from different time periods. Note that the Dead Sea Scrolls served as an invaluable aid in understanding the textual history of the Judeo-Christian Old Testament.

There also exists a number of cases where the same document's scribal errors can be easily identified (e.g. the Anglo-Saxon Chronicle).

In the case of DNA, however, we essentially only have the 'leaves' of the tree - we may not have access to enough ancient DNA to enable the kind of comparison and cross-checking needed. It is as if we only had books that were printed in 2002 available to analyse.

Does that make sense? How much ancient DNA is actually available? Can it be sequenced? Do we have samples along the same genetic lineage for multiple time-frames?

Valentine Pontifex

For entire organism: no way.

For genes it could be done. In fact it has been done for a gene for a visual pigment in archosaurs: the common ancestor of crocs and birds. From living organism the common ancestor's pigment was figured out. The putive pigment was artificially synthesized and it worked and suggested that they saw in dim light.
PubMed for peer reviewed paper

News article from Nature Science Update

Of course they don't call it texual criticism.

RufusAtticus

For pathogens, we do actually historic samples. There's been some interesting work on flu and HIV.

Dr.GH

Highly unlikely, WinAce. Here are some references on the posible parameters of a LCA, and some reasons that it is very unlikely that such an organisms molecular structure can be determined with any degree of certainty:

Arcady R. Mushegian and Eugene V. Koonin
1996 A minimum gene set for cellular life derived by comparison of complete bacterial genomes by , Proceedings of the National Academy of Science, USA, vol 93, p 10268 "Evolution of amino Acid frequencies in proteins over deep time: inferred order of introduction of amino acids into the genetic code."

Brooks DJ, Fresco JR, Lesk AM, Singh M.
2002 Evolution of amino Acid frequencies in proteins over deep time: inferred order of introduction of amino acids into the genetic code. Mol Biol Evol. 2002 Oct;19(10):1645-55.

Dyall, Sabrina D., Patricia J. Johnson
2000 “Origins of hydrogenosomes and mitochondria: evolution and organelle biogensis.” Current Opinion in Microbiology 3:404-411

Harris, J. Kirk, Scott T. Kelley, George B. Spiegelman, and Norman R. Pace
2003 The Genetic Core of the Universal Ancestor
http://www.genome.org/cgi/content/ab...GR-6528v1?etoc

Olendzenski, Lorraine, Olga Zhaxybayeva, J. Peter Gogarten
2000 “How Much Did Horizontal Gene Transfer Contribute to Early Evolution?: Quantifying Archaeal Genes in Two Bacterial lineages ” (Abstract) General Meeting of the NASA Astrobiology Institute.

Schwartz, Robert M., Margret O. Dayhoff
1978 “Origins of Prokaryotes, Eukaryotes, Mitochondria, and Chloroplasts” Science Vol. 199 395-403

Schopf, J. William
1994 “Disparate rates, differing fates: Tempo and modes of evolution changed from the Precabrian to the Phanerozoic” PNAC-USA v.91: 6735-6742


The definitive test of OOL research might require the discovery of primitive, extraterrestrial life.

WinAce

Thanks for the references, Dr. GH. I'll have to look them up. Although I'm discouraged by the fact that so much of earth history is apparently beyond our reach forever...

Intriguing. Is there a way to cross-reference information gathered from genetic comparisons with fossils or another line of evidence? For example, if we find a common ancestral gene of fruit-eating X and pollen-drinking Y that would have enabled the ancestor to eat meat, can we find morphologically intermediate meat-eating fossils? (Just tossing out random ideas here)

lpetrich

WinAce:
Can the methods of textual criticism (specifically, comparison between extant related species) give us startling insights into the content of the original ancestral genomes?

Actually, WinAce, there has been an enormous amount of research on this very subject -- molecular evolutionary biology. Research on this subject became feasible in the mid-1960's, when it became feasible to sequence whole proteins.

From The Bullfrog Affair,
Since then, "molecular phylogeny" methods have advanced as the quantity of sequence data has increased -- such methods are vital for interpreting the whole-genome data that has recently become available.

One important lesson is that the more functionally constrained some molecule is, the less it evolves -- as a result of it being selected for some constant function over the generations. Using this lesson and searching for "conserved" sequences has made possible the identification of numerous human genes by comparing the human-genome sequence to those of mice and fish.

And, if we can reconstruct the ancestral state of a genome, would it be feasible to splice it together and create a clone of the common ancestor between various species without having the original DNA preserved?

That can be done with individual proteins, at least if their sequences have a reasonable amount of conservation. And if enough ancestral genes can be reconstructed, then one may be able to do this with entire ancestral-organism genomes, though doing so may be very difficult.

lpetrich

There has also been a lot of work on molecular phylogeny -- family-tree construction by sequence comparison and related techniques.

It has often confirmed traditionally-recognized relationships and clarified ambiguous and controversial ones, though it has sometimes forced revisions of traditional ones.

Simply consider the differences between human hemoglobin and those of chimps, rhesus monkeys, rabbits, chickens, and fish, as reported on earlier in this thread.

And among unexpected conclusions has been cetaceans (dolphins, whales) being an offshoot of the artiodactyls (even-toed ungulates). The most closely-related one is, perhaps not surprisingly, the hippopotamus.

Finally, here is an online debate with creationist Walter ReMine about this very subject.

WinAce

"Anti-creationists raised this issue, noting the panda is only 17% efficient at assimilating bamboo. It's bad design, they said, a good designer would've endowed herbivores with proper enzymes![11]

A theory is especially potent when it turns critical objections into corroborating evidence. Message Theory does that.

We're concerned about planetary de-forestation, so consider the consequences if most higher-animals could efficiently convert forests into progeny - catastrophe for the system. Therefore, a designer should protect plants from limitless overgrazing. Multicellular animals' inability to efficiently digest cellulose is one-facet of ecological balance for the system."

I must have misread that. Did Remine actually say that the inability to digest something efficiently, which results in more feeding for the same amount of calories, prevents needless overgrazing? :banghead:

pz

Yes. Apparently, a theory is particularly potent when it turns blatant contradictions and absurd nonsense into corroborating evidence. Message Theory does that.