Ancient Fossils with Preserved Soft Tissues and DNA

Ancient Fossils withPreserved Soft Tissuesand DNA

Sean D. Pitman M.D.

Updated March, 2005

One of the earliest publishedreports concerned DNA extractedfrom ancient materials (i.e., greater than one million years old) involvedMagnolia leaves (with intactfragments measuring up to 820 basepairs) found in lake bottomsediments of Miocene age,supposedly 17-20 million years old.

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This find was quite interesting because themagnolia leaves were found in water logged clay deposits - i.e., they were still wet! Of course, DNA disintegrates fairly rapidly when in contact with water (complete

disintegration in less than 5,000 years).

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Yet, this experiment was repeated with severalscientists reporting the retrieval of authentic plant cpDNA in the 700-1500 bp sizerange.

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In commenting on the remarkably old DNA in the supposedly 17-million-year-oldmagnolia leaf, Savante Pääbo exclaimed, "The clay was wet, however, and onewonders how DNA could have survived the damaging influence of water for so long."

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Good question. However, most of the supposedly "ancient" DNA which has beenrecovered is from insects and plants preserved in

dry

amber, including a termiteestimated to be 25-30 million years old,

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a Hymenaea leaf thought to be 25-40 millionyears old

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and a weevil estimated to be 120-135 million years old.

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The weevil DNA, inparticular, was once thought to be 80 million years older than any other DNA specimenever extracted and sequenced.Even more amazing than this though are the findings of Dr. Cano, a microbiologist atCalifornia State Polytechnic University. What Dr. Cano did was dissect a Dominicanstingless bee trapped in amber, which was thought to be 25 to 40 million years old.What he found were very well preserved bacterial spores inside. In fact they were sowell preserved that they actually grew when placed in the right environment. In other words, they were still alive! And, interestingly enough, their DNA closely matched theDNA of modern bacteria that grow inside modern bees.

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Also, fairly recently, viablebacterial endospores and proteobacteria were isolated from primary (halite) salt crystalsdated at over 250 million years old.

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The experiments were conducted in dedicated

clean laboratory facilities. So, contamination is thought to be unlikely in this case. So, of course, the age of the crystals was subsequently questioned.

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Logically, since itstretches the imagination that any form of living thing could remain viable for such longperiods of time, perhaps the dating methods used to date the crystals were wrong?Good thinking! Also, it is interesting to note that the sequences from the study of Vreeland et al. [ref. 30] show only 1–3 substitution differences from contemporarybacterial sequences, whereas known mutation rates among related bacteria would havesuggested 59 differences.

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In this same line, the DNA extracted from amber, even though it was maintained in afairly dry environment, is also just as problematic as DNA sequences from ancient saltcrystals.

R. John Parkes commented in

Nature

concerning this and other similar phenomena by noting that, "There is also the question of how bacterial biopolymers canremain intact over millions of years in dormant bacteria; or, conversely, if bacteria aremetabolically active enough to repair biopolymers, this raises the question of whatenergy source could last over such a long period."

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Regardless of these serious problems, such discoveries have been widely reportedby the media without remark regarding the difficulty that these finds present for thestandard geological time scale. DNA, like all other biological macromolecules, isgenerally quite unstable and spontaneously breaks down - especially when hydrated or "wet". In living cells, DNA is maintained by repair mechanisms, but after death DNA self-destructs at a rather rapid rate. In a published review of the chemical stability of DNA,Tomas Lindahl (1993) noted, “Deprived of the repair mechanisms provided in livingcells, fully hydrated DNA is spontaneously degraded to short fragments over a time