DNA Recovery and Coal
dave hayward
discovery of Dino bones in a coal mine in Utah? It said they were well
preserved and that they were going to try and recover DNA from the bones.
I think it was the April issue so I hope it's not a fake article. Anyone
have any Info?
Dave
Mickey Rowe
: Does anyone know anything about an article in Earth magazine about the
Excerpts again from the dinosaur mailing list. Note, however, that
there has been some dispute over the findings to be discussed below.
I think that within the past month _Nature_ has published a suggestion
that the DNA found was a contaminant. With that in mind:
Date: Fri, 18 Nov 1994 17:14:27 GMT
From: Ron Baalke <BAA...@kelvin.jpl.nasa.gov>
To: dino...@lepomis.psych.upenn.edu
Message-Id: <9411181714...@kelvin.jpl.nasa.gov>
Subject: DNA Extracted from Dinosaur Bones
UTAH SCIENTIST SAYS HE HAS EXTRACTED DNA FROM DINOSAUR BONES
By JOHN NOBLE WILFORD
N.Y. Times
After two years of painstaking analysis and hundreds of unsuccessful
attempts, a scientist at Brigham Young University has extracted the
genetic material DNA from what he thinks are bone fragments of
80-million-year-old dinosaurs.
The surprise was that the recovered DNA bore little or no
resemblance to that of any modern animals. It is "like nothing we've
ever seen before," said Dr. Scott R. Woodward, an associate
professor of microbiology at the university in Provo, Utah, who
directed the study.
Other scientists, however, are skeptical of the research and want to
see the results tested further by independent laboratories.
In a report in Friday's issue of the journal Science, Woodward said
he had isolated DNA molecules from pieces of two ancient bones and
produced nine readable sequences from a strand of DNA for a
particular gene. It is the first report to be published in an
authoritative journal of an apparent success in isolating what is
presumably dinosaur DNA.
The bone fragments, possibly from a limb bone and a rib of a large
animal, were found in a coal mine in eastern Utah. They were
embedded in rock that is associated with dinosaur fossils when found
in other areas. But the fragments were too small to be identified
definitely as dinosaurian.
"On the basis of the circumstantial physical and geological
evidence," Woodward wrote, "it is likely that the bone fragments
belong to a Cretaceous period dinosaur or dinosaurs."
Despite this caution, Brigham Young issued a news release saying
that Woodward "has become the first researcher to extract DNA from
dinosaur bone," and in a telephone interview Wednesday, the
scientist did not contradict the statement. "I'm fairly confident
that we are dealing with dinosaur bones," he said.
Even if the bones are indeed dinosaurian, some scientists questioned
whether delicate DNA molecules could exist in bone for 80 million
years. They raised the possibility that the DNA could be
contamination from some organisms that had entered the bones later.
"Granted they have something, but I have no idea what it really is,"
said Dr. Mark A. Norell, a paleontologist at the American Museum of
Natural History in Manhattan. "I don't think they can show
definitely that those are dinosaur bone."
Woodward noted that scientists had recently found DNA in a weevil
preserved in 120-million-year-old amber. Others have recovered
20-million-year-old DNA from a fossilized magnolia leaf and from a
bee in amber.
A research team led by John R. Horner, a paleontologist at the
Museum of the Rockies in Bozeman, Mont., has had some success trying
to recover DNA from a 75-million-year-old Tyrannosaurus rex, but so
far, the results have not been replicated by others.
Paleontologists were perplexed by the finding that the supposedly
dinosaur DNA, when compared with modern DNA, did not appear to fit
into any known animal groups.
Woodward reported that the recovered DNA was at least 30 percent
different from the sequences of modern mammals, reptiles and birds,
which many paleontologists think are living descendants of
dinosaurs.
In an accompanying article in Science, Dr. Svante Paabo, a molecular
evolutionist at the University of Munich in Germany, was quoted as
saying, "The jury is still out until others can reproduce his
results."
Woodward said other laboratories would be given samples for
independent testing. But much of the material was destroyed in the
tests already done, and a collapsed tunnel has closed the coal mine,
preventing the search for more bone fragments.
Even if the material turns out to be dinosaurian DNA, Woodward
dispelled any notion that with this small bit of DNA, scientists
could somehow create living dinosaurs, in the manner of the movie
"Jurassic Park."
"I liked the movie and the book, but it's science fiction, pure
fantasy, and that's not going to happen," Woodward said in the
interview.
[I'm not editing these things, so forgive me for references to
previous conversations in the following message. Feel free to ask for
clarification if you desire it. -- MR ]
Date: Mon, 28 Nov 1994 14:04:13 -0500
From: rowe (Mickey Rowe)
Message-Id: <941128190...@lepomis.psych.upenn.edu>
To: dino...@lepomis.psych.upenn.edu
Subject: Woodward et al.
As promised, I'm writing about the recent claims of the dinosaur DNA
find from BYU. First off, the two references are:
Gibbons, A. (1994). "Possible Dino DNA Find Is Greeted With
Skepticism", _Science_, 266:1159.
and:
Woodward, S. R., Weyand, N. J. and Bunnell, M. (1994). "DNA Sequence
from Cretaceous Period Bone Fragments", _Science_, 266:1229-1232.
To clear up a bit of past confusion--no real attempt was made at
determining from what sort of cells the DNA might have been
extracted. Fragments from the interior of the bones were ground up
for the extraction experiments. Other bone samples were sectioned
and stained for viewing under a light microscope. These sections
indicated the possible presence of osteocytes (mature bone cells),
which were strongly stained by eosin and hematoxylin. I believe
that those stains indicate the presence of nuclear DNA. In any
case, for the current report, Woodward et al. cast their net
specifically for a section of mitochondrial DNA, more specifically
DNA which codes for cytochrome b (I suspect that they searched for
other sequences as well and reported only on the one in which they
achieved a success, but I'm basing that more on a comment in the
Gibbons article than on anything in the Woodward article).
In passing, they mention that the bone appeared to be woven rather
than lamellar. If I recall correctly, woven bone is an indicator of
rapid growth, like that typically seen (amongst modern animals) only
in birds and mammals.
As for the bones: bone 1 is thought to be a fragment from a long
bone. It's dimensions are 20 cm x 6 cm x 3 cm. It's not possible
to determine what bone it is let alone what sort of animal it might
have supported. Bone 2 appears to have been from a rib, and not
necessarily from the same animal as bone 1. It was 20 cm x 2 cm x 1
cm. Analysis of the constituents of the bones indicate that very
little mineralization took place--the composition is similar to that
of bones extracted from recently living animals.
Now for the sequences: 9 sequences were obtained with the help of
PCR, 7 from bone 1, and 2 from bone 2. A consensus sequence was
generated from the seven sequences from bone 1. (That is, each of
the seven sequences was given "one vote" on what each base should be
at each location along the strand, and the base indicated by the
majority of the seven strands was assigned to the corresponding
position along the consensus strand). All 9 of the strands were
then compared to the consensus strand, and all 10 strands (9
experimentally determined and the one consensus) were compared with
sequences reported from other animals.
I'm not a molecular biologist, so I don't know what sort of
variation you would expect to find between strands obtained and
amplified from modern organisms (anybody else want to chime in?).
However, what was found here was differences (arguments between the
sequences if you will) at around 9% of the sites. I'm having a bit
of difficulty determining the length of the strands they found and
would appreciate any available help. The text of the article claims
that the sequence found was 174 base pairs long. In the figure
showing all of the sequences, it looks to me like the *longest*
sequence is 134 base pairs long. In the Gibbons article it is
claimed that the *shortest* sequence was 134 base pairs long. In
any case, the sequences were all pretty short so you can't draw
strong conclusions from them, particularly in light of the
discrepancies between the individual sequences. As for the latter,
a very plausible explanation for these differences is that each of
the samples were damaged at some locations (since most people would
have told you that all 80 million year old DNA would be fubar,
finding evidence of damage at some sites doesn't exactly call for a
suspension of disbelief :-) However, in most cases the disagreements
are between the consensus sequence and only one or two of the actual
sequences, so it's a reasonable assumption that the the consensus
sequence is the "correct" sequence for the animal that gave us bone
1. There are 9 sites at which the sequences from bone 2 disagree
with the consensus sequence, but agree with each other. The authors
suggest this to mean that the bones were from different animals, and
that at these 9 sites, the two sequences from bone 2 are "correct".
With regards comparisons between these sequences and others from
contemporary animals, the authors say very little other than that
the data don't allow for the conclusion that the sequences are more
closely related to either mammals, or birds, or reptiles (their
word, not mine--I can only assume that they include box turtle,
garter snake, and alligator in the last category since they mention
those three animals by name in the list of additional sequences
obtained for comparison in their own lab).
Naturally there's more to the paper than what I've written, but I
don't want to go on forever unless people ask for more information.
The take home message is (from the last sentence of Woodward et
al.):
... this result demonstrates that the recovery of DNA from
well-preserved Cretaceous period bone may be possible.
Any stronger conclusion would be unwarranted embellishment IMHO.
--
Mickey Rowe (ro...@lepomis.psych.upenn.edu)
: Dave
--
Mickey Rowe (ro...@pender.ee.upenn.edu)
P.G.Davis
: Does anyone know anything about an article in Earth magazine about the
: discovery of bones in a coal mine in Utah? It said they were well
: preserved and that they were going to try and recover DNA from the bones.
: I think it was the April issue so I hope it's not a fake article. Anyone
: have any Info?
: Dave
The original article was by Scott Woodward et al. in Science last summer
(1994) . They isolated a portion of mDNA about 18? base pairs long they
tried to match this sequence using Genbank but no match was found. They
therefore assumed that it must be dinosaurian. About three weeks later
the aDNA expert (whose name escapes me for the moment but I think he is
Egyptian and works in Switzerland) stated that the DNA Woodward had found
was in fact a portion of human mDNA which had only just been isolated and
had not yet been assimilated onto Genbank etc. This in fact looks like the
truth and the bone was contaminated during collection/preparation.
Interestingly as a taphonomist I would have never chosen the bone that is
figured by Woodward et al. because it looks to a) weathered, b) abraded
and c) generally knackered by geological processes.
Hope this helps
Yours
PG
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Paul Davis | I always thought there was something
Dept. of Geology | fundamentally wrong with the universe
Uni of Bristol |
England | Arthur Dent - Philosopher and
e-mail paul....@bristol.ac.uk | wearer of dressing gowns
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