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--------------------------------------------------------------------------------


ANCIENT BONES — HOW OLD?

22 01 2021

Radiocarbon (14C) dating was developed by Nobel-Prize winning chemist Willard
Libby, and has become the predominant method to build chronologies of ancient
populations and species using the Quaternary fossil record. I have just
published a research paper about 14C dating of fossil bone reviewing the four
standard chemical pretreatments of bone collagen to avoid sample contamination
and generate accurate fossil ages: gelatinization, ultrafiltration, XAD
purification and hydroxyproline isolation. Hydroxyproline isolation is perceived
as the most accurate pretreatment in a questionnaire survey completed by 132
experts from 25 countries, but remains costly, time-consuming and not widely
available. I argue that (1) innovation is urgently required to develop
affordable analytical chemistry to date low-mass samples of collagen amino
acids, (2) those developments should be overseen by a certification agency, and
(3) 14C users should be more conceptually involved in how (much) 14C chemistry
determines dating accuracy. Across the board, scientific controversies like the
timing of Quaternary extinctions need not be fuelled by inaccurate chronological
data.

--------------------------------------------------------------------------------



Megafauna bones from the Quaternary fossil record. Top: excavation of a partial
skeleton of a short-faced kangaroo Procoptodon browneorum at Tight Entrance Cave
(Western Australia) [1]: these bones are close to the limit of radiocarbon (14C)
dating in a geological context 43000 to 49000 years old. Middle: metacarpal of
the extinct horse Hippidion cf. devillei from Casa del Diablo (Peru) 14C dated
at 11980 ± 100 years before present (BP) (CAMS-175039) following XAD
purification of collagen gelatin [2]. Bottom: collection of skeletal remains of
(mostly) red deer Cervus elaphus from El Cierro Cave (Spain) 14C dated at 15520
± 75 years BP on ultrafiltered gelatin (OxA-27869 and OxA-27870 average) [3].

--------------------------------------------------------------------------------

Scientists have widely been interested in the present and future state of
biodiversity. Ecologists (the main audience of this blog) have also looked into
the past with pioneering investigations addressing the composition of ancient
forests and the origins of agriculture in layers of fossil pollen accumulated in
lake sediments [4]. But it took us decades to see the fossil record as a useful
tool (combining biological, geochemical and molecular techniques) to answer
basic ecological questions. Some of those questions are critical for conserving
today’s biodiversity [5, 6]: for example, when did human impacts on ecosystems
become global or what extinct species have best tolerated past environmental
change and what that means to modern species? [7].

The study of (pre)historic biological events relies one way or another on our
ability to time when a certain animal, human, or plant occurred and what
environmental conditions they experienced, and relies on concepts borrowed
from archaeology (past human
activity), palaeontology (fossils), palaeocology (species responses to past
environments), and geochronology (age of fossils and/or their geological
context). Among the range of chronological methods available to date biological
and cultural samples [8], radiocarbon (14C) dating has become the most important
for dating bones aged modern to late Quaternary (last ~ 50,000
years). Hereafter, ‘bone’ comprises antler, bone, ivory and teeth. 14C dating of
bones is appealing at least for four reasons: 



 1. Conceptually simple (see video here): the more 14C found in a bone, the
    younger the bone. Counting 14C atoms by accelerator mass spectrometry (AMS,
    see the guts of an accelerator here) has outcompeted the original method
    of counting beta particles (measuring radioactivity, still used by some 14C
    laboratories) conceived by Willard Libby.
 2. Low-mass samples: we can date bone samples below 1 g, a crucial factor for a
    fragmented fossil record frequently represented by a single, incomplete bone
    per specimen (see video on how bones fossilise).
 3. Direct: if one is interested in timing when a species
    existed, directly dating a bone will often be more accurate
    than indirectly dating the surrounding soils and sediments, because fossils
    are frequently found outside the geological context of the death of the
    individual to which the bones belonged.
 4. Universal: more than 150 AMS facilities are doing 14C dating throughout the
    world, so the method is widely available wherever scientists do their work.

Most ages of fossil bone generated at modern AMS 14C laboratories are estimated
from collagen (a fibrillary protein with three strands of amino acids twisted
together like a rope). However, fossil collagen is not chemically inert but
incorporates carbon from the environment (soil, sediment, rain, ground
water) [9, 10]. AMS accelerators cannot differentiate 14C atoms belonging to a
fossil bone from 14C atoms that bone has taken up from the environment. Imagine
we are counting white beans in a plastic bag: we cannot tell whether different
beans came from different plants, orchards, regions or countries; they are just
beans as much as 14C atoms in a fossil bone are just 14C atoms. Contamination
with foreign 14C can cause errors in the estimation of the geological age of a
bone by tens to thousands of years, potentially distorting downstream inferences
like what climatic conditions (measured through a palaeoclimate archive) align
with a species’ extinction time (quantified from a time series of 14C dates).
Therefore, prior to dating, collagen is subjected to four major purification
steps — collectively known as ‘pretreatment’, which I summarise in the following
panel.

--------------------------------------------------------------------------------

increasing accuracy, complexity, cost & turnaround; decreasing datable
mass/sample →

pretreatment gelatinisation ultrafiltration XAD purification hydroxyproline
isolation chemistry removal of mineral (apatite) in cold acid, then heating in
slightly acidic water resulting in collagen gelatin gelatin filtered through a
30 kDalton (kDa) membrane gelatin broken into free amino acids in strong acid &
passed through a non-polar XAD resin that binds to contaminants gelatin broken
into free amino acids in acid & passed through a chromatographic column
isolating hydroxyproline by its structure dated fraction gelatin gelatin
molecules > 30 kDa all 18 amino acids amino acid hydroxyproline rationale
apatite more prone to uptake carbon contaminants than collagen large molecules
are collagen; small molecules are contaminants amino acids are free of
contaminants; collagen is not hydroxyproline is specific to bone

--------------------------------------------------------------------------------



Chemistry of collagen radiocarbon (14C) dating using accelerator mass
spectrometry (AMS). The ultimate goal is to count the collagen-specific 14C
atoms remaining in a bone sample (converted to gas or graphite) after removing
the 14C atoms that the bone has incorporated from the environment since the
individual (animal, human) died. What pretreatment to use balances (1) cost, (2)
purification efficiency, (3) turnaround time, (4) geological provenance, (5) the
true geological age of the fossil, (6) the size (mass) of the sample, and (7)
how the bone was handled from sampling to storage. Examples of two extreme
samples from low to high contamination (and collagen degradation) could be
a Holocene-age bone sampled yesterday in
southernmost Patagonia versus a Pleistocene-age bone from the banks of the
river Guadalquivir curated for fifty years in a museum.

--------------------------------------------------------------------------------

Robert Longin
Gelatinization is the minimum, if not final, pretreatment offered by the vast
majority of laboratories.
It mimics an ancient culinary trick: slow simmering of bone in hot water
dissolves collagen and produces a nutritious bone broth (gelatin). 
Adapted for 14C dating by Robert Longin as part of his PhD thesis at the
University of Lyon (France) and published in Nature in 1971 [11]. Erle Nelson
Ultrafiltration is the most popular pretreatment of collagen gelatin these
days. 
Developed in the 1980s by Erle Nelson at Simon Fraser University (Canada) [12],
used by several AMS labs in North America since the 1990s, and introduced to
Europe through Mike Richards’ PhD and first postdoc at Oxford University.
The Oxford Radiocarbon Accelerator Unit (ORAU) adopted ultrafiltration in June
2000, and other European labs followed at least 6 years later. Thomas Stafford,
Jr.
XAD purification uses non-polar resins that specifically bind to contaminants
after the collagen gelatine has been hydrolysed to free amino acids. 
Developed by Tom Stafford in the 1980s [13, 15], it features in the menu of 14C
services offered by several North American AMS laboratories.
The method has surprisingly not reached European facilities. Richard (Dizzy)
Gillespie
Dating hydroxyproline was hinted at in the 1960s [16] but Dizzy Gillespie was
the first author to publish 14C dates using hydroxyproline isolation in
1984 [14].
This pretreatment uses liquid chromatography to isolate individual amino acids
(hydrolysed from collagen) by their structure.
Hydroxyproline is an imino (or secondary) amino acid that animals produce in
vivo (metabolically, not from the diet).

Authors making key collagen-chemistry developments for AMS radiocarbon (14C)
dating. Gelatinisation alone and ultrafiltration will be safe for dating bone
from cold climates and depositional environments with weak soil formation like
caves but for the wrong reason; that is, absence or low occurrence of the
greatest single source of 14C contamination: humic/fulvic acids. These compounds
originate from the modification of plant matter, and form chemical bonds
(cross-links) with collagen that are not broken by gelatinisation or
ultrafiltration. Humates act on a collagen fibril like the tanning of a strip of
leather, once the tanning touches the leather at one point, it spreads over the
whole strip. This so-called Maillard reaction (honouring Louis Maillard) takes
place daily in everyone’s lives as it is what gives a loaf of bread or your
favourite biscuit its brown colour.

--------------------------------------------------------------------------------


QUESTIONNAIRE SURVEY

I have spent > 3 years collating 14C dates from the scientific literature almost
daily [e.g., 17]. Throughout, I have discovered that bone pretreatment is often
not reported by authors publishing 14C dates. Finding this information becomes a
detective task that I will discuss in a future post. My focus here is that (i)
if different 14C laboratories offer different pretreatments, and (ii) if
different pretreatments (sometimes the same pretreatment run by different
laboratories) can produce different 14C ages of the same bone, and (iii) given
that there are no universal guidelines about what pretreatment should be best
for what sample, then neglecting the chemistry of how a 14C date has been
generated eludes a critical criterion to rank the quality of 14C data. We
currently lack a comprehensive assessment and quantification of the magnitude of
this problem in published research.

With that concern in mind, I conceived my study. I asked 132 researchers, who
use, generate and/or publish 14C dates of human and megafauna bones, to answer
12 questions about their preferences and concerns about the four most widespread
pretreatments of collagen leading to AMS 14C dating (gelatinisation optionally
followed by ultrafiltration, XAD purification or hydroxyproline isolation). I
wanted to know the degree of consensus among top researchers in their fields
(particularly archaeologists, palaeontologists and geochronologists), working at
world-class research sites and/or AMS laboratories worldwide (25 countries). The
research paper has been published open-access here, including main text (pdf),
questionnaire design (html) + respondents’ raw responses (xlsx)+ supplementary
figures and tables (pdf). A talk I gave in February 2020 in the Flinders
University Ecology and Evolution Seminar Series about this work is
available here.

The questionnaire survey revealed that, for dating bone suspected to be severely
contaminated with foreign carbon, hydroxyproline isolation is the preferred
chemical option (39% of the respondents), followed by ultrafiltration (23%), XAD
purification (9%), and gelatinisation alone (<5%). 23% of the audience was
unsure of the reliability of what pretreatment to rank first. Before submitting
bone samples to a 14C laboratory, both contamination and the international
prestige of 14C laboratories are the top-ranked criteria respondents ponder to
choose pretreatment. And, one in every two respondents who submit bone samples
for dating to a 14C laboratory do not choose pretreatment themselves but ask or
let the 14C laboratory select pretreatment for them.

--------------------------------------------------------------------------------



Products of bone chemical pretreatment for radiocarbon (14C) dating. Top: Rib
fragment of a Mexican horse Equus conversidens from Wally’s Beach (Canada)
before pretreatment. Bottom-left: collagen extracted with an alkali (potassium
hydroxide, KOH) after decalcifying the bone, followed by acidification and
freeze-drying (3 days of work in total), giving an age of 13540 ± 40 years
before present (BP) (UCIAMS-127363) [18]. Bottom-right: gelatin obtained by
heating KOH-extracted collagen in pH 2 HCl (weak acidity) at 90 °C for 1 hour
giving an age of 11,495 ± 30 years BP (UCIAMS-127364) [18]. Purified gelatin
gave ages of 11685 ± 50 years BP by ultrafiltration after a solvent rinse
(OxA-37337), 11440 ± 30 years BP by XAD purification (UCIAMS-127351) and 11445 ±
55 years BP by hydroxyproline isolation (OxA-X-2736-10) [19]. Significance:
conservation glue (Butvar) makes the geological age of KOH-extracted collagen ~
2 millennia older than truth until its gelatin has been extracted, and humic
contamination likely makes the ultrafiltered gelatin ~ 2 centuries older than
dating all collagen amino acids (XAD) or only hydroxyproline.

--------------------------------------------------------------------------------

In my paper, I complemented the questionnaire survey with a literature review of
bone-contamination issues for 14C dating. I propose the following three areas of
future development:

 1. Universal standards: A certification agency seems much needed to oversee
    quality control across laboratories. The overarching principles of such an
    agency could be to enforce procedural consistency across 14C laboratories,
    to promote a network of research sites specialising on specific aspects of
    dating (e.g., types of samples like bone, charcoal, shell, etc.), and to
    supervise and speed up the transfer of chemistry developments from research
    to application at 14C laboratories. 
 2. Affordable accuracy: Molecular-level (primary and secondary amino acids)
    dating is expensive (costly reagents, equipment, highly skilled personnel)
    and not widely available. We need to make current protocols cheaper, and/or
    to develop alternative, affordable chemical protocols to isolate and date
    amino acids. Genomics illustrate that innovation cheapens technology and
    cheaper technology triggers innovation, so sequencing a genome has plummeted
    from US$100M to US$1K in 20 years. 
 3. Collective effort: Researchers must be more conceptually involved in how 14C
    data are generated, and journal Editors should not accept research
    manuscripts using 14C data without clear and replicable data-quality filters
    (including sample pretreatment). Provoking paper titles like “big data
    little help in megafauna mysteries” with regard to Quaternary
    extinctions [20] convey the message that data quality is as important as the
    most sophisticated modelling to make global inferences about past biological
    events.


DURING PEER REVIEW

Before my successful submission to Royal Society Open Science (RSOS), my
manuscript was rejected at the Editorial level three times for the following
reasons: (i) “your manuscript falls outside the scope of this journal”
(Scientific Reports, decision date = 20/07/2020), (ii) “not convinced that the
findings presented have the potential significance for publication in eLife”
(28/07/2020), and (iii) “not feel that your study represents the strength of
advance that we require for publication in PLoS Biology” (29/05/2020). Of
course, I hold no grudge against those decisions — rejections are normal
outcomes in a scientist’s work. But the above rationale of rejection contradicts
the facts that (i) these journals publish research built on 14C dates and
(ii) 14C dating is propelling advances in multiple scientific disciplines [21].
After all: what can be more important for scientific research than finessing
data quality?

One of the two RSOS reviewers pondered that “I worry that it [my article] will
scare potential users of radiocarbon labs into never attempting to radiocarbon
date bone” (RSOS has made reviewers’ comments and my responses to them
available here). I conclude this blog with my answer to that statement:

The overarching goal of my manuscript is to promote improvements rather than
discrediting the field of 14C dating. In that direction, I have now emphasised
the critical (current/future) role of 14C dating in scientific research in the
concluding section of my article: 

> “14C dating has meritoriously established itself as one of the most powerful
> tools for dating cultural and palaeontological deposits from the late
> Quaternary [22, 23]. The method is conceptually simple and well understood.
> Along with its prominence in the Quaternary sciences, its importance in modern
> research has been, and will be even more, heightened by the growing
> application of palaeoarchives and fossil materials to understand ongoing
> global ecosystem shifts and anthropogenic impacts on biodiversity and the
> environment [5, 6].”

--------------------------------------------------------------------------------


ACKNOWLEDGEMENTS

My paper was accepted for publication last December 2020, only days before
moving from Australia to Spain. I thank my dear colleagues at the Australian
Centre for Ancient DNA (ACAD) for the inspiring exchanges we have shared in the
last three years. I also appreciate the supreme feedback provided by Matthew
Collins, Dizzy Gillespie, and Tom Stafford during the conception and writing of
the paper.

I thank the 132 authors who participated in the questionnaire survey, and Alex
Bayliss, Corey Bradshaw, Tom Higham, Greg McDonald, Kieren Mitchell, Paula
Reimer, Mike Richards, John Southon and Chris Turney for their generous input at
different stages of conception and completion of my study. Photographs kindly
provided by Esteban Álvarez-Fernández (Cervus), Gavin Prideaux (Procoptodon),
Tom Stafford (Equus), Natalia Villavicencio (Hippidion), Christine Oberlin
(Robert Longin) and Mike Richards (Erle Nelson). My salary was funded by
Australian Research Council Discovery Project DP170104665, and publication fees
were paid by the School of Biological Sciences (University of Adelaide,
Australia).

Salvador Herrando-Pérez


REFERENCES

[1] Prideaux et al. 2010 Timing and dynamics of Late Pleistocene mammal
extinctions in southwestern Australia. Proceedings of the National Academy of
Sciences 107: 22157-22162 doi:10.1073/pnas.1011073107

[2] Villavicencio, Werdelin 2018 The Casa del Diablo cave (Puno, Peru) and the
late Pleistocene demise of megafauna in the Andean Altiplano. Quaternary Science
Reviews 195: 21-31 doi:10.1016/j.quascirev.2018.07.013

[3] Álvarez-Fernández et al. 2016 Nouvelles données sur le Magdalénien inférieur
de la Région Cantabrique : le Niveau F de la grotte de El Cierro (Ribadesella,
Asturies, Espagne). L’Anthropologie 120: 537-567
doi:10.1016/j.anthro.2016.09.001

[4] Moore 1986 Palaeoecology: unravelling human effects. Nature 321: 204
doi:10.1038/321204a0

[5] Dietl, Flessa 2011 Conservation paleobiology: putting the dead to
work. Trends in Ecology & Evolution 26: 30-37 doi:10.1016/j.tree.2010.09.010

[6] Fordham et al/ 2020 Using paleo-archives to safeguard biodiversity under
climate change. Science 369: eabc5654 doi:10.1126/science.abc5654

[7] Seddon et al. 2014 Looking forward through the past: identification of 50
priority research questions in palaeoecology. Journal of Ecology 102: 256-267
doi:10.1111/1365-2745.12195

[8] Walker 2005 Quaternary dating methods. Chichester, West Sussex, England:
Wiley.

[9] Collins et al. 2002 The survival of organic matter in bone: a
review. Archaeometry 44: 383-394 doi:10.1111/1475-4754.t01-1-00071

[10] Kendall et al. 2018 Diagenesis of archaeological bone and
tooth. Palaeogeography, Palaeoclimatology, Palaeoecology 491: 21-37
doi:10.1016/j.palaeo.2017.11.041

[11] Longin 1971 New method of collagen extraction for radiocarbon
dating. Nature 230: 241-242 doi:10.1038/230241a0

[12] Brown et al. 1988 Improved collagen extraction by modified Longin
method. Radiocarbon 30: 171-177 doi:10.1017/S0033822200044118

[13] Stafford et al. 1982 Isolation of proline and hydroxyproline from fossil
bone. Life Sciences 31: 931-938 doi:10.1016/0024-3205(82)90551-3

[14] Gillespie et al. 1984 Radiocarbon dating of bone by accelerator mass
spectrometry. Journal of Archaeological Science 11: 165-170
doi:10.1016/0305-4403(84)90051-7

[15] Stafford et al. 1987 Study of bone radiocarbon dating accuracy at the
University of Arizona NSF Accelerator Facility for radioisotope
analysis. Radiocarbon 29: 24-44 doi:10.1017/S0033822200043538

[16] Ho et al. 1969 Radiocarbon dating of petroleum-impregnated bone from tar
pits at Rancho La Brea, California. Science 164: 1051-1052
doi:10.1126/science.164.3883.1051

[17] Rodríguez-Rey et al. 2016 A comprehensive database of quality-rated fossil
ages for Sahul’s Quaternary vertebrates. Scientific Data 3: 160053
doi:10.1038/sdata.2016.53

[18] Waters et al. 2015 Late Pleistocene horse and camel hunting at the southern
margin of the ice-free corridor: Reassessing the age of Wally’s Beach,
Canada. Proceedings of the National Academy of Sciences 112: 4263-4267
doi:10.1073/pnas.1420650112

[19] Devièse et al. 2018 Increasing accuracy for the radiocarbon dating of sites
occupied by the first Americans. Quaternary Science Reviews 198: 171-180
doi:10.1016/j.quascirev.2018.08.023

[20] Price et al. 2018 Big data little help in megafauna mysteries. Nature 558:
23-25 doi:10.1038/d41586-018-05330-7

[21] Marra 2019 Hot carbon: carbon-14 and a revolution in science. New York,
USA: Columbia University Press.

[22] Swift et al. 2019 Micro methods for megafauna: novel approaches to Late
Quaternary extinctions and their contributions to faunal conservation in the
Anthropocene. Bioscience 69: 877-887 doi:10.1093/biosci/biz105

[23] Taylor, Bar-Yosef 2016 Radiocarbon dating. An archaeological perspective.
New York, USA: Routledge.


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INFORMATION

   
 * Date : Fri, 22 Jan 2021
 * Tags: AMS, AMS dating, bone, collagen, dating, ecology, palaeoecology,
   palaeontology, Radiocarbon dating
 * Categories : biodiversity, carbon, climate change, conservation, extinction,
   palaeo-ecology, research, science


2 RESPONSES

14 12 2021
Extinct megafauna prone to ancient hunger games – Global Ecology @ Flinders
(10:31:22) :


[…] a shift happened after, then humans did it. Biases in geochronological
inference (e.g., spatial, contamination), incorrect application of climate
proxies, poor taxonomic resolution, and not accounting for the […]

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14 12 2021
Extinct megafauna prone to ancient hunger games | ConservationBytes.com
(10:00:19) :


[…] a shift happened after, then humans did it. Biases in geochronological
inference (e.g., spatial, contamination), incorrect application of climate
proxies, poor taxonomic resolution, and not accounting for the […]

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> The science of ... saving life

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I am the Matthew Flinders Professor of Global Ecology at Flinders University.

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 * BirdLife International
 * Bright New World
 * Bush Heritage Australia
 * Conservation International
 * Foundation Earth
 * NatureServe
 * The Nature Conservancy
 * Wilderness Society
 * Wildlife Conservation Society
 * World Wide Fund for Nature


ENVIRONMENTAL SCIENCE

 * Hot Topics in Ecology
 * The Conversation (Environment)


GENERAL

 * Wild Forests
 * WildLeaks


JOBS

 * Conservation Careers
 * Conservation Job Board
 * Linkedin Jobs


LEARNED SOCIETIES

 * Australian Academy of Science
 * British Ecological Society
 * Ecological Society of America
 * Ecological Society of Australia
 * Society for Conservation Biology
 * Society for Ecological Restoration International


SCIENCE COMMUNICATION

 * Alliance of Leading Environmental Researchers and Thinkers (ALERT)
 * Australian Science Media Centre
 * Conservation Journal
 * Current Conservation
 * Hot Topics in Ecology
 * I Fucking Love Biodiversity
 * I Fucking Love Science
 * Royal Institution of Australia
 * The Conversation (Environment)




LOCATION

Flinders University
+61 8 8201 2090

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