Thursday, April 30, 2015

The Kalash Genetic Isolate: Ancient Divergence, Drift, and Selection

Qasim Ayub, Massimo Mezzavilla, Luca Pagani, Marc Haber, Aisha Moyuddin, Shagufta Khaliq, Syed Qasim Mehdi, Chris Tyler-Smith

(Link) pdf open access
Open access funded by Wellcome Trust

Abstract

The Kalash represent an enigmatic isolated population of Indo-European speakers who have been living for centuries in the Hindu Kush mountain ranges of present-day Pakistan. Previous Y chromosome and mitochondrial DNA markers provided no support for their claimed Greek descent following Alexander III of Macedon's invasion of this region, and analysis of autosomal loci provided evidence of a strong genetic bottleneck. To understand their origins and demography further, we genotyped 23 unrelated Kalash samples on the Illumina HumanOmni2.5M-8 BeadChip and sequenced one male individual at high coverage on an Illumina HiSeq 2000. Comparison with published data from ancient hunter-gatherers and European farmers showed that the Kalash share genetic drift with the Paleolithic Siberian hunter-gatherers and might represent an extremely drifted ancient northern Eurasian population that also contributed to European and Near Eastern ancestry. Since the split from other South Asian populations, the Kalash have maintained a low long-term effective population size (2,319–2,603) and experienced no detectable gene flow from their geographic neighbors in Pakistan or from other extant Eurasian populations. The mean time of divergence between the Kalash and other populations currently residing in this region was estimated to be 11,800 (95% confidence interval = 10,600−12,600) years ago, and thus they represent present-day descendants of some of the earliest migrants into the Indian sub-continent from West Asia.


Some Figures:

Figure 2. Kalash Demographic History
(A) PSMC analysis shows a low effective population size for the Kalash.
(B) Kalash effective population size estimated from LD analysis.
(C) MSMC analysis of the time of the split between the Kalash and African genomes (YRI, LWK, and MKK) and non-African genomes from East Asia (CHB and JPT), Europe (CEU and TSI), South Asia (GIH), and America (MXL).
(D) A UPGMA (unweighted pair group method with arithmetic mean) dendrogram shows the LD-estimated time of divergence between populations. The mean time of divergence between the Kalash and other populations from the Indian sub-continent is estimated to be 11,800 years ago (dashed red line). 


Figure 3. Shared Genetic Drift with Ancient Genomes
(A) Proportion of shared genetic drift (measured as f3 statistics) between extant world-wide HGDP-CEPH populations (including the Kalash) and the ancient Siberian hunter-gatherer (MA-1). The magnitude of the computed f3 statistics is represented by the graded heat key. The proportion of genetic drift shared between the Kalash and MA-1 is comparable to that shared between MA-1 and the Yakut, Native Americans, and northern European populations.
(B) Ternary plot of shared genetic drift with three ancient genomes: MA-1 (left), La Bran˜a 1 (middle), and Oetzi, the Tyrolean Iceman (right). The high proportion of genetic drift shared between the Kalash and MA-1 is comparable to that shared between MA-1 and Native Americans. In comparison with other populations from South Asia, the Kalash also share a higher proportion of genetic drift with La Braña 1 and Oetzi.


Discussion

The present study sheds light on the origins of the enigmatic Kalash population from Pakistan. We propose that the population represents an ancient genetic isolate rather than a recently split population showing extreme genetic drift, as suggested by earlier studies.(1,6)  The outlier status of these South Asians is corroborated by the fact that we found no evidence of recent admixture in the Kalash by using a variety of analyses, including TreeMix, f3, and linkage-based statistics. The fact that researchers also genotyped ten of these samples earlier by using the HGDP-CEPH panel and that these cluster with the samples genotyped in this study rules out the possibility of confounding results due to population sub-structure within the Kalash.
 
The ancient separation of the Kalash from a common Eurasian ancestor is supported by PSMC and MSMC analyses, which estimated that the Kalash split from East Asians (CHB and JPT as proxy) prior to splitting from Europeans and other South Asian populations. The split from Europeans (CEU and TSI) and South Asians (represented here by GIH) appears to have occurred during the Neolithic period, which is also supported by the decay of LD. LD decay showed that the Kalash were the first population to split from the other Central and South Asian cluster around 11,800 (95% CI ¼ 10,60012,600) years ago.  This estimate remained constant even after the addition of an African (YRI) population or when the Kalash were compared with different subsets of non-African populations.

The pairwise times of divergence with other Pakistani populations ranged from 8,800 years ago with the Burusho to 12,200 years ago with the Hazara. Although migration and undetected admixture in reference populations could bias our estimate of the time of divergence, using different subsets of population revealed no strong bias in the split between the Kalash and South Asians, which occurred after the split between Europeans and South Asian populations.

Since this split, the Kalash have maintained a low Ne of around 2,500 (95% CI ¼ 2,300–2,600), estimated from LD decay with no evidence of admixture. These Ne estimates are lower than those obtained from PSMC analysis because the latter method gives a single estimate of the cross-coalescence rate from the present to 24,000 years ago, whereas the linkage-based method gives us several estimates over the past 10,000 years. It is likely that PSMC analysis could not detect that the Kalash population suffered a continuous decline in effective population size. Taking into account the expected differences in Ne between autosomes and the Y chromosome, this is in agreement with the reported Ne of 237–1,124, which was estimated with observed and evolutionary mutation rates for Y chromosomal STRs. (34)

The Kalash represent a unique branch in the South Asian population tree and appear to be the earliest population to split from the ancestral Pakistani and Indian populations, indicating a complex scenario for population origins in the sub-continent rather than just the ancestral northern and southern Indian components identified previously. (35)  These Indo-European speakers were possibly the first migrants to arrive in the Indian sub-continent from northern or western Asia. This is supported by the higher level of shared genetic drift between the Kalash and the Paleolithic Siberian hunter-gatherer skeleton (MA-1) than between MA-1 and the other South Asian populations.

Whereas the Kalash have recently been reported to have European admixture, postulated to be related to Alexander’s invasion of South Asia,(6) our results show no evidence of admixture. Although several oral traditions claim that the Kalash are descendants of Alexander’s soldiers, this was not supported by Y chromosomal analysis in which the Kalash had a high proportion of Y haplogroup L3a lineages, which are characterized by having the derived allele for the PK3 Y-SNP and are not found elsewhere.(7)  They also have predominantly western Eurasian mitochondrial lineages and no genetic affiliation with East Asians.(4)

We observed that the Kalash share a substantial proportion of drift with a Paleolithic ancient Siberian huntergatherer, who has been suggested to represent a third northern Eurasian genetic ancestry component for present-day Europeans.(36,37) This is also supported by the shared drift observed between the Kalash and the Yamnaya, an ancient (2,000–1,800 BCE) Neolithic pastoralist culture that lived in the lower Volga and Don steppe lands of Russia and also shared ancestry with MA-1.(36,37)  Thus, the Kalash could be considered a genetically drifted ancient northern Eurasian population, and this shared ancient component was probably misattributed to recent admixture with western Europeans.

We also looked at how this long-term separation, isolation, and low effective population size affected the patterns of genetic variation in the Kalash. One striking example is the frequency of the derived allele for rs4988235, which has been linked to lactose tolerance.  The Kalash, like the MA-1, are fixed for the ancestral allele for this variant, whereas their neighbors in Pakistan have been observed to have moderate frequencies of the derived allele. Although this supports their long-term isolation, it is surprising in other ways because the Kalash have no reported lactose intolerance and indeed celebrate a ‘‘milk day’’ during their annual spring rituals.(38) This suggests that there might be additional derived lactase-persistence alleles in the LCT-MCM6 (MIM: 601806) region in this population.

Another example is the extremely high frequency (93%) of the stop-gain ACTN3 variant (rs1815739) associated with normal variation in human muscle strength and speed. (39) This variant was picked up as an outlier in the PBS test for selection in the Kalash. Simulations indicated that such a high frequency of the derived allele in the Kalash can only be obtained under a scenario that includes positive selection. The variant might be relevant in cardiovascular conditioning and muscle strength related to climbing up and down high mountain passes. Although ACTN3 has not been associated with adaptation to high altitude, RYR2, another gene with an intronic outlier variant (rs2992644) in PBS, has.(40)

It has been postulated that South Asia, which is now a densely occupied land, was encountered by the first populations of modern humans that ventured out of Africa more than 50,000 years ago. The exact route taken by these earliest settlers is not known, although it has been suggested that they traveled via a southern coastal route. (41,42)

The genetically isolated Kalash might be seen as descendants of the earliest migrants that took a route into Afghanistan and Pakistan and are most likely present-day genetically drifted representatives of these ancient northern Eurasians. A larger survey that includes populations from their ancestral homeland in Nuristan, Afghanistan, would provide more insights into their unique genetic structure and origins and help explain the complex history of the peopling of South Asia.

Wednesday, April 29, 2015

Accessing Developmental Information of Fossil Hominin Teeth Using New Synchrotron Microtomography-Based Visualization Techniques of Dental Surfaces and Interfaces

This is a great paper on cutting edge non destructive fossil hominin dental synchrotron imaging.  Life histories, including age at weaning, inter birth spacing and age at death can be determined from the study of hominin teeth.  Early hominin fossil teeth are very rare and not available for destructive testing.  Due to their hardness, hominin teeth are often the only hominin fossils that survive over hundreds of thousands of years.  The detailed morphology of teeth is information rich in terms of understanding life histories.  For these reasons, non-destructive testing procedures for early hominin teeth show great promise toward understanding the life histories of early hominins and human evolution.  (This research was funded by NSF Grant BCS 1126470, Harvard University, and the European Synchrotron Radiation Facility (Ec697).)

Adeline Le CabecNancy Tang and Paul Tafforeau
PLOS One
April 22, 2015
(Link) open access PLOS One paper
(Link) related movie


Abstract

Quantification of dental long-period growth lines (Retzius lines in enamel and Andresen lines in dentine) and matching of stress patterns (internal accentuated lines and hypoplasias) are used in determining crown formation time and age at death in juvenile fossil hominins.  They yield the chronology employed for inferences of life history. Synchrotron virtual histology has been demonstrated as a non-destructive alternative to conventional invasive approaches. Nevertheless, fossil teeth are sometimes poorly preserved or physically inaccessible, preventing observation of the external expression of incremental lines (perikymata and periradicular bands). Here we present a new approach combining synchrotron virtual histology and high quality three-dimensional rendering of dental surfaces and internal interfaces.  We illustrate this approach with seventeen permanent fossil hominin teeth. The outer enamel surface and enamel-dentine junction (EDJ) were segmented by capturing the phase contrast fringes at the structural interfaces. Three-dimensional models were rendered with Phong’s algorithm, and a combination of directional colored lights to enhance surface topography and the pattern of subtle variations in tissue density. The process reveals perikymata and linear enamel hypoplasias on the entire crown surface, including unerupted teeth. Using this method, highly detailed stress patterns at the EDJ allow precise matching of teeth within an individual’s dentition when virtual histology is not sufficient.  We highlight that taphonomical altered enamel can in particular cases yield artificial subdivisions of perikymata when imaged using X-ray microtomography with insufficient resolution.  This may complicate assessments of developmental time, although this can be circumvented by a careful analysis of external and internal structures in parallel. We further present new crown formation times for two unerupted canines from South African Australopiths, which were found to form over a rather surprisingly long time (> 4.5 years). This approach provides tools for maximizing the recovery of developmental information in teeth, especially in the most difficult cases.


Introduction

Scholars have long recognized the wealth of information preserved in dental hard tissues. Tooth microstructure has been used to study developmental defects, tooth formation times, and age at death (reviewed in [13]). Further, a strong correlation between dental development and important life history events has been suggested in human and non-human primates (reviewed in [47]). Life history can be described as series of developmental milestones in an individual’s life including birth, the duration of breast-feeding or weaning, as well as more complex aspects such as inter-birth intervals and lifespan; these events happen at different times and over different durations following species.

In order to determine growth periods and/or age at death of juveniles using a direct measurement independent of modern human or great ape standards, long-period incremental growth lines that course through the enamel (Retzius lines) and manifest on crown surfaces (perikymata) are the most commonly counted developmental features. Their periodicity however needs to be determined for calculating the crown formation time. This is achieved by counting the daily prism cross-striations between two successive long-period lines. This process is conventionally done by analyzing slices through the main cusp axis of the tooth under a microscope, and requires physical sectioning of the tooth. Other methods rely solely on the counts of cross-striations for determining age at death [810], but these approaches are extremely difficult to apply on fossils due to the high variability in the visibility of their enamel microstructure. In either case, these techniques are destructive, and are thus only rarely applied to valuable fossil specimens.

Retzius [11] was one of the first to observe long-period incremental growth lines in enamel on thin sections of vertebrate teeth, increments which have since been widely defined and described, especially in primates [1216]. Their etiology is still poorly understood [15,1721], although several explanatory hypotheses have been proposed to account for this growth disturbance: systemic origin [8,13,22], shift in the synchronization of different cellular biological rhythms [17] or even gastric disturbance (indigestion) caused by periodic feast days [23]. Structural variants of regular Retzius lines have been described, such as staircase-type Retzius lines [18] and S-shaped Retzius lines [24] while other lines running parallel to the developing front have been documented, e.g., irregular striae [19], pathological Wilson bands [2527], and chevron lines [28]. When Retzius lines reach the outer enamel surface (OES), they manifest as continuous wave-like structures around the circumference of the crown [1215,17,29]. First named perikymata by Preiswerk [30], these features are separated by grooves or imbrication lines following Pickerill’s description [31]. As early as 1854, Kölliker was one of the first to draw attention to the continuity between perikymata and Retzius lines which has then been confirmed by others [12,15,17,2933]. Newman and Poole [17] and others [34,35], reviewed in [3638] established the parallel between incremental growth features in enamel (Retzius lines, perikymata, cross-striations) and those existing in dentine (Andresen lines, periradicular bands, von Ebner lines). Dean [37] reports that periradicular bands are difficult to see because they are often packed close together, are shallower than perikymata, and lie beneath cementum, although they have been employed for reconstructions of developmental time [39]. Stress events often manifest as circumferential bands known as linear enamel hypoplasias on crown surfaces, in addition to irregular accentuated lines within the enamel (reviewed in [4042]).

Determination of the timing of these defects may provide insight into stress, and may facilitate matching synchronously-developing teeth within a dentition (e.g., [41,4346]). However, quantifying microscopic incremental features and documenting stress timing is often a serious challenge, since the clarity of Retzius lines within teeth is variable, and precise quantification of perikymata and hypoplasias is complicated by variation in their expression and the curvature of tooth surfaces [20,42]. Growth lines in teeth are conventionally observed from naturally-fractured teeth and histological (thin) sections under transmitted light microscopy. Nonetheless, perikymata counting from well-preserved tooth surfaces has the advantage of being non-destructive [47] and can be performed under a stereomicroscope or using scanning electron microscopy (SEM) with some preparation of the specimen (e.g., high resolution casts and sputter coating) [41], (reviewed in [48,49]]. Attempts for developing semi-automatic counting techniques of perikymata on isolated teeth with well-preserved outer enamel surfaces have so far demonstrated only limited success [50,51].

Histological assessments of incremental features often rely on physically-sectioned teeth, which limits material available for study, or on high-resolution impressions of tooth surfaces, which require accessible tooth germs or erupted teeth with well-preserved lateral surfaces. However, over the last decade, developments of propagation phase contrast X-ray synchrotron microtomography (PPC-SR-μCT) have permitted virtual histology, or non-destructive imaging of the internal aspects of dental tissues (e.g., [6,5254]). In addition to being non-destructive, PPC-SR-μCT data may be used to produce high resolution 3D models of OES, as well as virtual section planes of various orientations and thicknesses, which improve the visibility of growth lines (e.g., [6]). Propagation phase contrast scans reveal the interface between two materials as a double fringe (adjacent black and white halves, with the white being on the side of the denser material), which yields sharper surfaces than absorption scans. Importantly, the real physical interface between two materials is at the exact junction between these white and black fringes.

In brief, materials are characterized by their index of refraction (n) which is a combination of attenuation (β or μ) and phase shifts (δ), as n = 1- δ + iβ. Pure absorption occurs when the distance ‘D’ between the scanned object and the detector equals zero. In the case where transverse coherence of the beam is sufficient, such as in third generation synchrotron sources, when D increases but remains in the near field of the Fresnel diffraction region, phase dominates over absorption and the phase shifts resulting from the different densities of the matter become visible in the so-called ‘edge-detection regime’ [55,56]. In conventional CT, D remains small enough so that the phase is generally not detectable, except for small objects imaged at a resolution close to 1 μm, with average energies typically lower than 20 keV (see Figure 2 and the corresponding text in [57], and Figure 1 in [58]). The fringes related to the phase shifts represent one of the main advantages of synchrotron virtual histology for studies of dental development, as the phase contrast sensitivity to small density differences is orders of magnitude stronger than that of absorption (e.g., [52,59]). This approach facilitates the non-destructive observation of incremental growth lines in teeth, and yields exceptional microscopic clarity of surfaces and interfaces due to the strong phase fringes associated with these structures.

Here we describe and validate a new application of 3D virtual histology that enhances the identification and quantification of long-period growth lines on the OES, and stress pattern on both the OES and the enamel-dentine junction (EDJ). This is an alternative approach to conventional methods to determine tooth crown formation times and developmental defects, especially in the case of teeth with altered surfaces. This 2D-3D approach has been used to determine the age at death in juvenile dentitions that cannot otherwise be studied. This is the case for unerupted teeth that are not observable with other techniques, specimens inaccessible using classical histology due to conservation issues or 2D synchrotron paleohistology due to poor preservation of internal structures. The techniques presented in this paper have been developed during a broad comparative study involving Plio-Pleistocene juvenile hominins [60,61] and of the MH1 Au. sediba holotype [6264]. In the latter case, this combined 2D-3D approach has yielded age at death and overall dental development characterization despite poorly preserved external and internal structures. The goal of this paper is neither to challenge nor to solve potential methodological problems of previously published values of long-period line counts performed on teeth with good surface quality that are presently taken as references for comparison with our own results, but rather to propose new approaches to investigate specimens that would be inaccessible with other techniques.
The combination of 2D virtual histology and 3D high quality rendering of dental surfaces and interfaces facilitates detailed studies of fossil dentitions by enabling the use of any single fragmentary piece of information in a global approach. We present two case-studies of the lower canines of MLD2 (still enclosed in its crypt) and StW151, and we calculate their crown formation times. By maximizing the amount of information obtainable from rare and precious fossil specimens, this approach will allow us to better understand the evolution of human life history.


Images (they're fantastic!):


Fig 1. 3D Phong rendering and colored light system. Principle of the 3D Phong rendering illustrated with the URC of MLD11-30. Illumination of the 3D model simultaneously by two light sources (LS1 and LS2), each composed of three components (three first columns): ambient, diffuse and specular. Each of the three rows (left half of the picture) shows the individual effect of each component. The combination of all light components is presented in the fourth column. LS1 (middle row) employs a white hue and is oriented in a perpendicular direction to the computer screen (viewer’s perspective—labial side of the crown). Light source 2 has a low white ambient (5 in VGStudio MAX 2.2), an orange diffuse light of moderate intensity (35) and a pale blue specular component with a tenfold higher intensity than the orange light (about 200). Combined with LS1, LS2 is oriented from the top (for taking a first set of images during the rotation of the tooth when mounting a multiple view plate, see S1 Fig), and then from the bottom (second set of images, same conditions) to light the 3D model with a low angle incidence to make topographical and densitometric details more visible. Both sets of images were then combined in Adobe Photoshop to enhance and sharpen topographic details with a mask of high frequency reinforcement. This operation involved taking the top-light image and subtracting structures smaller than 20 pixels that were also present in the bottom-light image (low frequencies), resulting in the combination of unique details from each direction in the final 3D model (far right).


Fig 2. Topography and fine variation in density at the EDJ. Renderings of the EDJ of the ULC of StW151, with two white lights sources (default in VGStudio MAX 2.2). (A) The tooth rendered with ‘ScatterHQ’, which reveals only subtle density variation (gray values) at the EDJ. (B) The EDJ rendered with ‘Phong 3D’ and the ‘Normalize gradient’ commands; this renders only the topographical details of the EDJ surface, and omits shades related to density variation.


Fig 3. 3D rendering of the unerupted LLC of MLD2 showing perikymata. The unerupted MLD 2 LLC in its alveolar crypt, which filled with matrix during fossilization. Retzius lines could not be revealed in the virtual histological data, in spite of changing thickness and orientation of the virtual 2D slice, the two thick lines are likely parts of ring artifacts (A). Despite continuous contact between the OES and the sediment filling the crypt, and the noisy nature of the fringes at the OES, the enamel surface could be successfully segmented and rendered (B), revealing countable perikymata almost all the way from the cusp tip to the cervix. Linear enamel hypoplasias are also apparent encircling the tooth crown.

 
 
Fig 4. Enamel hypoplasia matching in the MLD11-30 URI2 and URC. Matching of the URI2 and URC of MLD11-30 based on linear enamel hypoplasias.  On the left-hand side, both teeth are shown in natural proportions: the incisor (left) is smaller than the canine (right). The transformation on the far right was created by enlarging the incisor to be the same size as the canine, so that its hypoplasia and perikymata pattern matches the canine. S2 Movie shows the procedure for matching.


Fig 5. Retzius lines and perikymata doubling in the LLI1 of KB 5223.  Virtual histological slices (grayscale images) showing subdivisions of Retzius lines (white arrows) in the LLI1 of KB5223 (labial view), and their corresponding expression as subdivisions of perikymata (white arrows) on the outer enamel surface. The dotted lines show the fidelity of 2D – 3D matching through horizontal alignment. The position of the labiolingual 2D section is indicated on the 3D model by the green stripe. See S1 Supporting Information (Section II) for a discussion about this phenomenon related to taphonomical alteration (local demineralization).
 

Fig 6. Complementarity of 2D and 3D developmental information illustrated for StW151 LLC and MLD11-30 URC.  When calculating the crown formation time of StW151 LLC, we use Retzius lines on a 2D virtual slice in the cervical area, since the 3D model does not show clearly identifiable perikymata in that region (A). The cervix of the MLD11-30 LLC (B) yields the largest variation for both inter- and intra-observer counts (S2 Supporting Information, Tab “Average deciles”). This is due to the presence of unequal subdivisions of perikymata and a poor visibility of the perikymata at the very bottom of the cervix. The exact alignment between the 2D slice (its thickness explains that the alignment appears not exact with the 3D, although it is) and the 3D model of the OES is shown by pink lines at the cervix and at a hypoplasia for StW151, and at the bottom edge of a fracture for MLD11-30.
 

Fig 7. EDJ matching in multiple teeth of a single individual.  The 3D models of the EDJs of the LRC (A) and LRM1 (B) of KNM-KP34725 are matched in (C) by superimposing a portion of each EDJ (red frames and arrows) following the stress pattern as a barcode on the EDJ and root surface (colored arrowheads). This is done with Abode Photoshop by rotation, translation, isometric scaling, perspective and skewing of the fragment of EDJ of the canine onto the fragment of molar that is taken as a reference. (The two apical thirds of the roots of the molar were out of the field of view during scanning, thus the roots appear to be cut in an abrupt manner.) 
 

Fig 8. Unwrapped external surface of the StW151 ULM1.  Virtual unwrapping of the outer surface of the StW151 ULM1 obtained from the concatenation of a single pixel-wide frames saved during the complete rotation of the tooth around its long axis. On the left side of the unwrapped surface, the tooth is viewed from the buccal side, and the mesio-buccal and disto-buccal roots can be seen in the front, while the lingual root is visible in the back. The lingual view, at the right of the unwrapped tooth, shows the lingual root in the front, and the two buccal roots in the back. Since not all points are at the same distance from the center of rotation of the tooth, some parts of the tooth can be distorted: the furcation area of the buccal roots is stretched in the middle of the unrolled tooth. Perikymata, periradicular bands and hypoplasias are visible and can be tracked across the tooth. Images are not to scale.
 

MLD2 and StW151: surprisingly long-forming canines
Synchrotron imaging has the considerable advantage here of yielding access to unerupted in situ teeth. Crown formation time of both MLD2 and StW151 appear to be relatively long (> 4.5 years, Table 1) compared to values published for other specimens (e.g., [48]). Our values fall at the lower end of the range reported for female great apes in [68]. The perikymata count could be comparable to that observed on the ULC of the ARA-VP-6/1 holotype of Ardipithecus ramidus that is 193 perikymata yielding a crown formation time of 4.29 or 4.82 years following the estimation of its periodicity at 7 or 8 days [78]. We would like to underline here the high variability induced by the use of periodicity ranges in the final results. This parameter has indeed been shown to be highly variable even within one single taxon [61]. The direct determination of long-period line periodicity represents a major advantage of developmental studies performed using PPC-SRμCT [6,46]. Therefore, crown formation times should be considered extremely carefully when no direct determination of periodicity is available. Moggi-Cecchi et al. [79] report a shorter crown formation time for the StW151 LLC. We suspect that their perikymata counts in the cervical area have been underestimated, as we realized that Retzius lines were much easier to identify on the 2D virtual slice than perikymata on the cervical area of the OES of this tooth (S4 Supporting Information). Nonetheless, other instances of canine crowns developing over an even longer period of time have been documented for Plio-Pleistocene South African specimens [61]. Since these crowns were not accessible or were too damaged for direct observation (both external and internal structures), these specimens could not be fully quantified from virtual 2D slices. The approach applied in the current study demonstrates how developmental information may be retrieved from unerupted teeth, even in the case of poor preservation, by combining multiple observational techniques of PPC-SRμCT. The crown formation time of the MLD2 LLC is strikingly long, and could be interpreted as resulting from errors in the perikymata counts, because of the complex surface topography of this tooth. Nevertheless, the fact that the StW151 LLC presents a crown formation time at least as long as that of MLD2, and that multiple counts of the MLD2 canine by three different observers end within a limited variability of results comparable to that of other well-preserved teeth, confirms our initial conclusion about the MLD2 LLC. Our results demonstrate that canine crown formation time in South African Australopithecines and maybe early Homo (depending on the taxonomic attribution of StW151) can sometimes be far longer and more variable than expected from previously published studies. More extensive study is necessary to assess whether such long canine crown formation times may be related to taxonomical status, sexual dimorphism, or natural variability [70,68]. In future dental developmental studies involving PPC-SRμCT, not only should individual periodicity be directly determined as in previous studies [6,46] but also a special focus should be set on determining cuspal daily secretion rates in at least one anterior and one postcanine tooth. This would constraint the reported range and take into account taxonomic and anatomical (tooth class) variability.

Stress pattern and its 3D visualization on the EDJ interface
Stress in enamel and dentine are commonly used to match teeth across a dentition as synchronous events [14,8083]. Although odontoblasts secrete dentine slightly in advance of ameloblasts secreting enamel, this difference in time can be treated as negligible for general dental development studies [84]. For the first time, we reveal the stress pattern on the EDJ resulting from subtle variations of density and topography on both sides of this interface. This is possible because phase contrast reveals this information with high sensitivity in the black and white fringes at the interface between the two materials (S13 Fig). Although matching the EDJ (Fig 7) of several teeth does not yield temporal information, as the Andresen lines are rarely visible on the EDJ interface, it creates a relative chronology of stress events that then allows one to exploit any single usable piece of developmental information (periodicity, and number of perikymata, Retzius lines in enamel, Andresen lines in dentine) within that framework (Fig 9).

Fig 9. Direct correspondence of 2D and 3D developmental information.  Matching of the incremental pattern between the standardized developmental slice of the ULC of STS2 and the 3D models of its EDJ and OES. Retzius lines or accentuated lines in the enamel on the 2D virtual slice allows the matching of a stress on the EDJ and OES. The number of long-period lines is indicated in square brackets between the major stress events highlighted on the 2D and 3D models, providing a quantitative overview of the time elapsed between stress. The long-period line count was performed on a high resolution image of the 2D slice to ensure a high definition of the growth lines. Further developmental information for this individual may be found in [61]. 

Conclusion

The main advantages of the 2D-3D rendering protocol presented in this study are: (i) enhanced topographic and densitometric details of the OES and stress patterns on the EDJ; (ii) enhanced visibility of developmental structures from high-quality images allowing for reasonably consistent inter- and intra-observer agreement; (iii) accurate visualization of long-period growth increments in enamel and developmental defects using a combination of virtual histological 2D slices and 3D models; (iv) novel possibilities for visualizing surfaces of well-preserved teeth still in crypt; and (v) facilitation of the matching of stress patterns across an individual's dentition.
This 2D-3D combination rendering approach for visualization of dental surfaces opens up new possibilities for detailed developmental studies on exceptional fossil hominins with well-preserved partially complete developing dentitions. We however draw the attention on the impact that resolution and partial volume effect can have on demineralized areas in the enamel subsurface, when subdivisions of perikymata are observed on the 3D renderings. On the one hand, special care has to be taken to ensure reaching robust results based on perikymata counts derived from X-ray images. In the vast majority of cases, there is no possible mistake about recognizing real perikymata on PPC-SRμCT data. Further, it allowed for the first time to determine crown formation times of two unerupted early hominin teeth that would not have been fully accessible with any other technique. These results suggest that the short formation time conventionally expected for early hominin lower canine crowns may be too restrictive; the two specimens presented here showed development times of more than 4.5 years. Dental development in general should consider using direct determination of the individual’s periodicity to avoid reporting very wide ranges. In addition, future PPC-SRμCT-based developmental studies may improve by trying to measure systematically CuDSR, which would contribute to constrain even more the reported ranges for both crown formation times and age at death. This innovative approach is being employed to generate a comprehensive and permanent digital record of developmental information in invaluable and fragile fossil hominin specimens. These developmental data will be made freely available online and will thus facilitate future comparative studies.

Hominin Teeth: Phong 3D rendering and colored light sources applied


Tuesday, April 28, 2015

The grooves on the island of Gotland in the Baltic Sea: a neolithic lunar calendar


Göran Henriksson
Astronomical Observatory, Uppsala University, Sweden
(Link) pdf

Introduction

On the island of Gotland, in the middle of the Baltic Sea, there exist about 3,600 groove cut in the bedrock or on big stones.  They can be found on the ancient shores of lakes and in connection and in connection with the coastal settlements and finds of the Neolithic Pitted Ware Culture.  The grooves have a typical length of 50-110cm, width of 5-10cm, and depth of 1-10cm.  They follow closely a circular arc in both the length and width cross-sections (Fig. 1; 2).  The surface is very smooth and they must have been cut by a stable machine using quartz sand and water (Fig. 3).

Saturday, April 25, 2015

Genes Don't Cause Racial-Health Disparities, Society Does

Researchers are looking in the wrong place: White people live longer not because of their DNA but because of inequality.

Jason Silverstein
Apr 13, 2015
The Atlantic

Eurogenes Admixture results for Motala HGs, Stora Förvar 11 Mesolithic and Samara HGs

 














(Link) to the spreadsheet

(Link) to the blog post where "Davidski" has posted the spreadsheet in the comments section.

Note that Swedish Motala HGs mysteriously show 100% "EuroHG" Ancestry.  Maybe it's just me, but I don't think I've ever seen an Admixture run that consistently weights as 100% in a particular component at K=10 over multiple samples from the same population.  There is almost always some variation at low level between the samples.

Looking at some of the other data in this run, the Mesolithic sample, Stora Förvar 11, also from Sweden, is shown as having approximately 17.7% "North Caucasus" ancestry:

Summarizing the Stora Förvar 11 sample, components for > 5% on this K=10 Eurogenes Admixture run: 
 
"Early European Farmer": 8.3%,
"North Caucasus": 17.7%,
"EuroHG": 71.3%
 
This Stora Förvar 11 sample was found on Stora Karlsö, a small island off the west coast of the larger Swedish island of Gotland, in the Baltic Sea. The remains were dated to 7,500 to 7,250 years ago.  They were found in a late Mesolithic context.
 
In comparison, the Samara HG results on the same run are as follows:
 
Summarizing Samara HG components for > 5% on this K=10 Eurogenes Admixture run: 
 
"Early European Farmers": 0%,
"North Caucasus": 26.5%,
"Amerindian": 9.25%
"EuroHG": 64.2%

The Samara hunter-gatherer sample I0124 is from Samara, near the Volga River in Russia. The sample is dated to 5650–5555 BC.
 
So, at least on this Admixture run, it is quite apparent that "North Caucasus" ancestry was already established both in the Baltic Sea and on the Volga River in the Mesolithic.  The Samara_HG Sample and the Stora Förvar 11 are quite similar, as is the Karelia I0061 sample (which you can check for yourself by looking at the spreadsheet.)
 
The major difference is that the Samara HG sample has some Amerindian like ancestry that does not appear in Western Europeans. 
 
Looking at the Stora Förvar 11 and Karelia samples, it is obvious that there is no need to argue for mass migration from the Steppe during the Neolithic or Bronze Age to explain the "North Caucasus" component in modern European populations.   This component was already present in Northern European populations in the Mesolithic.
 
In any event, it would be a fool's errand to try to use estimates of the proportion of this "North Caucasus" ancestry in populations of the Neolithic and Bronze age to try to pinpoint the source of Indo-European languages in a Steppe specific Bronze Age population within the last 5,000 years.  This component was obviously already widely distributed all the way from Gotland to the Steppe by the Mesolithic.  (. . . As I have argued for the last four months.)
 
But, hey, some people are fools and ignore their own data . . . and want to get their papers published in Nature, Science and the Society for American Archaeology by inventing salacious scenarios to grab attention for their projects. The bar is sometimes low.  What else can I say?
 
Map of Northern Europe, showing the Island of Gotland.
 
Related Posts on this Blog:
 

Thursday, April 23, 2015

What I'm reading now: Coevolution of Composite-Tool Technology, Constructive Memory and Language

I guess I'm a little late to the party, but in any case, for the last few days, I've been enjoying this deeply considered multi-disciplinary paper from 2010 by Stanley Ambrose.

Coevolution of Composite-Tool Technology, Constructive Memory, and Language
Implications for the Evolution of Modern Human Behavior
Current Anthropology
Volume 51, Supplement 1, June 2010
(Link) open access

Abstract:  The evolution of modern human behavior was undoubtedly accompanied by neurological changes that enhanced capacities for innovation in technology, language, and social organization associated with working memory. Constructive memory integrates components of working memory in the medial prefrontal cortex to imagine alternative futures. Enhanced mental time travel permits long range strategic planning. Within this broadly conceived area of cognitive neuropsychology, I will focus on two stages of the evolution of cognitive faculties for planning. The first involves executing complex sequences of actions involving manufacture of multicomponent artifacts; the second involves enhanced planning through information sharing, which required the establishment of extended regional social interaction networks based on trust and cooperation. Both stages were probably accompanied by important innovations in grammatical speech.

Wednesday, April 15, 2015

World’s oldest stone tools discovered in Kenya

Science Magazine
Michael Balter
(Link)

SAN FRANCISCO, CALIFORNIA—Researchers at a meeting here say they have found the oldest tools made by human ancestors—stone flakes dated to 3.3 million years ago. That’s 700,000 years older than the oldest-known tools to date, suggesting that our ancestors were crafting tools several hundred thousand years before our genus Homo arrived on the scene. If correct, the new evidence could confirm disputed claims for very early tool use, and it suggests that ancient australopithecines like the famed “Lucy” may have fashioned stone tools, too.

Until now, the earliest known stone tools had been found at the site of Gona in Ethiopia and were dated to 2.6 million years ago. These belonged to a tool technology known as the Oldowan, so called because the first examples were found more than 80 years ago at Olduvai Gorge in Tanzania by famous paleoanthropologists Louis and Mary Leakey. Then, in 2010, researchers working at the site of Dikika in Ethiopia—where an australopithecine child was also discovered—reported cut marks on animal bones dated to 3.4 million years ago; they argued that tool-using human ancestors made the linear marks. The claim was immediately controversial, however, and some argued that what seemed to be cut marks might have been the result of trampling by humans or other animals. Without the discovery of actual tools, the argument seemed likely to continue without resolution.

Now, those missing tools may have been found. In a talk at the annual meeting of the Paleoanthropology Society here, archaeologist Sonia Harmand of Stony Brook University in New York described the discovery of numerous tools at the site of Lomekwi 3, just west of Lake Turkana in Kenya, about 1000 kilometers from Olduvai Gorge. In 2011, Harmand’s team was seeking the site where a controversial human relative called Kenyanthropus platyops had been discovered in 1998. They took a wrong turn and stumbled upon another part of the area, called Lomekwi, near where Kenyanthropus had been found. The researchers spotted what Harmand called unmistakable stone tools on the surface of the sandy landscape and immediately launched a small excavation.

More tools were discovered under the ground, including so-called cores from which human ancestors struck off sharp flakes; the team was even able to fit one of the flakes back to its original core, showing that a hominin had crafted and then discarded both core and flake in this spot. The researchers returned for more digging the following year and have now uncovered nearly 20 well-preserved flakes, cores, and anvils apparently used to hold the cores as the flakes were struck off, all sealed in sediments that provided a secure context for dating. An additional 130 pieces have also been found on the surface, according to the talk.

“The artifacts were clearly knapped [created by intentional flaking] and not the result of accidental fracture of rocks,” Harmand told the meeting. Analysis of the tools showed that they had been rotated as flakes were struck off, which is also how Oldowan tools were crafted. The Lomekwi tools were somewhat larger than the average Oldowan artifacts, however. Dating of the sediments using paleomagnetic techniques—which track reversals in Earth’s magnetic field over time and have been used on many hominin finds from the well-studied Lake Turkana area—put them at about 3.3 million years old.

Although very recent research has now pushed back the origins of the genus Homo to as early as 2.8 million years ago, the tools are too old to have been made by the first fully fledged humans, Harmand said in her talk. The most likely explanation, she concluded, was that the artifacts were made either by australopithecines similar to Lucy or by Kenyanthropus. Either way, toolmaking apparently began before the birth of our genus. Harmand and her colleagues propose to call the new tools the Lomekwian technology, she said, because they are too old and too distinct from Oldowan implements to represent the same technology.

Researchers who have seen the tools in person are enthusiastic about the claim. The finds are “very exciting,” says Alison Brooks, an anthropologist at George Washington University in Washington, D.C. “They could not have been created by natural forces … [and] the dating evidence is fairly solid.” She agrees that the tools are too early to have been made by Homo, suggesting that “technology played a major role in the emergence of our genus.”

The claim also looks good to paleoanthropologist Zeresenay Alemseged of the California Academy of Sciences here, a leader of the team that found cut marks on the Dikika animal bones. (At the meeting, another team member presented new arguments for the cut marks’ authenticity.) “With the cut marks from Dikika we had the victim” of the stone tools, Alemseged says. “Harmand’s discovery gives us the smoking gun.”

On aurait découvert les plus anciens outils au monde

Sciences et Avenir
4/15/2015

Plus vieux que le genre humain lui-même, ces outils sont datés de 3,3 millions d'années et ont été mis au jour au Kenya.

 
Le lac Turkana, au Kenya, photographié depuis la Station spatiale internationale par l'astronaute italienne Samantha Cristoforetti. C'est dans cette région que les outils ont été découverts.
© ESA/NASA/SIPA
 
ÉCLATS ET ENCLUMES

Les plus anciennes pierres taillées, exhumées à l’est du Kenya, auraient 3,3 millions d’années (voir notre carte plus bas) ! C'est ce que viennent d'annoncer des chercheurs new-yorkais lors du dernier meeting annuel de la société de paléoanthropologie, qui se tenait du 14 au 15 avril 2015 à San Francisco (Etats-Unis). Soit 700 000 ans de plus que les plus anciens outils connus à ce jour… Et leur découverte suggère que des ancêtres des hominidés façonnaient déjà des outils des centaines de milliers d’années avant que le genre Homo ne s’épanouisse. Car une découverte récente a eu beau vieillir le genre humain de 400.000 ans, le tout premier des Homo n’aurait que 2,8 millions d’années.

Les chercheurs auraient mis au jour plus d’une centaine d’éclats, de "cœurs" (ou blocs initiaux ) et d’ "enclumes" qui pourraient être la signature d’un atelier très archaïque de taille d’outils préhistoriques. Le tout reposait dans des sédiments datés de 3,3 millions d’années grâce aux techniques éprouvées du paléomagnétisme.

Comment ont été faits ces "premiers outils sculptures" ?

À partir d’une pierre, les hominidés débitent grossièrement des éclats qui leur serviront à couper, râcler, etc. Ils sculptent aussi de gros galets sur lesquels ils aménagent différents types de tranchants. Ce type primitif d'outils, connus sous le nom de "choppers", se retrouvent en Asie comme en Afrique et au Moyen-Orient. (Voir à ce sujet les dessins d’Eric Boeda dans Sciences et Avenir de Janvier 2008).
 
Les plus anciennes pierres taillées connues jusqu’à présent venaient de Gona en Ethiopie et étaient datées de 2,6 millions d’années. On parle à leur sujet  de "galets aménagés" ou encore d'industrie "Olduwayenne", parce qu'elles été trouvées pour la première fois, dès les années 1960, dans la gorge d’Olduvaï en Tanzanie. A l'époque, les chercheurs les attribuaient à l'Homo habilis (l'homme habile). Depuis, les spécialistes sont nombreux à penser que d'autres hominidés que nos ancêtres directs Homo auraient pu façonner des outils à leur main. En 2010, le site d’El Dikka, en Ethiopie, a ainsi livré des os vieux de 3,4 millions d’années - l'âge de Lucy et de sa famille australopithèque - portant des entailles de coupe, possiblement laissées par des outils, mais la découverte reste très discutée, comme l'explique le journaliste Michael Balter, qui a suivi la conférence de paléoanthropologie de San Francisco pour le site d’actualités de la revue américaine Science.

Fabriqué par le Kenyanthrope ?

Cette fois, c’est le site de Lomekwi, à l’est du lac Turkana, au Kenya, qui a livré de multiples outils " intentionnellement façonnés ", a expliqué Sonia Harmand de l’université Stony Brook à New York devant un parterre de paléoanthropologues. Or, ces trésors d’artefacts – "qui ne peuvent en aucun cas être le résultat de fractures accidentelles de la roche" selon la chercheuse – ont été trouvés à quelque pas du site qui avait déjà livré le curieux Kenyanthrope Platyops. Un ancêtre possible de l'homme, doté d’une drôle de face plate et vieux de 3,2 millions à 3,5 millions d’années. De là à imaginer que c’est cet hominidé qui a fabriqué les plus anciens outils au monde, il n'y a qu'un pas… La controverse ne fait sans doute que commencer. La découverte de Sonia Harmand, d'Hélène Roche (CNRS) et de leurs collègues devra faire l’objet d’une publication dans une revue de science spécialisée afin de pouvoir être discutée par les spécialistes du monde entier.

Les hominidés en Afrique entre 3 et 4 millions d’années:

Tuesday, April 14, 2015

A place in time: Situating Chauvet within the long chronology of symbolic behavioral development

Genevieve von Petzinger, April Nowell
Journal of Human Evoltion
Volume 74, September 2014, pages 37-54
 
Abstract
 
Since the discovery of the Grotte Chauvet (Ardèche, France) in the mid-1990s, there has been a debate regarding the accuracy of assigning this site to the Aurignacian period. The main argument stems from a perceived lack of agreement between the radiocarbon age of the imagery (>32,000 years BP [before present]) and its stylistic complexity and technical sophistication, which some believe are more typical of the later Upper Paleolithic. In this paper we first review the evidence for symbolic behavior among modern humans during the Aurignacian in order to explore the question of whether Chauvet's images are anachronistic. Then, using a database of non-figurative signs found in Paleolithic parietal art, we undertake a detailed comparison between Chauvet's corpus of signs and those found in other French Upper Paleolithic caves. While we conclude that there is substantial evidence to support an Aurignacian date for Grotte Chauvet, we also suggest that it may be time to revisit some of the cultural boundaries that are currently in use in Paleolithic archaeology.

Genevieve von Petzinger: Ice Age Rock Art Geometric Signs


Sunday, April 12, 2015

Anonymous Online Use of the Internet: Major Research Institutes Lack an Open Policy

Recently, I emailed the Broad Institute of MIT and Harvard, the Max Planck Institute, the University of Adelaide (Australia), and several other institutions regarding their online policy. 

My letter to each institute said [more or less] the following:

_____________________________________________________

Dear University/Institute X,

I have recently noticed the use of online blogs and forums which publish and disseminate non-public information on ancient DNA studies.   Some of this information is making its way into publication and into subliminal promotion of genetic ancestry testing companies from whom certain entities stand to profit.

Some of these forums may be authored or used by faculty and staff of your institution.

I would like to inquire about your policy regarding online use of pseudonyms by staff and professors.

Does the University/Institute X have an online ethics policy, and if so, is this policy publicly available?

Is the anonymous use of online pseudonyms allowed by professors at University/Institute X?

Is the anonymous creation and use of online blogs allowed by professors at University/Institute X?

Is the anonymous use of pseudonyms permitted by professors and researchers that collaborate with University/Institute X?

Are public and private research funding disclosure requirements being met with regard to these anonymous posts?

What policies and practices does University X employ to ensure ethical online behavior of University X researchers and their collaborators?

Thank you in advance for the information.

__________________________________________________


It's been several weeks.  No answer.  Apparently, none of these research institutes have an online policy, or they simply do not answer questions sent to them by members of the public.  This does leave me wondering whether major research institutes even care to request that faculty adhere to a code of ethics and to funding disclosure requirements when using the internet. 

Friday, April 10, 2015

"They Couldn’t Take My Soul": Anthony Ray Hinton on His Exoneration


Calling for “More than a Moratorium” on Human Germline Modification

Posted by Jessica Cussins on April 9th, 2015 on the blog Biopolitical Times, the blog of the Center for Genetics and Society
(Link)
 
Untitled Document Three high-profile scientific statements published in quick succession last month called for various kinds of moratoria on research on and/or use of gene-editing techniques that would result in genetically modified humans. The statements were prompted by reports that human sperm, eggs or embryos have already been created using such techniques in China and the US, and that papers are forthcoming.

These calls from within the scientific community are important, and highlight scientists’ desires not to have their discoveries used for means they condemn. But even among this limited group of scientists, there isn’t a clear consensus about what an appropriate solution looks like. The statement in Nature argues that in vitro research should be part of a moratorium because there is unlikely to ever be a justifiable therapeutic application that warrants the associated risks, while the statement in Science calls for extensive in vitro research to explore possible clinical applications straight away.

Jennifer Doudna, lead author of the Science statement and one of the pioneers of the CRISPR/Cas9 system, gave a lecture at UC Berkeley yesterday in which she raved about how popular the technique has become in the past couple years. She expressed her desire to spread the technology even more widely, beginning with a campus workshop this summer to teach students how to use it themselves. It’s not clear, however, if Doudna’s vision for a free and open CRISPR future will pan out given the heated patent fights already stirring up.

In reality, scientists have the most to gain from the development of these technologies (whether for good or for ill), and for this reason alone are probably not the right people to be guiding international policy. Writing in The Guardian, science, technology and society policy scholars Sheila Jasanoff, J. Benjamin Hurlbut, and Krishanu Saha make a strong case that “Human genetic engineering demands more than a moratorium.” They argue that merely waiting until we have more technical knowledge misses the point:
The answer to how we should act does not lie in the technological details of CRISPR. It is our responsibility to decide, as parents and citizens, whether our current genetic preferences should be edited, for all time, into our children and our children’s children… Decisions such as whether or not to edit human genes should not be left to elite and invisible experts[.]
Patricia J. Williams, writing in The Nation, reminds us that so much more is at stake in the question of whether to genetically modify the human species than just the health of an individual resulting child.
As sociologist Nikolas Rose has observed, the very project of medicine seems to have shifted from a metric of health versus disease to one of ever-expanding perfectibility of the species itself… The post-War aversion to eugenics—the understanding that despite great variability from one human to another, no one life is worth more than another—has eroded.
Writing in The Hastings Center’s Bioethics Forum, Gregory E. Kaebnick reminds us of an important limitation of any gene editing technique at the moment:
[I]dentifying the correct genetic changes is the real issue, though, and CRISPR/Cas9 doesn’t even address this problem. In fact, no gene editing tool can solve the second problem, any more than a word processing tool can by itself solve the problem of how to write the next great American novel. To identify the “correct” genetic changes, we need to understand what the targeted gene does, but also how it interacts with other genes, and also how the genome interacts with environments. We’re not there.
And at Ivy Magazine, Jamie Metzl summarizes the dangers of human germline modification, including:
[P]lain hubris….When we tinker with systems we don’t fully understand, it is very likely we’ll make mistakes….A genetics arms race, especially if different societies have different ideas about the desirability of genetic selection and engineering….Start[ing] to see our children as consumer products.
Metzl invites readers to visit his website and read his novel Genesis Code, and notes that “This may be the most important issue of our lifetime, and yet it hasn’t entered into public consciousness."

These articles are welcome, and necessary, contributions to the public debate at a time when some “practical bioethicists” (all of whom have argued in favor of human germline enhancement) can see only “emotive panic” in the call for broad engagement with this consequential decision for the human future.

It is also nice to see stem cell biologist Paul Knoepfler take these transhumanist-leaning Oxford bioethicists to task for their “one-sided verbiage”:
So experimentally de novo creating designer babies with gene edits that the resulting genetically modified people could then pass along to future generations forever with unknown consequences is really not so different than say getting your vision corrected, stepping outside to smoke a cigarette, changing ones friends or allowing new generations to use the Internet?
I don’t think so.
Other scientists continue to be vocal critics, too. Eric Lander, founding director of the Broad Institute of MIT and Harvard, told C. Simone Fishburn of BioCentury that there is no therapeutic application he can think of that would justify gene editing in human germline cells.
Huntington's patients are heterozygous; 50% of the embryos are just fine, so you can use IVF. There's no case for using germline gene editing in Huntington's because we have a simple technology for people with the disease… We need to truly ban this from a moral standpoint.
Amazingly, despite such widespread disapproval for barreling ahead with this level of manipulation of future humans, it seems that commercial ventures have already been established to utilize precision gene editing techniques. OvaXon is a joint venture between OvaScience and Intrexon that promises to develop “new applications to prevent the transmission of inherited diseases by gene-correcting egg precursor cells for applications in human and animal health.”

A sentence from the article in The Guardian is worth repeating: “Knowing science does not teach us how to live well with its power.” The increasing collapse of barriers between scientific endeavor, commercial enterprise, and careerist aspiration mean that we can no longer casually defer to scientists as voices of objectivity. Moving forward, we desperately need to broaden the conversation about the desirable uses of this technology to include students and teachers, public health workers, reproductive and disability and racial justice advocates, concerned members of the public, and more. There is surely as much to learn and consider about the social and policy implications of germline modification proposals as about their technical details.
Previously on Biopolitical Times: