Tuesday, July 29, 2014

Kotz-a-tó-ah, Smoked Shield, Distinguished Warrior

   Kotz-a-tó-ah, Smoked Shield, a Distinguished Warrior
   Painting of George Catlin, painted 1834
" . . . another of the extraordinary men of this tribe [Kiowa], near seven feet in stature, and distinguished, not only as one of the greatest warriors, but the swiftest on foot, in the nation. This man, it is said, runs down a buffalo on foot, and slays it with his knife or his lance, as he runs by its side!” (Catlin, Letters and Notes, vol. 2, no. 43, 1841, reprint 1973; Gurney and Heyman, eds., George Catlin and His Indian Gallery, 2002)
Smithsonian American Art Museum

Saturday, July 26, 2014

Chronology of the Grotta di Fumane

22 Jul 2014

Super post on the latest at the Fumane Cave. 

[A note to the authors of PalaeoChron, your blog doesn't feed!]

Friday, July 25, 2014

Comparative Performance of Two Whole Genome Capture Methodologies on Ancient DNA Illumina Libraries

, , , , , , , ,

(Link) open access


1. The application of whole genome capture (WGC) methods to ancient DNA (aDNA) promises to increase the efficiency of ancient genome sequencing.

2. We compared the performance of two recently developed WGC methods in enriching human aDNA within Illumina libraries built using both double-stranded (DSL) and single-stranded (SSL) build protocols. Although both methods effectively enriched aDNA, one consistently produced marginally better results, giving us the opportunity to further explore the parameters influencing WGC experiments.

3. Our results suggest that bait length has an important influence on library enrichment. Moreover, we show that WGC biases against the shorter molecules that are enriched in SSL preparation protocols. Therefore application of WGC to such samples is not recommended without future optimization. Lastly, we document the effect of WGC on other features including clonality, GC composition and repetitive DNA content of captured libraries.

4. Our findings provide insights for researchers planning to perform WGC on aDNA, and suggest future tests and optimization to improve WGC efficiency.

Fig. 1. WGC preferentially retrieves longer fragments in sequencing libraries. The read length distribution of pre-capture and post-capture libraries is shown for (a) double-stranded libraries (DSL) and (b) single-stranded-libraries. In (a) the x axis is split in <90 bp and >90 bp to adjust the scale and better illustrate the higher concentration of short reads in the pre-capture libraries (pink line) and the bias observed against these in capture experiments (green and blue lines) where longer fragments are preferentially retrieved. (b) Illustrates that the relative gain of shorter fragments obtained by building a SSL, is lost by capturing these types of libraries. The plot shown in (c) depicts the bioanalyzer profile of the bait libraries revealing that for WISC a wider tail is observed for longer baits, which might explain the stronger bias in favor of longer fragments by this particular method.


By comparing the performance of WISC and MYbaits in enriching for endogenous human DNA in ancient DNA extracts, we have been able to pinpoint potential factors influencing the dynamics of WGC experiments. The assessment of the subtle differences between both approaches to in-WGC enables us to draw insights on two variables that may the affect capture efficiency – bait length distribution and hybridization time. Our data furthermore provides insights into the effect of blocking agents, and first insights into the performance of whole-genome enrichment methods on SSL.

Although the experimental design and parameters used in this study seem to suggest an apparent benefit of one of the methods over the other, we strongly caution that batch effects could be playing an important role under these settings, hence discourage such interpretation from our results. Likewise, it is worth considering that even though there is a certain convenience in using a pre-made kit (MYbaits), our observations point to specific factors that can be optimized in the in house method (WISC) namely bait length distribution and hybridization parameters. Knowing the relevance of such parameters in WGC, gives users the flexibility of customizing their capture experiment to match the particularities of each aDNA library (see below).

Role of bait length distribution on the efficiency of WGC

Bait length distributions (Fig. 1c) differ mainly in that WISC shows a wider range and longer bait lengths. This in principle could account for the marked retrieval of longer reads in the WISC compared with the MYbaits experiments (Figs. 1a-b).  Following this rationale, the higher success of the latter could be explained by its ability to better access a fraction of the sequencing library, specifically that with the smaller fragments, while this fraction remains inaccessible due to the higher concentration of longer baits used in WISC. An important consequence of this feature was the poor and even unsuccessful outcome of capturing SSL, which include a higher fraction of short fragments, with either method. At the same time, this limitation reveals an important area for future development in the context of WGC experiments.

Although there was a small, yet consistent, benefit in the MYbaits over the WISC, it would be rash to conclude that the MYbaits method always outperforms WISC.  These results were generated using a single batch of WISC bait versus a single batch of MYbaits. Given that (i) bait lengths will likely vary between batches as a result of initial template DNA fragmentation, and (ii) our hypothesis that bait length may play a key role in retaining shorter DNA fragments, we believe it is more than likely our results simply reflect the fact that in these batches tested the WISC bait were slightly longer than the MYbaits. Future studies that examine the role of bait length in capture success will be needed to further examine this hypothesis.

Wednesday, July 23, 2014

The Resettlement of Northern Europe

Felix Riede
The Oxford Handbook of the Archaeology and Anthropology of Hunter-Gatherers
Edited by Vicki Cummings, Peter Jordan and Marek Zvelebil
Print Publication Date: April 2014


As the climate began to ameliorate after the last Ice Age, pioneer plants, animals, and people began to resettle northern Europe. The recolonization of the North European Plain and the maritime and mountainous landscapes of Scandinavia is associated with variants of the Magdalenian techno-complex. Structured by the successive maturation of landforms as well as by a number of catastrophic environmental changes, this process took the form of a series of colonization pulses followed by contractions and renewed colonization efforts. With the introduction of important new technologies such as the bow and arrow, watercraft, and fishing technology as well as domesticated dogs, this demographically and environmentally dynamic period saw the expansion of the geographic as well the behavioural dimensions of the hunter-gatherer niche. Underwritten by extensive mobility, trade, and exchange networks, these forager populations were able to explore and settle even the most remote parts of Arctic northern Europe early during the Holocene.

Recent developments in the study of the Upper Paleolithic of Vasco-Cantabrian Spain

Lawrence Guy Straus
Quaternary International
4 June 2014
(Link) (not open access)


This is an updated review of recent (post-2004) developments in the study of the rich Upper Paleolithic (40–10 uncal. ka) record from the Spanish “wing” of the classic Franco-Cantabrian culture area, composed of the provinces of Asturias, Cantabria, Vizcaya, Guipúzcoa and northern Navarra. Numerous new/ongoing excavations, radiometric dating assays, paleoenvironmental, artifact and faunal analyses are summarized here and their implications for understanding the Middle–Upper Paleolithic transition and the succession of anatomically modern human adaptations in this narrow, mid-latitude strip bounded to the north by the Gulf of Gascony and to the south by the Cantabrian Cordillera. Constants in this record are the balance between regionally distinctive characteristics (in terms of ecology, faunas, artifacts, subsistence and art) and the reality of connections to the Upper Paleolithic cultures of France and the rest of Iberia; the role of the region as a glacial-age refugium; the fundamental continuity of human settlement with movements between the coastal lowlands and the adjacent montane interior; the intensification of subsistence through situational specialization and overall diversification, with periods of intensive demographic and environmental stress; underlying facts of lithology and the differential availability and utilization of flints and non-flint raw materials for different types of tools; the demographically critical role of intra- and extra-regional social networks within the context of valley-defined local band territories. The review proceeds along the lines of traditionally defined cultural traditions: Aurignacian sensu lato, Gravettian, Solultrean, Magdalenian and Azilian, although it is recognized that these are archeological constructs and that there is both considerable variability within each of these concepts and a considerable degree of similarity cross-cutting all of them.

Tuesday, July 22, 2014

Dusk at a small lake, Lassen Volcanic National Park

Dusk at a small lake, Lassen Volcanic National Park, California
Nurse's Song

When the voices of children are heard on the green,
And laughing is heard on the hill,
My heart is at rest within my breast,
And everything else is still.

‘Then come home, my children, the sun is gone down,
And the dews of night arise;
Come, come leave off play, and let us away
Till the morning appears in the skies.’

‘No, no, let us play, for it is yet day,
And we cannot go to sleep;
Besides, in the sky the little birds fly,
And the hills are all cover'd with sheep.’

‘Well, well, go and play till the light fades away,
And then go home to bed.’
The little ones leapèd, and shoutèd, and laugh'd
And all the hills echoed.

Sunday, July 20, 2014

Margaret Hamilton, Mathematician and Computer Scientist, Played Key Role in Space Program



Hamilton as Lead Apollo Flight Software Designer
(Link) Wikipedia
(Link) NASA Office of Logic Design
Margaret Hamilton (born 1938) is an American former NASA scientist, and founder and CEO of software development company Hamilton Technologies, Inc. At NASA she was Director of the Software Engineering Division of the MIT Instrumentation Laboratory, later the Charles Stark Draper Laboratory, which played a key role in the success of the Apollo space program.

NASA Research

At NASA Hamilton was responsible for helping pioneer the Apollo on-board guidance software required to navigate to/from and land on the moon, and its multiple variations used on numerous missions (including the subsequent Skylab.) She worked to gain hands-on experience during a time when computer science and software engineering courses or disciplines were non-existent.

In the process, she produced innovations in the fields of system design and software development, enterprise and process modelling, preventative systems design, development paradigm, formal systems (and software) modelling languages, system-oriented objects for systems modelling and development, automated life-cycle environments, methods for maximizing software reliability and reuse, domain analysis, correctness by built-in language properties, open-architecture techniques for robust systems, full life-cycle automation, quality assurance, seamless integration (including systems to software), distributed processing systems, error detection and recovery techniques, man/machine interface systems, operating systems, end-to-end testing techniques, and life-cycle management techniques.

These in turn led her to develop concepts of asynchronous software, priority scheduling, and man-in-the-loop decision capability, which became the foundation for modern, ultra-reliable software design.

Apollo 11

Preventing an abort of the Apollo 11 mission has been attributed to her work. Just three minutes before the Lunar lander reached the Moon's surface several computer alarms were triggered. The cause of the alarms was an overload of incoming to the Apollo Guidance Computer (AGC). Due to its robust architecture, the computer was able to keep running, as the Apollo onboard flight software was developed using an asynchronous executive so that higher priority jobs (e.g. important for landing) could interrupt lower priority jobs. A 2005 re-analysis concluded that a hardware design error in the rendezvous radar provided the computer with faulty information even while in standby mode.

Margaret Hamilton, on the design of the Apollo 11 Guidance Computer software:
". . . the computer was being asked to perform all of its normal functions for landing while receiving an extra load of spurious data which used up 15% of its time. The computer (or rather the software in it) was smart enough to recognize that it was being asked to perform more tasks than it should be performing. It then sent out an alarm, which meant to the astronaut, I'm overloaded with more tasks than I should be doing at this time and I'm going to keep only the more important tasks; i.e., the ones needed for landing ... Actually, the computer was programmed to do more than recognize error conditions. A complete set of recovery programs was incorporated into the software. The software's action, in this case, was to eliminate lower priority tasks and re-establish the more important ones ... If the computer hadn't recognized this problem and taken recovery action, I doubt if Apollo 11 would have been the successful [M]oon landing it was.
—Margaret Hamilton, Letter to Datamation, March 1, 1971
Margaret's current activities as of February 2010 include fulfilling her role as the founder and CEO of Hamilton Technologies, Inc., a business developed around the Universal Systems Language (USL) which is in turn based upon her Development Before The Fact (DBTF) paradigm for systems and software design.
Margaret Hamilton has published 130 papers, proceedings and reports concerned with the 60 projects and 6 major programs in which she has been involved.

A selection:
  • M. Hamilton, S. Zeldin (1976) "Higher order software—A methodology for defining software" IEEE Transactions on Software Engineering, vol. SE-2, no. 1, Mar. 1976.
  • M. Hamilton (1994), “Inside Development Before the Fact,” cover story, Editorial Supplement, 8ES-24ES. Electronic Design, Apr. 1994.
  • M. Hamilton, Hackler, W.R.. (2004), Deeply Integrated Guidance Navigation Unit (DI-GNU) Common Software Architecture Principles (revised dec-29-04), DAAAE30-02-D-1020 and DAAB07-98-D-H502/0180, Picatinny Arsenal, NJ, 2003-2004.
  • M. Hamilton and W.R. M. Hackler (2007), “Universal Systems Language for Preventative Systems Engineering,” Proc. 5th Ann. Conf. Systems Eng. Res. (CSER), Stevens Institute of Technology, Mar. 2007, paper #36.

Forty Five Years Ago Today

David Woods, video editor
(his books)

Apollo 11 Lunar Surface Journal, The First Lunar Landing
Corrected Transcript and Commentary Copyright © 1995 by Eric M. Jones
All rights reserved.

Blog notes:

The first moon landing was forty five years ago, today.  As a child, I watched many of the moon landings and was fascinated with the details of the radio communication.  In this video, you can hear the challenges the Apollo 11 mission faced with radio communication and with different kinds of background noise.  (Some of it is also engine noise.  Today, with radio and telephony, you rarely hear radio noise because it is filtered out using digital and analog filters and other noise and error rejection schemes.)

For most of the descent, the Eagle lunar lander is controlled by the flight computer, the Apollo Guidance Computer (AGC), which among other things, is fed data by a radar system which can "see" the lunar surface. 

The full transcript of the lunar descent is available at the NASA site Apollo 11 Lunar Surface Journal, The First Lunar Landing (see above for the link).

The video starts at 102:32:35 into the transcript.

At about 5:17 into the video, or 102:38:04 into the transcript, you can hear Aldrin say "we got good lock on", meaning that the radar and AGC have acquired information about the lunar surface and are flying under computer control with the radar information.

The "P" annotations on the video refer to the computer programs that are being run during the descent.  The AGC programs were:

P63 - Landing maneouver braking program
P64 - Landing maneouver approach phase
P65 - Landing phase - auto
P66 - Rate of descent landing
P67 - Manual landing phase

From the Apollo Guidance Computer wiki page:

At about 5:40 in the video, "Buzz Aldrin gave the Apollo Guidance Computer (AGC) the command '1668' which instructed it to calculate and display DELTAH (the difference between altitude sensed by the radar and the computed altitude). This added an additional 10% to the processor work load causing executive overflow and a '1202' alarm. After being given the "GO" from Houston Aldrin entered '1668' again and another '1202' alarm occurred. When reporting the second alarm Aldrin added the comment "It appears to come up when we have a 1668 up". "

"Luckily for Apollo 11, the AGC software had been designed with priority scheduling. Just as it had been designed to do, the software automatically recovered, deleting lower priority tasks including the '1668' display task, to complete its critical guidance and control tasks."

"The problem was not a programming error in the AGC, nor was it pilot error. It was a peripheral hardware design bug that was already known and documented by Apollo 5 engineers. However because the problem had only occurred once during testing they concluded that it was safer to fly with the existing hardware that they had already tested, than to fly with a newer but largely untested radar system. In the actual hardware, the position of the rendezvous radar was encoded with synchros excited by a different source of 800 Hz AC than the one used by the computer as a timing reference. The two 800 Hz sources were frequency locked but not phase locked, and the small random phase variations made it appear as though the antenna was rapidly "dithering" in position even though it was completely stationary. These phantom movements generated the rapid series of AGC cycle steals."

Again at about 9:30 into the video, there are low priority alarms, '1201' and '1202', which are again over-ridden by the AGC.  The AGC continues to control the flight profile, processing high priority tasks, and ignoring low priority tasks.

At 10:30 into the video, Armstrong takes the AGC out of the controlled P64 approach phase program and into a P66 rate of descent manually controlled landing.  He pitches the profile of the Eagle forward, to maintain speed, in order to fly across Crater West boulder field.  Once across the boulder field, at about 11:05, he pitches back to slow down.

They land with 20 seconds of fuel remaining.