Academic publishing: a case study

Humans: from the beginning is a single-volume guide to the whole of the human past, from the first apes to the first cities (for more information, go to www.humansfromthebeginning.com). It took me nearly five years to research and write, and my intention was to release it initially as an eBook on the Amazon Kindle platform (I may eventually also release it as a print-on-demand paperback but currently have no plans to do so). To produce an eBook from my source files was certainly not going to be a trivial task – the work as a whole ran to around 250,000 words in 32 chapters, together with an introduction and a number of maps, infographics and plates and illustrations. In addition, each chapter was comprehensively referenced. Although not a textbook as such, Humans: from the beginning draws extensively on journal articles and other academic literature, and each source used was properly cited using Harvard-Anglia referencing.

In this post, I will document the steps I took to turn my source files into an eBook meeting the same standards of production values and professionalism as an academic book produced by one of the major publishing houses. Please note that the work is a case study rather than a comprehensive guide. Obviously no two books are alike, and not all the material here will necessarily be relevant to your needs. Conversely, you may find that some of your needs and questions are not directly addressed. If so, however, there should be enough material here to point you in the right direction. Please also note that a basic knowledge of HTML and CSS is assumed.

Becoming a micropublisher

The basic questions I needed to address were:

1. How to ensure that my self-published eBook was as professional in its production values as any produced by a major publishing house;

2. Mastering the basics of producing an eBook for the Kindle platform;

3. How best to use the eBook format to provide ease of access to the roughly 1,500 academic sources my book cited;

4. How else I could take advantage of the eBook format by offering features not available in a traditional book;

The importance the first of the above cannot be overstated. We live in a world in which self-publishing has finally come of age, liberating authors from the often frustrating task of trying to persuade publishers and/or literary agents to take them on. However, they now face a fresh set of problems in that they now have sole responsibility for tasks that could once be left to their publishers. The author is now in effect a micropublisher, and if they do not achieve the same standards of professionalism as a larger-scale publisher their work – however good – will be unlikely to be taken seriously.

The first and most obvious requirement for a book is a good book cover. This should not be daunting; my book featured a stone hand-axe superimposed on a horizon over which dawn is breaking. The breaking dawn represents the long, slow rise of our modern world; the hand-axe is a stone tool of a type that remained in use more or less unchanged for one and a half million years. In many cases, things need not even be that complicated. For this work I selected a simple textured background, available from the Amazon Cover Creator.

The next step was to obtain an ISBN Number for my book. Although this is not obligatory for an Amazon Kindle book, I felt it would be advisable. Large-scale publishing houses do not release books without ISBN numbers, as a micro-publisher I wanted to do the same. In the UK, ISBN numbers are the responsibility of the Nielsen ISBN Agency (please note that their site is a bit temperamental with some browsers). The minimum purchase is a block of ten numbers for a price of £132.00 inclusive of VAT. This might sound like overkill, but bear in mind that if do intend to release your book as a paperback as well as an eBook, you will require an ISBN number for each format. Academic non-fiction is frequently re-issued as new editions, each of which will also require a fresh ISBN number.

You also need to give a name to your publishing house. Note that this is a purely a label and not a limited company: you do not have to register anything with Companies House. However, you do need to choose a name that does not conflict with that of any other publishing house. It is also advisable to steer clear of names suggesting an association with well-known organisations or individuals. “Beckham Books” might sound catchy, but unless you happen to share your surname with the former England footballer it is probably best avoided. A Google search should confirm whether your chosen name is likely to be acceptable, but Nielsen has the final say.

I also registered web domain names for my book title and for the name of my publishing house. I set up a promotional website for the book: this is a fairly straightforward non-self-hosted WordPress blog; the web domains www.humansfromthebeginning.com  and www.humansfromthebeginning.co.uk both redirect to it. The site itself features a brief biography of the author (i.e. myself), a preview extract and links to where the book may be purchased on www.amazon.co.uk and www.amazon.com (it’s worth noting that although I’m a UK-based publisher, the bulk of my sales have been in the United States).

Intellectual Property

Fail to respect the intellectual property of others and solicitor’s letters could start landing on your doorstep.

As noted above, my work was fully referenced in accordance with standard academic practice. I was also sparing in my use of exact quotes, preferring where possible to paraphrase. Exceptions were made when the quote was obviously intended by its author to be humorous; there I was careful to fully-attribute the quote in writing in addition to providing a citation. Although I did not do so in my book, be aware that quoting lines from songs or printed matter that are not out of copyright will require permission from the copyright holder.

My book included a number of photographic images and here I was careful to either i) obtain the permission of the copyright holder, or ii) ensure that it was available for use under Creative Commons. In the first instance, I actually used only one image which was licensed for use at a very reasonable fee. In all cases, I provided full attribution, identifying sources and copyright holders, with details of the relevant Creative Commons licences where applicable. A caveat is that you can come across items that should not have been listed under Creative Commons, for example photographs that have been taken in museums and other places where photography is not permitted or is for personal use only (the same applies, of course, to any photographs you might take yourself).

eBook Basics

Pretty well any of the remarks above could be applied to traditional books as well as eBooks, but before going any further into the details of how I converted the finished manuscript of Humans: from the beginning into an eBook, here is a very brief introduction to eBooks and how they differ from printed books. An eBook is a book-length electronic document comprising text and images that is readable on a computer, mobile device or dedicated e-reader (such as the Amazon Kindle). Many eBooks are electronic versions of printed books, but many (including mine) do not have a printed counterpart. Though many would argue that eBooks lack the charm of printed books, they do have a number of advantages. The most obvious is that large numbers of eBooks can be stored on a device no larger than a single printed book.

Other important advantages are:

1. An eBook does not require an index, as all text is searchable. To somebody like myself, who constantly needs to look up items in reference books, printed indices are a constant source of frustration as time and time again what I am looking for is either not in the index at all, or a listed page (often the only one) contains absolutely no reference to the required subject matter (the printed book equivalent of the dreaded 404 Not Found message). Furthermore, you can only look up subjects. If you want to look up a phrase you happen to remember as part of the text you want to find, there is no way to do so.

2. Navigation within an eBook is quick and easy. Instead of referring to the Contents for the page number of the desired chapter and then turning to that page, you can be taken there at a single click. While this might not seem like a big deal in itself, in a non-fiction eBook the same approach can be used to provide easy access to references, glossary items and visual matter.

3. The reader of an eBook is not stuck with the publisher’s choice of font and can select from a number of fonts. Text size, page colour, margin size and line spacing are also reader-selectable. It is actually possible for the publisher to mandate the choice of font in an eBook, but Amazon discourages the practice and I did not do so.

4. An important difference between a printed book and an eBook is that in the latter, the concept of the page number is completely meaningless. The amount of text displayed at any one time on an e-reader will depend on a) the physical size of the device and b) the choice of font size selected by the user.

There are two major eBook formats, the open EPUB standard and Amazon’s in-house MOBI/KF8. The Kindle e-reader, as one might expect, uses the latter format. Despite this, we need not concern ourselves greatly with MOBI/KF8, because Amazon provides a tool known as KindleGen that will convert an EPUB file to a MOBI/KF8 file. The output file, which has a file extension of .mobi, is Kindle-compatible. KindleGen can also accept files in HTML or XHTML, and Amazon recommends its use for publishers wishing to create Kindle books in-house.

Two quick and dirty practical exercises

As a preliminary exercise, I needed to familiarise myself with the basics of producing an eBook and getting it on to a Kindle. As a starting point, I downloaded the Amazon Kindle Publishing Guidelines, which are available as a .pdf file. Google ‘Amazon Kindle Publishing Guidelines’ to obtain the latest version of this document. I then downloaded and installed the KindleGen tool provided by Amazon (the procedure is explained in the publishing guidelines) and I also downloaded and installed Notepad++, a freeware file-editing tool with some very powerful features including the ability to run Regular Expression (RegExp) scripts. Throughout the conversion exercise I was using MS Word on a PC running under Windows 7.

The following is a quick and dirty practical exercise to put a mini-eBook onto a Kindle e-reader. Note that from now on I will use the term ‘Kindle e-reader’ to mean any device capable of reading a Kindle eBook. These include not just dedicated devices such as the Kindle Paperwhite and the Kindle Fire (the latter basically a customised Android tablet) but also iPhones, iPads, Android devices or laptops running the appropriate Kindle app or software.

For this exercise, you will require such an e-reader, together with an Amazon account. Your Kindle e-reader will have an email address in the format {my Kindle email address}@kindle.com. This will be the address you set up when you registered the device and you can remind yourself by going to the Amazon website and selecting Your Account -> Manage Your Kindle -> Manage Your Devices.

To convert a document and load it onto your kindle, you will need to use a slightly different email address: {my Kindle email address}@free.kindle.com. Simply email any small document (MS Word, .rtf or .html) to this address, putting ‘Convert’ in the subject. Conversion usually takes no more than a few minutes. You then will receive an email advising you that the conversion has been completed.

Go to Your Account -> Manage Your Kindle. In ‘Your Kindle Library’ you will see your newly-converted document at the top of a list of your Kindle documents. Assuming your Kindle e-reader is connected to the internet, your document should appear as downloadable to it (exactly how it is displayed depends on your device as the implementation varies from platform to platform). I found this exercise to be a useful introduction, but as I shall explain shortly, it is not suitable for producing a full-sized eBook. There is really only one way to accomplish this, and it is to use the KindleGen tool provided by Amazon. Here is a second quick and dirty practical exercise, this time using KindleGen for converting an HTML file.

Set up a directory on your PC and create a command line .bat file with the following command:

c:/kindlegen/kindlegen.exe {myfile}.htm>errors.txt

Running the command line file will generate the files {myfile}.mobi and errors.txt. The latter will contain one or two warning messages, because we are not at this stage converting a genuine eBook. However, the {myfile}.mobi can be read on a Kindle or Kindle-enabled device. Send the file to the {my Kindle email address}@free.kindle.com email address, and download it to your device as before. This might seem very simple, but now try exporting your lengthy manuscript from your word processor to HTML, converting it with KindleGen and trying to read the resulting .mobi file on your device. If your Word document contained a Table of Contents, this will appear as a series of hypertext links to the chapters of your book. The links will work – but they will be very slow. If you have kept each chapter of your book as a separate document (as I did) and haven’t at any stage combined them into a single massive manuscript (as I did periodically for test purposes and to circulate to interested parties) then there is no need to try this: just take my work for it).

Here’s why – eBook files are basically HTML files contained in a wrapper. Your eBook may be thought of as a website, and hypertext links work exactly the same way as they do on a website. Now imagine a website that held all its content on a single, massive page. Any hypertext linking within it would run pretty slowly. Of course, websites consist of many pages, with hypertext links typically taking you from one page to another. That is exactly how your eBook needs to be structured if your readers are to enjoy what Amazon term a ‘good reading experience’.

Preparing your manuscript for conversion to an eBook

As noted above, I kept each chapter of Humans: from the beginning as a separate MS Word document. The ‘manuscript’ to be converted into an eBook comprised MS Word documents for the 32 chapters, an introduction and a glossary, together with a title page, copyright notice, acknowledgements and attributions. The chapters and introduction (though not the glossary) were referenced using the MS Word citations tool. In addition there were maps, infographics and plates and illustrations. These I decided to keep separate from the main text on the grounds that a reader would find it easier to access them from a central index than would be the case if they were embedded in individual chapters. My task was to transform this into an EPUB document that could in turn be converted to the Kindle-compatible KF8 format with Amazon’s KindleGen tool.

The first step was to convert each Word document into an HTML file. MS Word provides a ‘filtered HTML’ export option from .doc and .docx files, but unfortunately this still produces a considerable amount of junk. Indeed, many books recommend simply copying the contents of each Word document into a flat text file. I feel that this is throwing out the baby with the bathwater, as you will lose all of your formatting in the process.

I created a series of styles to cover all aspects of formatting in each chapter – one each for chapter heading, section headings within each chapter, and body styles. I used the styles to handle indentation and before and/or after line spacing. I entirely eliminated the use of tabs, spaces and carriage returns to accomplish this. The result is that when exported to HTML, the body text of each document will comprise a series of series of paragraphs that lend themselves to formatting with cascading style sheets. In an eBook, as in a website, formatting is carried out using classes contained in a .css file.

The next issue I faced was references, of which my book contained large quantities. In an eBook, the reader should be able to look up a reference by simply clicking a hypertext link. They can then return by either 1) clicking a link on the reference that takes them back, or 2) using the ‘back’ function on their e-reader. The first method requires additional HTML coding and has the problem that it will always return the reader to the same point regardless of how many times the particular reference is cited in the text. As I was constantly citing multiple instances of references, I decided that the first method, though easier to implement, was actually the most suitable in my case.

While I was working on my book, I used Harvard-Anglia referencing (author(s), year; e.g. Smith, 2012) to save having to constantly look up what was being cited. However, the presence of large numbers of references cited in this style can interfere with the reading experience, so for the purposes of publication I switched to Nature referencing (as used in the science journal Nature), where the reference is assigned a number that refers to its entry in the bibliography. The references in my book are broken down by chapter, meaning that each chapter has its own bibliography. The methods I will describe apply to the referencing system I have just described, but they could be adapted for other systems if desired.

I first applied a style to the references. This served two purposes: firstly, the formatting could be again controlled through the cascading style sheets, and secondly it facilitated the attachment of hypertext links. To accomplish this, I created the following Word macro:

Sub ApplyCitationStyle()

Dim stylename As String

Dim exists As Boolean

Dim s As Style

Dim fld As Field

stylename = “In-Text Citation”

‘Check if the style already exists.

exists = False

For Each s In ActiveDocument.Styles

If s.NameLocal = stylename Then

exists = True

Exit For

End If

Next

‘If the style did not exist yet, create it.

If exists = False Then

Set s = ActiveDocument.Styles.Add(stylename, wdStyleTypeCharacter)

s.BaseStyle = ActiveDocument.Styles(wdStyleDefaultParagraphFont).BaseStyle

s.Font.Superscript = True

End If

  

‘Now that the style really exists, select it.

Set s = ActiveDocument.Styles(stylename)

   

‘Apply the style to all in-text citations.

For Each fld In ActiveDocument.Fields

If fld.Type = wdFieldCitation Then

fld.Select

Selection.Style = s

End If

Next

End Sub

The macro formats the references with a style called “In-Text Citation”, which results in them being displayed as superscripts. It isn’t actually necessary for it to do so, as you will have to implement superscripting with your cascading style sheets. The important point is that the references are now spanned by the style.

For each chapter document, I saved a copy and switched from Harvard-Anglia to Nature referencing before running the ApplyCitationStyle macro; I then inserted the bibliography at the bottom of the document using the Word ‘Insert Bibliography’ feature. For Nature referencing, this appears as a table, but I converted it to straight text and formatted it using a Word style. At the end of these steps, I had a series of ‘well behaved’ MS Word documents, one per chapter plus one for the introduction. These were ready for export into a series of HTML files, two per document, one to hold the text and the other the bibliography of that document.

From Word to HTML

Before beginning the conversion process, I set up a directory structure to hold my files. This would eventually form the backbone of my eBook:

1. Within a directory called ‘Build’, I created two subdirectories; ‘META-INF’ and ‘OEBPS’ (the subdirectory names are required by the EPUB standard; the name ‘Build’ was my choice);

2. Within ‘OEBPS’, I created three subdirectories; ‘content’, ‘css’ and ‘images’;

‘css’ held the .css file (as one might expect);

3. ‘images’ was used to hold the image JPEG or GIF files associated with my work; I created subdirectories within it for each category of image: these were ‘maps’, ‘infographics’ and ‘pictures’, together with a subdirectory named ‘cover’ to hold the book cover JPEG file;

4. Within ‘content’, I created the subdirectories ‘text’, ‘references’ and ‘toc’, together with one directory for each category of images (i.e. ‘maps’, ‘infographics’ and ‘pictures’);

5. The ‘text’ subdirectory held the files making up the main body of the text, i.e. chapters, introduction, glossary, title page, copyright notice, acknowledgements and attributions;

6. The ‘references’ subdirectory held my bibliography files;  

7. The ‘toc’ subdirectory held table of contents files, as will be discussed later;

8. The three image subdirectories held the container files which display the image files (maps, infographics, and plates and illustrations) and accompanying explanatory texts;

I was now ready to begin the export process and produce two HTML files for each document: one for the document text and one for the bibliography. For chapters, I used the naming convention ChxxN.htm and ChxxR.htm, where xx is the chapter number with leading zero and the suffixes ‘N’ and ‘R’ identify the chapter text and bibliography files respectively (‘N’ simply referred to the Nature referencing convention). Other main body text files I simply called by name, i.e. Introduction.htm, Glossary.htm, etc. The only bibliography file not following the ChxxR.htm convention was that pertaining to the Introduction; I called it IntR.htm. These conventions were purely of my own choosing, but the code described below is based on them. Using other naming conventions would require the code to be modified accordingly.

I exported each of Word files to HTML by saving as ‘Web page, filtered’ and opening the resulting file in Notepad++. Each still contained a significant amount of junk, and I also needed to wrap double-quotes (“) around the CSS class names, which was readily accomplished by Search and Replace. Note that the .CSS classes don’t necessarily have to have the same names as the corresponding Word styles and it was possible to rename them at the same time as I added the double-quotes. For example, I renamed In-Text Citation to Citation.

Next, I copied and pasted the formatted paragraphs and the bibliography from each HTML extract file to publishable HTML files set up using the following general template, taking care to ensure that encoding was set to UTF-8 for all files. Note that KindleGen will fail if this is not done.

Each document text file has the following format:

{my text heading}

[Body text copied from the export file goes here]

Where:

1. {my CSS file name} is the name of the css file (HFTB.css in my case)

2. {my div id} is a unique capitalised identifier, based on the name of the file, e.g. CH05, INTRODUCTION, GLOSSARY;

3. {my text heading} is the chapter name or name of the text as will appear in the eBook (e.g. 22: Of rice and men);

4. TOC.htm is a table of contents file for the main text, to be discussed below; the code provides a return hyperlink;

Each bibliography file has the following format:

{ my chapter name}

[Bibliography copied from the export file goes here]

Where:

1. {my CSS file name} is the name of the .css file (HFTB.css in my case)

{my chapter name} is the title of the chapter;

2. CH{ chapter number} is a four-character text string corresponding to the chapter number with leading zero, e.g. ‘CH05REF’ (the reference section for the introduction is ‘INTREF’);

3. RefTOC.htm is a table of contents for the bibliography, to be discussed below; the code provides a return hyperlink;

At this stage, I had two HTML files, ChxxN.htm (chapter text) and ChxxR.htm (bibliography) for each chapter (xx = chapter number with leading zero). Unfortunately, as noted above, the files still contained random junk, which I had to identify and remove by manual editing.

Commonly-occurring junk includes:

1. Unwanted spaces and other blank characters preceding and within HTML tags, and following after HTML close tags;

2. Unwanted tags, leading to non-well-formed HTML;

3. Unwanted Style attributes.

I now needed to establish hyperlinks from the citations in chapter text files to the corresponding references in the bibliography files. To this end, I used Regular Expression (RegExp) search and replace terms in Notepad++.

For each set of chapter text and bibliography files, I proceeded as follows:

1.      Open the bibliography file in Notepad++;

2.      Go to Search/Replace and select Regular Expression mode;

3.      Enter the search string

(\d+).;

4.      Enter the replace string

$1 where xx = chapter number, with leading zero (e.g. CH05) and {my reference style} = the style used to format the bibliography entries;

5.      Click Replace All and save the file;

6.      Open the chapter text file in Notepad++;

7.      Go to Search/Replace and select Regular Expression mode;

8.      Enter the search string Citation”>(\d+)

;

9.      Enter the replace string Citation”>$1

where xx = chapter number, with leading zero (e.g. CH05);

10.  Click Replace All;

11.  Enter the search string Citation”>(\d+),;

12.  Enter the replace string Citation”>$1, where xx = chapter number, with leading zero (e.g. CH05);

13.  Click Replace All;

14.  Enter the search string (\d+)

,(\d+)\;

15.  Enter the replace string $1

,$2 where xx = chapter number, with leading zero (e.g. CH05);

16.  Click Replace All repeatedly until you receive the message “Replace: All 0 occurrence was replaced” [sic];

17.  Save the file;

With the above set of processes completed for each of my MS Word chapter files, I had completed the process of exporting main manuscript to HTML.

Logical and Physical TOCs

A Kindle eBook has two tables of contents (TOC): a logical TOC and a physical (or HTML) TOC. The logical TOC allows readers to navigate between chapters when using a Kindle e-reader. The exact implementation depends on the device used, but in general the reader will be presented with a list of the book’s contents and will be able to navigate to the chapter of their choice. The physical TOC, on the other hand, will be encountered when the reader pages through the book from the beginning. Just where it occurs is up to the publisher, but I located it after ‘Acknowledgements’ and before ‘Introduction’ near the start of the book. It serves the same purpose as the logical TOC, allowing the reader to navigate to the chapter of their choice. Unlike the logical TOC, it cannot be summoned on demand, other than via the logical TOC itself.

In the EPUB 3.0 standard, the logical and physical TOCS can be accommodated in the same HTML file. Previous implementations required the logical TOC to be placed in a separate .nav file, in which the order of appearance for each item has to be coded explicitly. This means a simple re-ordering of the content requires recoding every single entry, which is tedious to say the least. For this reason, I adopted the EPUB 3.0 standard although EPUB 2.0 was suitable in every other respect.

In my implementation, both TOCs were accommodated in a file named TOC.htm, which resides in the content/toc subdirectory. In principle, both TOCs should also be able to share the same code but in practice this was found to cause problems with some implementations.

The TOC.htm file has the following format:

http://www.w3.org/1999/xhtml

xmlns:epub=“http://www.idpf.org/2007/ops” xml:lang=“en”>

Contents

[Physical TOC goes here]

[Logical TOC goes here]

Table of Contents

Go to Beginning

The physical TOC consisted of a series of entries, one for each item directly referenced from it:

{text description}

Where:

1. {my CSS class} is a CSS class to format the line;

2. {file name} is the target file name including extension, e.g. Ch05N.htm;

3. {file div id} is the div id (see above) of the target file, e.g. CH05;

4. {text description} is the text appearing within the

tags of the target file (see above), e.g. “27: An enigmatic civilisation”;

The logical TOC comprises an ordered list enclosed within a

element.

[Logical TOC entries go here]

The logical TOC entries take the form:

{text description}

In theory there is no reason why the ordered list could not serve as the physical as well as logical TOC. It should be possible to suppress the (unwanted) automatic numbering that appears on an ordered list; however on some Kindle e-reader implementations this does not work, and the automatic numbering still appears.

Other TOCs

The logical and physical TOCs described above are mandated (or at least highly recommended by Amazon) and for my eBook, provide navigational access to all the items in the content/text directory. The EPUB standard provides for the nesting of TOCs so that, for example, an entry marked ‘References’ could be expanded into the bibliography list by chapter. Unfortunately, the Kindle platform does not support nesting for the logical TOC, but there is no restriction on using physical TOCs. 

Accordingly, I provided four additional TOCs: one for accessing the bibliography (RefTOC.htm), one for accessing the maps (MapTOC.htm), one for accessing the infographics (FigTOC.htm), and one for accessing the plates and illustrations (PicTOC.htm). All were in turn accessible from the main TOC.

The RefTOC.htm file has the following format:

References

[Bibliography entries go here]

The bibliography entries have the following format:

{chapter title}

Where:

1. {my CSS class} is a CSS class to format the line;

2. {chapter no.} is the chapter number with leading zero (for the introduction the target bibliography file is IntR.htm);

3. {chapter title} is the text appearing within the

tags of the target bibliography file, e.g. “27: An enigmatic civilisation”;

The MapTOC.htm, FigTOC.htm and PicTOC.htm files follow the same general format as RefTOC.htm and hyperlink to the container files which display the book’s visual matter. As with the bibliography files, the container files contain return hyperlinks to their respective TOCs.

The Glossary

I provided a glossary in which commonly-encountered terms were defined and explained. Entries could be accessed alphabetically from within the glossary via a hyperlinked alphabet, or via hyperlinks in the main body of the book’s text. Unfortunately, there was no quick and easy way of doing this and it was necessary to insert the relevant links on an individual basis. Again, as most glossary items were multiply accessed, no return link was provided and the reader returns by use of the ‘back’ function on their Kindle e-reader.

The content.opf file

The content.opf file sits in the OEBPS directory and is central file of an EPUB package. It defines the structure of the eBook and holds its metadata. Very briefly, it contains four sections: the section, section, section and section. The section provides metadata, which is essentially data about data rather than content. In this implementation, metadata is supplied for the ISBN number, book title, author name, publisher name, date of publication, book description, and subject. The section provides a list of paths, identifiers and properties for each file in the package; and the section lists in order of appearance the identifiers for each file in the package, thus defining the order in which they would appear were the reader to page through the entire book.

The  content.opf file has the following format:

                       

urn:isbn:{my ISBN no.}

15

en-gb

{my book title}

{author name}

aut

{my publisher}

{yyyy-mm-dd}

{yyyy-mm-dd}T{hh:mm:ss}Z

{a brief description of the book}

{my subject 1}

{my subject 2}

{my subject 3}

           

[One entry for each of the content files from the content/text/ subdirectory]

[MapTOC]

                       

[One entry for each of the container files from the content/maps/ subdirectory]

[One entry for each of the map image files (in all cases, {type} = JPEG)]

[FigTOC]

                       

[One entry for each of the container files from the content/infographics/ subdirectory]

[One entry for each of the infographic image files (in all cases, {type} = GIF)]

[PicTOC]

[One entry for each of the container files from the content/pictures/ subdirectory]

                       

[One entry for each of the picture image files (in all cases, {type} = JPEG)]

[RefTOC]

[One entry for each of the bibliography files from the content/references/ subdirectory]

[One entry for each of the HTML and image files in the package; {id ref} will be either the div id for the HTML files or the unique id based on image name for the image files]

Building the package

At this point, the package was almost complete. It remained only to add the container.xml file to the META-INF directory and the mimetype file to the Build directory.

The container.xml file simply tells an eReading device where to find the content.opf file, and it has the following format:

 

   

 

The mimetype file defines the file as an EPUB and ZIP file. It is a text file with no file extension containing a single line of text:

application/epub+zip

The next step was to zip the whole package up into an EPUB file and then convert this to a Kindle-compatible MOBI/KF8. In the Build directory, I set up two .bat files; compress.bat and mobimake.bat. I also installed the Zip.exe utility in the Build directory.

Format of compress.bat:

zip {my book}.epub -DX0 mimetype

zip {my book}.epub -rDX9 META-INF OEBPS

Format of mobimake.bat:

{my KindleGen path}/kindlegen.exe {my book}.epub>errors.txt

Having set up these files, I ran compress.bat to produce an EPUB file, which in my case was called hftb.epub. Before converting this to the MOBI/KF8 format, it was necessary to check it for errors. There are many free websites that will upload and validate an EPUB file; I used this one: http://validator.idpf.org/ (note that it does not have a www. prefix). Once I had ironed out the inevitable errors, it was time to take the final step and run mobimake.bat. This created the MOBI/KF8 file, which in my case was called hftb.mobi. It also outputs the file errors.txt, which lists errors, warnings and approximate deliverable file size. This latter figure forms the basis of the ‘delivery fee’ that is charged by Amazon to the author against the royalty payment for each sale.

Testing and release

With the book now built, the final stage was testing. This entailed individually testing every single hyperlink in the book and also checking for formatting errors. This was a laborious procedure for a long book, but I viewed it as essential. A small number of issues were identified, which were easy to fix but would have made the book seem less polished as a product had they been allowed to remain. Testing was carried out on four platforms: a dedicated Kindle device, an iPhone, a Nexus 7 Android tablet and a PC. Full testing was carried out only on the latter.

On 4 March 2014, I uploaded Humans: from the beginning to the Amazon Kindle bookshelf, and it has been in sale ever since. In the weeks that followed, a few errata came emerged, highlighting another advantage of the eBook over its printed counterpart. It was simply necessary to make corrections and upload the corrected version. Previous purchasers receive this free of charge, similar to the way that apps on a smartphone are periodically updated. I added a ‘release note’ with the updated version as a new page located after the bibliography.

Review finds no evidence for Neanderthal ‘inferiority’

Archaeological record of Neanderthals was not dissimilar to that of contemporary modern humans

A paper by Paola Villa and Wil Roebroeks in open access PLOS ONE has reviewed archaeological evidence for the view that the ‘inferiority’ of Neanderthals to modern humans was responsible for their demise.

Villa and Roebroeks considered a number of commonly-proposed hypotheses for the extinction of the Neanderthals. These included the views that Neanderthals lacked the capacity for syntactic language and symbolic behaviour; that they had only a limited capacity for innovation, and their technology was inferior to that of modern humans; and that they were less efficient hunters than modern humans, with a less varied diet. 

In every case, Villa and Roebroeks were able to demonstrate that the available archaeological does not support the hypothesis. For example, there is evidence for Neanderthal symbolic behaviour that is as strong as anything claimed for modern humans from the African Middle Stone Age, even if the controversial Châtelperronian data is ignored. While the pace of technological change was slow, the same could be said of the later part of the African Middle Stone Age after modern humans emerged. There is also good evidence that Neanderthals were efficient hunters, and that they enjoyed a varied diet.

The question, then, is if Neanderthals were not technologically and cognitively disadvantaged over modern humans, why did they die out? Villa and Roebroeks suggest multiple factors played a part including low population densities in comparison to the incoming modern humans; and possible male sterility arising from interbreeding with modern humans. Eventually, they suggest, the Neanderthals were swamped and assimilated by the increasing numbers of modern immigrants.

References:

1. Villa, P. & Roebroeks, W., Neandertal Demise: An Archaeological Analysis of the Modern Human Superiority Complex. PLoS One 9 (4), e96424 (2014).

Link:

PLOS ONE
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0096424

Ancient DNA reveals differences between Neanderthal and modern human lineages

Study also confirms that Neanderthal populations were small and isolated

 Researchers have analysed genetic sequences from Neanderthal remains found in Spain, Croatia and southern Siberia. The results indicated that the genetic diversity of Neanderthals is very low in comparison to that of modern humans, suggesting that they lived in small, scattered populations.

Genes associated with skeletal morphology were found to be more changed in the lineage leading to Neanderthals than they were in the lineage leading to modern humans, implying that Neanderthals underwent more skeletal changes than modern humans.

Conversely, genes associated with pigmentation and behavioural characteristics were to be more changed in the modern lineage. The team researchers also identified amino acid substitutions in Neanderthals and modern humans. These can change the structure and function of proteins, and may underlie phenotypic differences (differences in observable characteristics) between the two species.

Reference:
Castellano, S., et al Patterns of coding variation in the complete exomes of three Neandertals, PNAS (2014); published ahead of print April 21, 2014, doi:10.1073/pnas.1405138111

Link:
http://www.pnas.org/content/early/2014/04/16/1405138111.short?rss=1

Ancient Egyptians tamed cats 2,000 years before earliest generally accepted evidence

Sacrificial burial from Predynastic Hierakonpolis dates to 3800 – 3600 BC

The remains of six cats were found in a circular pit in an elite graveyard: an adult male, an adult female and two pairs of kittens. The cats were sacrificed as part of a funerary ritual. The ages of the kittens suggest that they belonged to two different litters; furthermore the adult female was too young to have been the mother.

The relationship of the male cat to the kittens cannot be determined. If all these animals were taken from the wild, then four different captures would have been required (the male, the female and each pair of kittens). It is unlikely that this could have been accomplished in short period prior to the sacrifice. Furthermore, the slightly different ages of the kittens suggest they were born outside the natural reproductive cycle of Egyptian wild cats, with a single birth season on spring. It therefore seems likely that the cats were bred in captivity or at least in close association with humans.

The traditional view is that domesticated cats first appeared in Egypt during the Middle Kingdom around 4000 BC or possibly 300 years earlier during the latter part of the Old Kingdom, but this finding pushes the date back to the Predynastic Naqada IC-IIB period (3800 – 3600 BC).

However, the earliest evidence for an association between humans and cats is a 9,500 year old burial from Cyprus containing the remains of a human and a cat.

Open Access http://dx.doi.org/10.1016/j.jas.2014.02.014

Reference:

1. van Neer, W., Linseele, V., Friedman, R. & de Cupere, B., More evidence for cat taming at the Predynastic elite cemetery of Hierakonpolis (Upper Egypt). Journal of Archaeological Science 45, 103-111 (2014).

Fifty years of Homo habilis

 The first human species - or was it?

Fifty years ago, the British anthropologist Louis Leakey and two colleagues reported the discovery of a new human species, Homo habilis (‘handy man’), in the journal Nature. Homo habilis lived at least 1.9 million years ago and remains the earliest-known widely-recognised human species to this day. The new species was described from fossils recovered at Olduvai Gorge, Tanzania between 1960 and 1964, but the story of its discovery began more than three decades earlier in 1931, when Leakey first investigated this now world-famous site.

Leakey believed that humans had evolved from African apes, as Darwin had originally suggested. By the early twentieth century however, this view had fallen out of favour and an Asian origin was widely favoured. The earliest-known human species at that time was Homo erectus, which had been discovered in late nineteenth century and was then known only in Asia. Although Neanderthals had been discovered some decades before that, Homo erectus was the first human species to be discovered that lived significantly before Homo sapiens and its brain was only around two-thirds the size of a modern brain.

However, in 1924, Australian anthropologist Raymond Dart had studied an apelike fossil found at a lime quarry at Taung, near Johannesburg, South Africa. He noted that the spinal column entered the skull through the centre rather than the back, suggesting that it was a biped and therefore a very early human – although its brain was no larger than that of a chimpanzee. Dart named it Australopithecus africanus (southern ape from Africa). The discovery switched the focus back to Africa, and in the decades that followed, australopithecines were also found in East and Central Africa. What was missing was a human ancestor intermediate between the australopithecines and Homo erectus.

Leakey became interested in Olduvai Gorge when fossilised human remains were found there, though ironically these later turned out to be a comparatively recent burial. Olduvai Gorge is probably the best-known fossil site in the world, and is now a UNESCO World Heritage site. A steep-sided ravine in Eastern Serengeti, it was formed when a stream carved its way through sedimentary rock, revealing seven main archaeological layers going back two million years. It was originally known as Oldoway Gorge; but it and Olduvai are mispronunciations of the local name Oldupai Gorge, which in turn comes from the Maasai word for the wild sisal plant growing in the gorge.

The 1931 expedition failed to discover any fossils, but a number of stone tools were found. These included a rudimentary stone chopping tool that was made by chipping flakes off a stone cobble to produce a weighty, sharp-edged cutting tool capable of cutting into animal carcasses. The tool is now on display in the British Museum, which at 1.8 million years old is the oldest object in the museum’s collection. Leakey classed the find as Oldowan, for the then still-current name Oldoway Gorge. The tool was found in Bed I, the lowest, earliest archaeological level at the site; more sophisticated stone hand-axes were found in higher, later levels. Leakey believed that the site recorded a sequence leading from the simple chopping tools in the lowest levels to the far more sophisticated tools in the higher Bed IV. The search was now on for the maker of the Oldowan tools, but Leakey’s work was interrupted by the breakup of his marriage and the outbreak of the Second World War.  

In 1951, he returned to Olduvai Gorge with his second wife, Mary, and in 1959, after several fruitless seasons, the Leakeys were finally rewarded with the discovery of the fossil skull of a young adult in the same archaeological layer that had yielded the stone cobble tool. It was small-brained and large jawed, with massive chewing teeth. The new species was designated Zinjanthropus boisei; ‘Zinj’ is an ancient Arabic word for the coast of East Africa, and the name also honours expedition sponsor Charles Boise. The skull was given the affectionate nickname of ‘Dear Boy’ by Mary Leakey. Now known as Paranthropus boisei, ‘Dear Boy’ belonged to an offshoot of the australopithecine lineage that is thought to have been an evolutionary dead end. Could this have been the maker of the cobble tools? It seemed doubtful.

The Leakeys were then joined in the field by their son Jonathan, and in November 1960 Jonathan and Mary found a lower jawbone with 13 teeth still in place, together with finger, hand and wrist bones. Over the next three years further fossils were recovered and analysed with the help of primatologist John Napier and anthropologist Phillip Tobias. They came from a species with a larger brain and smaller teeth than ‘Dear Boy’. Louis Leakey believed that this was this was the real toolmaker. The new species was announced in the journal Nature in April 1964 and given a name proposed by Raymond Dart – Homo habilis.

Compared to the australopithecines, the skull of Homo habilis was less massively-built, and the upper and lower jaws were within the size range of both Homo erectus and modern humans. The feet were humanlike, as were the thumb joints – but it was shorter in stature and much smaller-brained than a modern human. Males averaged 5 ft. 1 in and females 4 ft. 1 in; the brain size of around 600 cc was far less than the 1350 cc average for a modern human, or even the 750 cc human minimum proposed by British anthropologist Sir Arthur Keith in the late 1940s. This figure lies midway between the largest gorilla brain and the smallest modern human brain. Homo habilis was nevertheless significantly taller and bigger-brained than the australopithecines. However, the limb proportions were still apelike, with proportionately long arms and short legs, suggesting that Homo habilis retained some apelike tree-climbing abilities.

The Olduvai fossils are 1.8 million years old. Most remains are from East Africa; but the skull STW 53 from Sterkfontein, South Africa, may also be Homo habilis. The oldest tentative fossil evidence for Homo habilis to date is AL 666-1, a 2.33-million-year-old upper jawbone recovered at Hadar, Ethiopia, but the oldest uncontested Homo habilis remains are only 1.9 million years old. The most recent Homo habilis fossil currently known is a 1.44-million-year-old partial upper jawbone from Koobi Fora, Kenya. These dates – if both correct – imply that the species survived for almost a million years. Homo habilis is not known to have left Africa, but it has been suggested that it might have been the ancestor of Homo floresiensis, the so-called ‘hobbit people’ from the Indonesian island of Flores.

The Oldowan stone tool tradition associated with Homo habilis was the most primitive of all stone tool traditions. We now know that such tools were also made by some of the later australopithecines and might have a response to deteriorating climate as the Earth entered the current series of ice ages 2.5 million years ago. It is possible that as the climate deteriorated, preferred food types became unavailable and australopithecines added more meat to their diet. The increased need to butcher carcasses led to the development of stone tools. Early Homo erectus also used Oldowan tools before switching to the more advanced hand-axes seen in the upper levels at Olduvai Gorge. However, many Homo erectus groups, particularly in the Far East, persisted with the Oldowan stone cobble tools.

Plaster casts of the inside of Homo habilis braincases have shown that the sulcal and gyral patterns (ridges and furrows that give the human brain its wrinkled look) were more humanlike than apelike. The frontal and parietal lobes are enlarged, and that the Broca’s Area was expanded in comparison to the same region in australopithecines and modern apes. The frontal lobes, which control higher brain functions including planning and reasoning, are located at the front of the brain. Behind them, on the top and on each side of the brain are the parietal lobes, which carry out a wide range of functions including spatial awareness and the processing of sensory information.

Broca’s Area is named for nineteenth century physician Paul Broca who demonstrated a connection with speech. Damage leads to Broca’s aphasia, where patients are unable to speak in a grammatically correct manner. This suggests some linguistic abilities, though recent research shows that the Broca’s Area is also associated with tool-making. It is possible that its expansion was linked to enhanced tool-making skills as well as or possibly instead of the use of language.

However, the late australopithecines that made stone tools had brains no larger than their forebears, so tool-making alone doesn’t explain why Homo habilis needed a bigger, better brain. Bigger brains might sound like a good idea, but the same could be said of owning a Rolls-Royce. The problem in both cases is that they are expensive to run, and there is a pretty good case for trying to get by without. Brain tissue requires over 22 times as much energy as an equivalent amount of muscle tissue. In a modern human, the brain uses around 16 percent of the body’s energy budget despite making up just 2 percent of the body’s overall mass. While the energy costs of the smaller Homo habilis brain were less than those of a modern human brain, they were still considerable.

A possible answer is the social brain hypothesis, a theory which links the brain size of primates to the size of their social group. The enhanced brainpower is needed to keep track of the complex social relationships that are normal in many primate societies – not just human ones. Larger, more co-operative social groupings in Homo habilis society might have been an evolutionary response to the deteriorating climate and reduced availability of food.

Just where Homo habilis belongs in the human family tree remains contentious, even half a century after its discovery was announced. Even its membership of the human league is now questioned, with some seeing it as the anthropological equivalent of the now ex-planet Pluto and arguing that it should be reclassified as an australopithecine.

Although most textbooks describe Homo habilis as the ancestor of Homo erectus, the view has been called into question. Recent fossil finds indicate that Homo habilis persisted alongside Homo erectus for hundreds of thousands of year at Koobi Fora, Kenya. This makes it unlikely that the latter evolved from the former, and instead it has been proposed that both shared a common ancestor about two million years ago. If it were to turn out that the disputed AL 666-1 upper jawbone was something other than Homo habilis, then this scenario would become likely as the oldest examples of the two species would then be practically the same age. Another possibility is that the true ancestor of Homo erectus is the recently-discovered australopithecine species Australopithecus sediba. Australopithecus sediba lived in South Africa two million years ago, with limb proportions said to be more humanlike than Homo habilis.

Do the fossils assigned to Homo habilis even represent a single species? The variation in Homo habilis fossils is considerable and it has been suggested that these actually represent two species. Some examples have a broader, flatter face and larger teeth than others, and it is has been proposed that these be assigned to a second species known as Homo rudolfensis. On the other hand, it has been claimed that the degree of variation between skulls assigned to Homo habilis, Homo rudolfensis and Homo erectus is actually no more than that between five early Homo erectus skulls found at Dmanisi, Georgia, and it has accordingly been suggested that all three are actually the same species. The problem with this view is that it does not explain the more apelike limb proportions of Homo habilis.

It is this detail together with the small brain size that has led some to believe that Homo habilis should be reclassified as an australopithecine. Quite simply, it is too unlike Homo sapiens to be regarded as a human species. However, there is no consensus on the issue. Studies have been conducted to determine whether it can be included in Genus Homo on the basis of anatomical characteristics shared with other members, but these have proved inconclusive.

If Homo habilis individuals could somehow have been aware that they would one day become the subject of such deliberations, it is unlikely that they would have been overly concerned. It should not be forgotten that they might have existed for as long as a million years, which is a testament to their success as a species.

Ancient DNA study provides additional insight into Neolithic transition in Scandinavia

Hunter-gatherers were absorbed into farming communities

A newly-published genetic study of ancient DNA obtained from prehistoric human remains in Sweden has provided a fresh insight into the transition to agriculture in Scandinavia.

The ability to obtain DNA from the remains of prehistoric people has in recent years added a new dimension to the long-running quest to understand the demographics of the transition from hunter-gathering to farming in Neolithic Europe. Studies based on living populations have been unable to provide definitive answers, as ancient genetic signals are often blurred by far more recent events.

Researchers at Stockholm University and Uppsala University obtained genetic material from the remains of six hunter-gatherers and four farmers from the Scandinavian Neolithic, dating to around 5,000 years ago, together with a late Mesolithic hunter-gatherer from 7,500 years ago. The samples were obtained from mainland Sweden and the Swedish island of Gotland.

It was found that the genetic diversity of the hunter-gatherers was far lower than that of the farmers and of any present-day Eurasian populations, suggesting that their population sizes were very small. Fluctuating climatic conditions and/or restricted carrying capacities might have affected hunter-gatherer population sizes. It is also possible that the genetic diversity of the hunter-gatherers never recovered from population crashes occurring during the Last Glacial Maximum when European populations were confined to a few ice-free refugia.

A significant finding was that the hunter-gatherer and farming populations were genetically distinct from one another, confirming the view that agriculture was spread across Europe by migrating farmers, rather than by indigenous hunter-gatherers simply taking up farming. In other words, it was farmers and not just farming that spread.

The researchers also found evidence for genetic admixing between the hunter-gathering and farming communities – but it was one way. Hunter-gatherers apparently married into the farming communities, but not the other way round. Thus the expanding farming communities assimilated indigenous hunter-gatherers.

The study, published in the journal Science, is part of a recently-launched initiative to investigate ancient human remains in Scandinavia. Known as the Atlas project, it is being conducted by researchers at Stockholm University and Uppsala University.

References:

x

1.  Skoglund, P. et al., Genomic Diversity and Admixture Differs for Stone-Age Scandinavian Foragers and Farmers. Science (2014).

Bronze Age pastoralists played key role in spread of crops in Central Asia

New archaeobotanical data highlights cereal cultivation by mobile groups during period 2800 to 1200 BC.

Mobile pastoralism first appeared on the steppes of Central Asia during the fourth millennium BC, and was established by the early part of the third millennium BC. Nomadic groups were also responsible for introducing copper, tin, ceramics and bronze metallurgy into the Inner Asian Mountain Corridor between the Altai and Pamir mountain ranges.

However, much less is known of the Central Asian herders’ use of domesticated cereals and the integration of farming into their mobile economies. Botanical evidence for farming on the steppes and mountains of Central Asia has not been previously documented prior to 800 BC, leading to the traditional view that there was a sharp division between nomadic pastors and sedentary farmers in Eurasia and elsewhere.

This view has now been challenged by newly-published archaeobotanical data from four Bronze Age sites in the region. The highland steppe sites of Tasbas and Begash in eastern Kazakhstan, and Ojakly and the unnamed site of 1211/1219 in the Murgab Delta region of Turkmenistan are all believed to have been used as seasonal camps by mobile pastoralists as part of their annual round. Features of these sites include semi-subterranean houses and storage areas.

At Tasbas, wheat and unidentifiable cereal grains were recovered from a funerary urn dating from between 2840 to 2500 BC; and wheat, barley and broomcorn millet dating from between 2450 to 2100 BC were found at Begash. This is the earliest evidence for the use of domestic crops in the region. By 1450 – 1250 BC, cereals were present in far greater quantities at Tasbas: barley, wheat, broomcorn millet and foxtail millet, together with peas. The high density of seeds found in soil suggests that the crops were cultivated locally and not obtained by trading with farmers. Barley chaff used as binder in mud bricks also suggests local cultivation.

The two sites in Turkmenistan date to between 1700 and 1500 BC and have yielded broomcorn millet, barley and wheat. By this time, sedentary farming communities had emerged in the region, and both sites lay close to specialised farming villages. It is likely that the pastoralists obtained their barley and wheat from these, but the farmers did not grow broomcorn millet. Thus it appears likely that the mobile pastoralists were responsible for introducing this crop into the region.

In conclusion, the wheat and broomcorn millet at the two Kazakh sites is earliest evidence for spread of crops into the region – wheat from southern Central Asia and broomcorn millet from East Asia. The seasonal migrations of the pastoralists who used these sites resulted in extensive interactions between local communities throughout the mountainous regions of Central Asia. These interactions resulted in the spread in both directions of crops and agriculture between China and Central Asia among sedentary and mobile groups by the second millennium BC.

The findings indicate that domesticated crops reached Central Asia 2,000 years earlier than previously believed, and highlight the key role of mobile pastoralists in transmitting crop repertoires and transforming agricultural economies in the region. They break down the sharp divide previously thought to exist between nomads and farmers in prehistoric Central Asia.

References:

x

1.  Spengler, R. et al., Early agriculture and crop transmission among Bronze Age mobile pastoralists of Central Eurasia. Proceedings of the Royal Society B 291 (1783) (2014).

x

Fishing was rapidly abandoned by first farmers in Britain and Ireland

Lipid residue study finds evidence for dramatic change in diet during Neolithic transition

Agriculture reached Britain and Ireland around 4000 BC, but the means by which the transition from hunting, fishing and gathering occurred has been debated for many years. One view is that indigenous Mesolithic people acquired domesticated crops and animals from continental Europe, but retained much of their existing lifestyle. Another is that Neolithic farmers arrived from the continent and spread rapidly. This latter scenario proposes that a rapid acculturation of indigenous Mesolithic people followed.

Previous work has considered stable carbon isotope signatures of bone collagen extracted from Mesolithic and Neolithic human remains. The results suggested that in coastal environments, the Mesolithic diet included a significant amount of marine protein, but that of the Neolithic farmers was predominantly terrestrial-based. However, doubts have been expressed about the sensitivity of the bone collagen stable isotope analysis to low-protein diets; quantities of less than 20 percent marine protein in the diet would be undetectable. Possible Neolithic shell middens from Scotland and Ireland suggest that seafood continued to be eaten.

To address this uncertainty, researchers analysed lipid residues recovered from Neolithic pottery sherds from coastal sites in Britain, the Scottish Isles, and Ireland. To extend the chronological period, material was also included from sites dating to the Bronze Age through to the Viking period. The results confirmed the near-complete absence of marine protein from the Neolithic diet and the strong presence of dairy products. This remained the case during the Bronze Age, and it was not until Viking times did marine protein again become a significant dietary item.

Similar studies in the Baltic region indicate a different pattern. There, hunting, gathering and fishing continued alongside farming. The contrasting patterns occurring at the same time in different regions suggest geographically-distinct ecological, demographic and cultural influences dictating the adoption of agriculture. The rapid shift to an intensive dairy economy is consistent with the low frequency of lactose intolerance among modern inhabitants of northwest European archipelagos. The evolutionary processes driving lactase persistence in adults would have been driven by the increasing importance of dairy products in the diet.

References:

x

1.  Cramp, L. et al., Immediate replacement of fishing with dairying by the earliest farmers of the northeast Atlantic archipelagos. Proceedings of the Royal Society B 281 (2014).

x

Copper awl points to non-local origin for metallurgy in southern Levant

Artefact was imported centuries before Late Chalcolithic.

The southern Levant became a major centre for metallurgy in Southwest Asia during the Late Chalcolithic period from 4500 to 3800 BC. Artefacts from this period include eight massive gold rings weighing a total of almost 1 kg (2.2 lb.) from the Nahal Qanah Cave, Israel, and prestige copper items from a cave at Nahal Mishmar near the Dead Sea, which display lost wax casting technology.

However, the origins of this metalworking tradition have remained obscure until recently. Now a newly-published report has suggested that the roots of southern Levantine metallurgy might be found in an earlier, non-local tradition. Tel Tsaf in the Jordan Valley was excavated between 2004 and 2007. The main period of occupation of the site occurred during the Middle Chalcolithic, and dates to between 5100 and 4600 BC. The mud-brick complex included courtyard buildings and grain silos, two of which had been repurposed as graves. Artefacts from the site included elaborately painted pottery and over 2,500 beads made of ostrich egg-shells and stone. Many artefacts were of non-local origin, including obsidian items from Anatolia or Armenia, a shell from the Nile and pottery from northern Syria or Mesopotamia. Animal remains included large numbers of cattle and pigs and the capacity of the grain silos has been estimated at around 15 to 30 tons. Wealth and food surpluses were being accumulated at Tel Tsaf far in excess of anything else known in the region during this period; and the site had access to long-distance exchange networks throughout Southwest Asia.

From one of the silo-graves was recovered a badly-corroded copper awl. The awl is a 41 mm (1.6 inch) pin made from cast copper, with a rounded cross-section. The maximum diameter is 5 mm (0.2 inch), narrowing to 1 mm (0.04 inch) near the tip. The burial held the remains of a woman aged around forty, and other grave goods included an ostrich-shell bead necklace with 1,668 beads.

Chemical analysis indicated the metal composition of the awl included 6 percent tin and 0.8 percent. Although corrosion may have altered the chemical composition of the awl, the presence of tin suggests that it was not of local origin. Copper items of such a composition have not been found in the Late Chalcolithic or the Early Bronze Age of the southern Levant, nor does it match the composition of local native copper. It is thought that the alloy is natural, as it unlikely that artificial copper/tin alloys were being produced at this stage. Tin bronze is not known from the region until the Middle Bronze Age, around the second millennium BC. Thus the awl not only predates all previously-known metal artefacts in the southern Levant by several centuries, it also predates all known tin bronze items in the region by around 3,000 years.

Assuming that the awl is not of local origin, then it must have reached Tel Tsaf via long-distance exchange networks. Metallurgy must have diffused to the southern Levant from the north. At first, artefacts were imported and it was not until some centuries later that they were produced locally. Thus it can be seen that the elaborate Late Chalcolithic metallurgy of the southern Levant developed from an earlier, non-local tradition.

That the awl was found in an elaborate grave suggests that at this stage, metal items were seen as rare and prestigious. The residents of the courtyard building where the grave was found apparently belonged to a family or group that controlled the local cultivation and storage of grain as well as long-distance trade. Their wealth may have either led to or been the result of a trade in luxury items obtained from sources very remote from Tel Tsaf.

References:

x

1.  Garfinkel, Y., Klimscha, F., Shalev, S. & Rosenberg, D., The Beginning of Metallurgy in the Southern Levant: A Late 6th Millennium CalBC Copper Awl from Tel Tsaf, Israel. PLoS One 9 (3), e92591 (2014).x

Did Neolithic switch to agriculture drive selection for lighter skin colour in Europeans?

Study finds evidence of strong positive selection for skin, eye and hair pigmentation over last 5,000 years.

Why do people living in the tropics have dark skin whereas those living in higher latitudes have lighter skin? The traditional explanation is that is an evolutionary balancing trick between protection from skin cancer on one hand and the synthesis of Vitamin D by skin cells on the other. Dark skin results from higher levels of the pigment melanin: for those living nearer the equator, higher melanin levels provides a better protection from the sun’s more intense UV radiation; conversely, for those living at latitudes where UV radiation is weaker, the protection is not required and high melanin levels would block the production of Vitamin D.

However, things may not be quite so straightforward. A study carried out in 2012 at the University of Porto in Portugal considered alleles (variants) of four genes known to be associated with pigmentation, using samples taken from present-day Portuguese and sub-Saharan Africans. The evolutionary history of the four genes was estimated using a statistical model (Monte Carlo) to simulate the effects of genetic drift, natural selection and mutation. It was found that three of the alleles linked to lighter pigmentation did not start to sweep through European populations until around 11,000 to 19,000 years ago – at least 40,000 years after modern humans left Africa (Beleza, et al., 2012).

Two recently-published studies have investigated ancient DNA extracted from prehistoric human remains in Europe. The first study, published in the journal Nature, considered the pigment genes of DNA obtained from human remains found at the Mesolithic cave site of La Braña-Arintero, near León, Spain. The remains were identified as those of a male hunter-gatherer, who lived 7,000 years ago. He was found to have been dark-skinned and blue-eyed. Although present-day Spaniards are darker-skinned than northern Europeans, they are far paler than Africans (Olalde, et al., 2014). The result again suggests that paler skin colour was a fairly late development.

The second study, published in the journal PNAS, considered the pigment genes TYR, HERC2 and SLC45A2. TYR produces the enzyme tyrosinase, which is used as a catalyst in the production of melanin. HERC2 is responsible for determining eye colour; and SLC45A2 is involved in the distribution and processing of tyrosinase and other pigment-producing enzymes. The various alleles of these genes are responsible for different colours of skin, hair and eyes. Researchers extracted ancient DNA from 63 Chalcolithic (6500 to 5000 years old) and Bronze Age (5000 to 4000 years old) individuals from Ukrainian sites on the Pontic-Caspian steppe. 43 individuals yielded DNA from which the pigment genes could be sequenced, and these were compared with those of present-day Ukrainians.

The researchers found that the pigmentation of the prehistoric population differed from that of the present-day Ukrainians. The latter have 8.5 times as many alleles of TYR related to light skin colour as did their prehistoric forbears. Alleles of HERC2 related to blue eye colour were also far more common in the present-day population. However, none of these lighter pigmentation alleles are present in African populations. Thus it seems that the shift to lighter pigmentation was underway in the Chalcolithic and Bronze Ages, but it was at that stage incomplete – despite the immense passage of time since modern humans had left Africa. Computer simulations showed that these effects could not be explained by genetic drift alone, and that natural selection must have been a factor (Wilde, et al., 2014).

The team speculated that selection for lighter skin colour was related to the change in diet following the arrival of agriculture. The diet of hunter-gatherers was more likely than that of the farmers to include items rich in Vitamin D, such as fish and liver. To make up the difference, individuals needed to be able to synthesise it more efficiently – hence a lighter skin colour. At the same time, the trend to lighter hair and eye colour may have been the result of sexual selection: the initially-unusual colouring might have been more attractive to the opposite sex (the researchers noted that this phenomenon has been documented in guppies).

References:

1.  Beleza, S. et al., The timing of pigmentation lightening in Europeans. Molecular Biology and Evolution 30 (1), 24-35 (2012).

2.  Olalde, I. et al., Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European. Nature 507, 225-228 (2014).

3.  Wilde, S. et al., Direct evidence for positive selection of skin, hair, and eye pigmentation in Europeans during the last 5,000 y. PNAS (Early Edition) (2014).

Deep Impact?

Why an asteroid impact is unlikely to have caused the Late Quaternary mass extinction.

The Pleistocene world was dominated by large mammals, flightless birds and reptiles. These included mammoths, mastodons, giant ground sloths, camels, sabre-tooth cats, giant beavers, and giant deer with antlers spanning 3 m (10 ft.). In Australia, there lived the hippopotamus-sized Diprotodon optatum that weighed in at 2.8 tonnes, and was the largest marsupial of all time. These animals are collectively known as the megafauna, a term applied to animals with an adult weight of 45 kg (100 lb.) or more. Between 50,000 and 10,000 years ago, many of these great beasts vanished in one of the largest extinction events since the demise of the dinosaurs. Australia and the Americas were hardest hit, but no habitable continent remained unscathed. Overall, about 180 large mammal species and over 100 entire genera perished (Barnosky, et al., 2004; Lyons, et al., 2004; Koch & Barnosky, 2006; Barnosky, 2008). Usually referred to as the Late Quaternary extinction event, it was recognised by early geologists towards the end of the eighteenth century.

The cause of this mass extinction has long been debated and there remains a lack of consensus to this day. Climate change and human activity were put forward as possible causes as far back as the early nineteenth century, and both are hotly championed to this day. One of the more controversial theories, first proposed in 2007, is that around 12,900 years ago, Earth suffered multiple airbursts and surface impacts from fragments of a comet or asteroid that had previously broken up in space. In North America, the bombardment caused devastating shock-waves and continent-wide forest fires that brought about the extinction of the megafauna. While the overall effects were far less severe than those of the impact now believed to have killed off the dinosaurs, they were still sufficient to trigger a global ‘impact winter’. This in turn precipitated Younger Dryas climatic downturn.

Evidence for the supposed impact was claimed in the form of a 12,900-year-old carbon-rich layer or ‘black mat’. The layer has been identified at around fifty Clovis sites in North America. It is said to contain material consistent with an impact, including magnetic mineral grains, soot, carbon spherules and so-called nanodiamonds. The latter are minute diamonds formed when carbon particles are subjected to intense heat and pressure by an explosion (Firestone, et al., 2007; Haynes, 2008; Kennett, et al., 2009). More recently, evidence for impacts has also been claimed from Younger Dryas boundary sites in Mexico, Belgium, the Netherlands, Germany and Syria (Israde-Alcántara, et al., 2012; Bunch, et al., 2012). Anomalous levels of platinum, said to be due to the impact of a large iron meteorite, have also been reported from Greenland ice core samples dating to the Younger Dryas boundary (Petaev, et al., 2013).

In theory this is all sounds highly feasible, but in practice the timing is a little suspicious. Other factors were in play at the time, and it is not necessary to invoke an extraterrestrial impact to explain the onset of the Younger Dryas. Named for the arctic-alpine flowering plant Dryas octopetala that flourished in the northern tundra at that time, the Younger Dryas marks the final stage of the Pleistocene. It lasted from 12,900 until 11,600 years ago and both its onset and termination were fairly abrupt (Taylor, et al., 1997; Severinghaus, et al., 1998). During the preceding Bølling-Allerød warm period, the North American ice sheets retreated. The resulting meltwater formed a vast glacial lake known as Lake Agassiz, larger than all the modern Great Lakes put together. Beginning 13,000 years ago, Lake Agassiz released a series of freshwater discharges into the Arctic Ocean, through what is now the drainage basin of the Mackenzie River (Murton, et al., 2010). The conventional view is that the great volume of freshwater disrupted the Gulf Stream, halting the flow of warm seawater from the tropics to higher latitudes. The result was to plunge the Northern Hemisphere back into glacial conditions. Effects in the Southern Hemisphere are less certain, though evidence of cooling has been found there also (Moreno, et al., 2001).

That an extraterrestrial impact should occur at more or less the same time as the freshwater discharge strikes me as being a rather implausible coincidence. It should also be noted that other studies have failed to find evidence for the nanodiamonds (Daulton, et al., 2010), and that there is no evidence for the continent-wide conflagration supposedly triggered by the impact. Evidence for burning is better attributed to climate change-generated increases in natural wildfires (Marlon, et al., 2009). Similarly, the magnetic grains can be accounted for by a constant influx of micrometeorites from space (Surovell, et al., 2009). The ‘black mats’ do not occur throughout the whole of North America, but rather are located predominantly in the west. They may be algal mats or ancient soils associated with regional increases in moisture (Gill, et al., 2012). The source of platinum anomaly may be extraterrestrial, but this remains unproven and more evidence is needed. All in all, I am sceptical about the impact theory, although it certainly cannot be ruled out.

References:

1. Barnosky, A., Koch, P., Feranec, R., Wing, S. & Shabel, A., Assessing the Causes of Late Pleistocene Extinctions on the Continents. Science 306, 70-75 (2004).

2. Lyons, K., Smith, F. & Brown, J., Of mice, mastodons and men: human-mediated extinctions on four continents. Evolutionary Ecology Research 6, 339–358 (2004).

3. Koch, P. & Barnosky, A., Late Quaternary Extinctions: State of the Debate. The Annual Review of Ecology, Evolution, and Systematics 37, 215–250 (2006).

4. Barnosky, A., Megafauna biomass tradeoff as a driver of Quaternary and future extinctions. PNAS 105 (Suppl. 1), 11543–11548 (2008).

5. Firestone, R. et al., Evidence for an extraterrestrial impact 12,900 years ago that contributed to the megafaunal extinctions and the Younger Dryas cooling. PNAS 104 (41), 16016–16021 (2007).

6. Haynes, V., Younger Dryas ‘‘black mats’’ and the Rancholabrean termination in North America. PNAS 105 (18), 6520–6525 (2008).

7. Kennett, D. et al., Nanodiamonds in the Younger Dryas Boundary Sediment Layer. Science 323, 94 (2009).

8. Israde-Alcántara, I. et al., Evidence from central Mexico supporting the Younger Dryas extraterrestrial impact hypothesis. PNAS 109 (13), E738-E747 (2012).

9. Bunch, T. et al., Very high-temperature impact melt products as evidence for cosmic airbursts and impacts 12,900 years ago. PNAS 109 (28), E1903-E1912 (2012).

10. Petaev, M., Huang, S., Jacobsen, S. & Zindler, A., Large Pt anomaly in the Greenland ice core points to a cataclysm at the onset of Younger Dryas. PNAS 110 (32), 12917-12920 (2013).

11. Taylor, K. et al., The Holocene–Younger Dryas Transition Recorded at Summit, Greenland. Science 278, 825-827 (1997).

12. Severinghaus, J., Sowers, T., Brook, E., Alley, R. & Bender, M., Timing of abrupt climate change at the end of the Younger Dryas interval from thermally fractionated gases in polar ice. Nature 391, 141-146 (1998).

13. Murton, J., Bateman, M., Dallimore, S., Teller, J. & Yang, Z., Identification of Younger Dryas outburst flood path from Lake Agassiz to the Arctic Ocean. Nature 464, 740-743 (2010).

14. Moreno, P., Jacobson, G., Lowell, T. & Denton, G., Interhemispheric climate links revealed by a late-glacial cooling episode in southern Chile. Nature 409 , 804-808 (2001).

15. Daulton, T., Pinter, N. & Scott, A., No evidence of nanodiamonds in Younger–Dryas sediments to support an impact event. PNAS 107 (37), 16043-16047 (2010).

16. Marlon, J. et al., Wildfire responses to abrupt climate change in North America. PNAS 106 (8), 2519–2524 (2009).

17. Surovell, T. et al., An independent evaluation of the Younger Dryas extraterrestrial impact hypothesis. PNAS 106 (43), 18155-18158 (2009).

18. Gill, J. et al., Paleoecological changes at Lake Cuitzeo were not consistent with an extraterrestrial impact. PNAS 109 (34), E2243 (2012).

Return from Beringia

Linguistic study suggests Ice Age groups migrated back to Central Asia from Bering land bridge.

The New World was the last habitable part of the globe to be settled by humans. Today, Alaska is separated from eastern Siberia by the Bering Strait, which is 55 km (18 miles) wide, but this has not always been the case. Throughout the period from 25,000 years ago until as late as 10,000 years ago, sea levels were so low that the strait and parts of the adjoining Chukchi and Bering Seas became dry land. The result was a landmass stretching from the Verkhoyansk Range in eastern Siberia to the Mackenzie River in northwestern Canada (Hoffecker, et al., 1993). Known as Beringia, this so-called ‘land bridge’ was 1,600 km (1,000 miles) from north to south and linked Asia to North America. The region remained dry and cold, but free of ice. It is thought to have been an open landscape covered with grasses and herbaceous tundra and steppe vegetation (Guthrie, 2001; Zazula, et al., 2006). It is via the Beringia land bridge that humans are long believed to have first reached the New World, but the number of migrations and their timing have been hotly debated for many decades.

Much of our understanding of these migrations has come from archaeological and genetic data. The genetic results suggest that the New World was populated in three migrations: a major migration associated with the First Americans or Paleoindians; a second migration associated with Na-Dene language speakers distributed mainly in northwestern Canada, Alaska and along the Pacific Coast; and a third migration associated with Eskimo-Aleut language speakers, who are restricted to the Aleutian Islands and the Arctic (Reich, et al., 2012).

A third approach to understanding prehistoric migrations is comparative linguistics. In 1986, the American linguist Joseph Greenberg (1986) used this method in an attempt to identify the number of migrations into the New World. It has long been known that languages evolve over time, and that there are language ‘families’ or groups of languages that share common origins. Greenberg began by assuming each group of migrants spoke their own language and that over time a language family arose from each founding language. In earlier work going back to the 1960s, Greenberg claimed that there were three language families: Amerind, Na-Dene and Aleut-Eskimo. His conclusion – now vindicated by genetics – is that there were three migrations.

Up until now, however, linguists have been unable to link the three language groups to those in Asia. It has long been suspected that there is a linguistic connection between the Na-Dene languages and the Yeniseian languages of Siberia, but it remains unproven. A new study has investigated the possible relationship, using phylogenetic methods to build up a linguistic family tree. In the last decade, computational phylogenetic tools developed primarily to study relationships in evolutionary biology have been adapted for use in the field of historical linguistics. These new techniques have been used to study prehistoric migrations and language classifications as far back as the latter part of the last Ice Age.

The researchers applied the technique to 40 languages spoken across North America and Asia. The resulting family tree was used to test various migration hypotheses. The results suggested that there was an early dispersal of Na-Dene populations along the North American coast and a Yeniseian migration back into Siberia. This was followed by a dispersal of Na-Dene languages into the North American interior. The study does not contradict the widely-accepted scenario that the New World was settled from Beringia, but complicates it with the insight that some groups in Beringia migrated back in the opposite direction (Sicoli & Holton, 2914).

References:

1. Hoffecker, J., Powers, R. & Goebel, T., The Colonization of Beringia and the Peopling of the New World. Science 259, 46-53 (1993).

2. Guthrie, D., Origin and causes of the mammoth steppe: a story of cloud cover, woolly mammal tooth pits, buckles, and inside-out Beringia. Quaternary Science Reviews 20, 549-574 (2001).

3. Zazula, G. et al., Vegetation buried under Dawson tephra (25,300 14C years BP) and locally diverse late Pleistocene paleoenvironments of Goldbottom Creek, Yukon, Canada. Palaeogeography, Palaeoclimatology, Palaeoecology 242, 253–286 (2006).

4. Reich, D. et al., Reconstructing Native American population history. Nature 488, 370–374 (2012).

5. Greenberg, J., Turner, C. & Zegura, S., The Settlement of the Americas: A Comparison of the Linguistic, Dental, and Genetic Evidence. Current Anthropology 27 (5), 477-497 (1986).

6. Sicoli, M. & Holton, G., Linguistic Phylogenies Support Back-Migration from Beringia to Asia. PLoS One 9 (3), e91722 (2914).

Chauvet cave paintings may be far more recent than generally believed

French archaeologists claim that prehistoric artwork thought to be 36,000 years old is actually 10,000 years younger.

Chauvet Cave is located near the village of Vallon-Pont-d’Arc, Ardèche in southern France. The cave was discovered in 1994 by a team of cavers led by Jean-Marie Chauvet, for whom the site was named. It was the most important cave painting find since the discovery of Lascaux by a group of teenagers during World War II. Unlike the 18,000-year-old Lascaux cave paintings, which became a major tourist attraction after the war and deteriorated badly as a result, Chauvet was rapidly taken over by the French government and a strict conservation program was put in hand.

The artwork comprises 425 panels, depicting rhinoceroses, lions, bears, mammoths, horses, bison, ibex, reindeer, red deer, aurochs, muskoxen, panthers, and the earliest-known representation of an owl turning its head through 180 degrees. Hand prints, red dots and a partial image of a woman associated with a bison have also been discovered.

Radiocarbon dates indicating that the paintings are around 36,000 years old are widely accepted. This would date them to the late Aurignacian period, and make them twice as old as Lascaux. Put another way, the radiocarbon dates suggest that Lascaux is separated from Chauvet by the same interval of time that separates it from the first landing on the Moon. However, archaeologists Jean Combier and Guy Jouve have cast doubt on the great antiquity of the Chauvet paintings.

They argue that on stylistic grounds, the Chauvet artwork cannot be associated with the Aurignacian period. Instead, they claim, the artwork shows affinities to that of the more recent Gravettian and Solutrean periods. Therefore the oldest paintings at Chauvet cannot be more than 26,000 years old. The later ones might even be contemporary with Lascaux.

That Chauvet dates to the Solutrean period was the initial impression of Jean Clottes, one of France’s most eminent prehistorians. Clottes made his assessment in 1995, before any radiocarbon dates were available. His dating of the artwork on purely stylistic grounds was subsequently dismissed as ‘foolhardy’ – but could it be that relying purely on radiocarbon dates is equally unwise?

When first introduced in the 1950s, radiocarbon dating revolutionised archaeology and Willard Libby, the American chemist who pioneered the technique, was awarded the Nobel Prize in Chemistry in 1960. However, radiocarbon dating is not infallible. For example, it is very easy for a sample to become contaminated with more recent organic material that will slew results.

In the case of Chauvet, radiocarbon dates were obtained from wood charcoal used as black pigment. However, Combier and Jouve suggest fossil carbon was used as well as charcoal. This was available at Vagnas, a village not far from Vallon-Pont-d’Arc, where there was a quarry yielding lignite and bitumen. A pigment comprising a mixture of fresh charcoal and fossil carbon would present as being significantly older than one containing fresh charcoal alone.

Combier and Jouve note that such a mixture would also have a different isotopic signature to that of pure wood charcoal, i.e. the proportions of the stable carbon isotopes carbon-12 and carbon-13 would differ between the two. It would thus be possible to show whether or not the Chauvet dates were suspect. Such an anomaly has been detected at another cave site, Candamo Cave in Spain, although in this case the ‘old’ carbon leeched into the pigment from the limestone walls of the cave through the action of bacteria.

Accordingly, Combier and Jouve suggest that fresh radiocarbon dates should be obtained for Chauvet, and they believe that it extremely important that more than one laboratory carries out the work.

References:

1. Clottes, J., Cave Art (Phaidon, New York, 2008).
2. Combier, J. & Jouve, G., Chauvet cave’s art is not Aurignacian: a new examination of the archaeological evidence and dating procedures. Quartär 59, 131-152 (2012).
3. Combier, J. & Jouve, G., Nouvelles recherches sur l’identité culturelle et stylistique de la grotte Chauvet et sur sa datation par la méthode du 14C. L'Anthropologie ( (in press) doi:10.1016/j.anthro.2013.12.001) (2014).
4. Mellars, P., A new radiocarbon revolution and the dispersal of modern humans in Eurasia. Nature 493, 931-935 (2006).