DNA testing – Part 3 – Follow-up

June 5, 2017 at 10:27 pm | Posted in Health, History, Online services, Science | 1 Comment
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I’ve written before on DNA testing. In the first article in 2015, I compared the 4 prominent services for personal DNA testing. I chose 23andme. I then reported the broader results. Now I have some updates to that discussion.

It’s turned out the Y chromosome has had a lot more mutation than the maternal line so they had to update the haplogroup naming conventions last year. The original paternal haplogroup name is no longer current and the tree more complex. In my case, the guys wandered further too.

A few terms for the major testing:
Autosomal is the 22 pairs of chromosomes in the cells nucleus, excluding the pair of sex chromosomes. It’s the broad overview and allows you to match to other family members, etc.

Y-DNA is the Y or male sex chromosome. It traces your male line back: fathers, fathers, father, etc. You need to be a male or have a male member of the family tested for this one.

mtDNA – mitochondrial DNA comes from the mitochondria. It is passed down from mothers to both sons and daughters. It traces the mothers line back: mothers, mothers, mothers, etc.

Haplogroup – those that share a common ancestor based on haplotypes, groups of genes inherited from a single parent. We all have a paternal and maternal haplogroup. Haplogroups can be viewed in a tree structure of sequential mutations.

They can trace these 2 lines back roughly 100,000 years now for well-tested populations.

23andMe
Skip forward 2 years and 23andMe has finally upgraded my data to their new site format as promised. For a while, they were offering health results only to Canada and the UK due to US restrictions on “diagnosis.” With the site redesign, they’ve removed a lot of the more detailed health analysis and focus now on general markers like lactose intolerance, sleep depth, and so forth. Gone are more diagnostic things like Celiac and Parkinson’s markers.

Reporting is more centralized and distributed to tabs to support smaller screens. It surprised me to discover printing the reports (for me to PDF) gave a more complete view.

A new report on the Maternal line (haplogroups) goes back as far as the National Geographic’s “Deep Ancestry” report (below) although the second has slightly more detail.

The paternal haplogroup name was updated but there’s a gap between the tree map in the paternal section and the specific haplogroup named. As I discovered on FTDNA below, it’s also less specific.

Genographic
Meantime, I had also decided to take advantage of a sale on National Geographic’s Genographic Project. I wanted to support their work, and it offers more of a deep ancestry approach.

Here a deviation has taken place. Family Tree DNA used to do all their testing, allowing you to load your DNA test results into FTDNA (below) afterwards for free. However, for US customers, Helix is now doing their testing. They’re using a newer system that is not compatible with FTDNA. If you get the Helix test (white box, spit not swab), you can’t download the genome after either.

But as I’m Canadian, I still got the black, cheek swab kit to send to FTDNA in Texas.

My first impression of the Genographic results wasn’t positive – they didn’t notify me when the results were up. And the first presented report is “Genius” matches. It displayed famous people (not geniuses) who had some unmentioned genetic match. Essentially a pointless report.

The Regional Ancestry report had quite different percents from 23andMe but I suspect was less accurate due to the much smaller testing population.

What I did enjoy was the Deep Ancestry reports. This showed the maternal and paternal lines over thousands of years, migrating across vast distances as the ages changed.

There is also a Hominin report for the percent of Neanderthal DNA. This varied substantially from the 23andMe result as well.

Another disappointment was printing. The reports didn’t print well and the official printable report that summarized much of the above was missing all the maps even though the reports refer to them. I had to use screen captures for the maps and assemble them with the reports myself.

Given that 23andMe now includes very similar reports and has a great deal more other ones, it’s certainly preferable. It’s possible the Helix testing for Americans offers more reports or detail but that’s unclear. I suspect 23andMe would still be superior.

Family Tree DNA
Because I got the old Genographic kit, I could transfer the results to Family Tree DNA for free. This allowed downloading the Genome file and offered a few basic reports.

One of note though was the Y-DNA haplotree. This went much further than 23andMe, offering a Haplogroup that was 15 steps more detailed. And there they offered a further test (at a cost) to take it a few steps further.

From this, I discovered the links between the 23andMe paternal map and their designation of my haplogroup plus further steps that FTDNA named.

One of the bigger differences with FTDNA is their a la carte approach to ordering tests. You send in or transfer one sample and then pay just for the tests you want when you want them. Where the others above include autosomal, mtDNA, and Y-DNA, FTDNA lets you choose. Y-DNA is of no use for women, for example, as they don’t have the Y chromosome.

You can also choose the degree of testing for the mt and Y reports. If you’re a male and test all 3 at the basic level, it will cost you more than these others. But for serious researchers, there is a level of detail available you don’t see in the one-size services.

The site has many “projects” where members discuss details of their research. The one’s I looked at required the Y67 test to join as they were specific to certain haplogroups.

FTDNA offered me a significant autosomal discount, so I ordered the Family Finder test to connect with a few relatives on the system. This gave me the Matches section and Chromosome browser, similar to what 23andMe has. The Origins reports where too general to be of much use. They did not match known family regions either.

Also note they’re using the oldest technology now.

Conclusions
I’d still recommend 23andMe for the overview. Their reports are broader and bring a more complete perspective. They use newer tech and have a larger customer base which increases accuracy and matches.

Family Tree DNA is superior if you want to explore genealogy in greater detail. They have more detailed test options but use older tech and are more expensive. Just understanding the value of their options requires a serious exploration.

National Geographic Genographic Project loses much of it’s advantage as others begin to include deep ancestry reporting. With their migration to the newer tech, it can’t be uploaded to FTDNA nor the genome downloaded for other services.

Ancestry also includes a DNA testing service but this would only be helpful if you use their services already. The family tree building software is sophisticated but is an ongoing expense.

From some of the commentary I’ve read on-line, serious researchers use several of the services for different features and to connect with different populations. As the number tested grows, the detail levels will increase. Added features will make going back in and taking a look around again useful, even for the casually curious.
David

Johnny Appleseed

December 24, 2016 at 2:55 pm | Posted in History | Leave a comment

When I was young, we used to sing grace before family meals. To engage us more, our mother had my sisters and I take turns leading grace. We each got to choose ours and I chose Johnny Appleseed. It was lively and brief.

“Oooooh, the Lord is good to me, and so I thank the Lord, for giving me the things I need, the sun and the rain and the apple seed. The Lord is good to me.”

This turns out to be called the Johnny Appleseed Traveling Song or the Swedenborgian hymn. Johnny Appleseed’s real name was John Chapman. He was an eccentric orchardist and Swedenborgian missionary. While he planted many apple trees, he did so in nursery’s. He didn’t plant apple trees everywhere he went as told in the legends, nor was his story like The Man Who Planted Trees. He encouraged planting apple trees and his plantings were spread widely. But his barefoot traveling was mostly as a missionary. He evidently didn’t believe in grafting, growing only native species suitable for cider and applesauce. More.

Certainly a character though, and the stories probably contributed to the popularity of apples in North America.  And yeah, a little off-season but recent events brought him to mind.
David

Quoting Shakespeare

November 28, 2016 at 12:31 pm | Posted in History | Leave a comment

Have you ever said “for goodness sake”? What about “rant” or “a wild goose chase”? You may not think you quote Shakespeare on a regular basis but a surprising number of phrases can be traced back to his plays. “Zany”, eh? We don’t know which phrases where common at the time and which where original Shakespeare witticisms, but his plays have ensured they’ve lasted hundreds of years.

Here’s a list of 50 phrases from the Bard. It will leave you “Bedazzled”.
David

Kiva’s History

June 12, 2016 at 12:26 pm | Posted in Economoney, History, Internet, Online services | Leave a comment
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I began micro-loaning with Kiva in 2008 and have written various articles on the subject. I’ve now given 24 loans in 17 countries. In one case, the local lending organization failed, impacting the loan repayment. In another, there was a small loss due to currency exchange values. But the rest of the loans have been doing fine – farmers, students, grocers, groups, and more. A small infusion has kept the process going and slightly expanded the number of loans I can make. The cost for me has been tiny compared to the impact. As the funds are repaid, I reloan them.

Kiva has recently released a video showing their history. It also gives a sense of it’s impact. This is a better repayment rate than in the west.

On YouTube

Music Sequencing

April 16, 2016 at 2:44 pm | Posted in Computers, Hardware, History, Music, Software | 1 Comment
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If you’re not a musician, you may be unaware of one trend in modern music –  sequencing.

Many years ago, sequencing software first arose in tools like Cakewalk. You added a track for each instrument and placed “notes” that used MIDI data. MIDI is a digital language for music data that allowed various devices, instruments and computers to talk. It could produce synthetic notes from pre-defined instruments. Computer sound cards of the day added MIDI instruments to their repertoire.

Old Cakewalk
(the software looks complex but is mainly a series of modules. Tracks, sequencing, notation, mixer, etc.)

You could compose complex songs in such software, or just use it for background tracks like drums and bass.

Over time, the ability to add pre-recorded sample sounds of live instruments was added, greatly expanding the quality and flexibility.

You sometimes hear sequencing software used in live performances to duplicate studio techniques that can’t be easily reproduced on stage – like a backup orchestra. It may sound like prerecorded content – which might also be used – but sequencing software allows adjusting the tempo and changing other details live that can’t be done with recorded content.

A friend of mine, who is not a musician, composes entire songs with samples in sequencing software. He markets the resulting albums on-line and makes a small income from his hobby. Such software now has thousands of instruments available and more can be added.

A parallel development was in instruments like drum pads where rubber pads could be used to trigger pre-programmed drum sets. This allowed drummers to expand their available drums but also to practice much more quietly.

drum pad
Similarly, piano keyboard controllers came out that were used to trigger software or other keyboards (via MIDI) rather than having built-in sounds. They were just a keyboard – like another form of your computer keyboard.

Over time, “pad controllers” were added to other instruments like keyboards as it was easier to play drums or trigger events with pads than keys. Then the controllers became instruments in themselves. They’re used to trigger digital events in computer software – either an individual sound sample (like playing an instrument) or an entire pre-programmed sequence.

nanopad
This shifted sequencing from a software process into a performance process. Recorded as a sequence, any errors can be easily corrected, samples upgraded, and so forth before recording a final song.

Unlike a typical instrument where this key is middle C, and that one is C5; pad controllers are entirely programmable. Any given pad can be anything. And then be something else for the next song. Better controllers have pads that are both touch and pressure sensitive so they can be quite expressive, giving contours to the programmed sound.

Controllers are also inexpensive compared to traditional instruments as the basics are simple. They’re a group of fancy buttons. All the sounds and intelligence are in the software. That’s where you do the programming, assigning sounds to keys. Then you can record the result – as a song or as a sequence to further polish.

In this example, notice how even voice is used as an “instrument” via pre-recorded samples. Also notice the sound samples being played have various lengths – some short, some longer. This is different from a normal instrument.

You have to have good spatial memory for this.
Here’s someone with 2:

A basic 16 pad unit with “lite” versions of the needed software is only about $30. It also works with pretty much any sequencing software like the free Hydrogen drums. (a dedicated drum sequencer, what might be called a software drum machine)

At first, people used pads for programming sequences. But pretty quickly, they began using them in live performance too. I saw a single live musician with a digital drum pad lay down the bass drum beat, then the next drum, then the next, building up over a dozen instruments, then jamming over the top. It has an interesting crescendo effect. One musician playing multiple parts in a kind of time dilation.

A related example:

The next stage of that was recording acoustic instrument samples live into a sequencer and then having that play back while they added other layers. The lines between live and recorded, acoustic and digital all blur.

Here’s an example – watch them use the foot pedal to mark the end of a sample recording. The pedal is carefully triggered so the sequence repeats from that point. (this is called looping) Notice a pad controller also being used but they’re using various triggers.

You don’t see pad instrumentalists on mainstream radio much yet. It’s a new style of musician – but they’re quite common on the net. It will be fascinating to see where this evolves.
David

The Pitchforks are Coming

July 2, 2014 at 5:30 pm | Posted in Economoney, History, Media | 2 Comments

An essay from a .01%er, Nick Hanauer, on why the increasing disparity between the wealthy and the poor is bad for everyone. And why a living wage will restore the middle class and help support the wealthy to stay such.

As he correctly observes, no civilization has Ever lasted when this income disparity has continued. It either becomes a police state or a revolution. Always. The question is only when.

He gives a few real examples where his ideas have worked while observing how trickle-down is not working. “the highest rate of job growth by small businesses are San Francisco and Seattle. Guess which cities have the highest minimum wage? San Francisco and Seattle.

Dear 1%ers, many of our fellow citizens are starting to believe that capitalism itself is the problem. I disagree, and I’m sure you do too. Capitalism, when well managed, is the greatest social technology ever invented to create prosperity in human societies. But capitalism left unchecked tends toward concentration and collapse. It can be managed either to benefit the few in the near term or the many in the long term. The work of democracies is to bend it to the latter. That is why investments in the middle class work.

I’m not an economist but I agree the imbalance needs correction – for so many reasons.
David

Hardware Commons

June 10, 2014 at 10:30 am | Posted in Design, Economoney, Hardware, History, Internet, Media, Science, Technology | Leave a comment

Just as software has it’s open source and licensing has Creative Commons, open knowledge of hardware is crucial for us to grow as a society in healthy ways. I recently wrote a similar article on network infrastructure – an open Internet.

Why is this even an issue? Current laws concentrate knowledge into property rights for economic control rather than the common good. Corporate structures, treated legally as a person and thus given the same rights, are concentrating economic activity into monopolies. The result is the concentration of knowledge and wealth in a progressively smaller group, the so-called 1%. (although that’s overstating it now) This has historically destabilized and destroyed civilizations.

If we’re going to learn the lessons of history, we need more balance and a more diversified economy. We need opportunity in the commons and that is best served by accessible knowledge.

This increased access to knowledge is hugely important…it acts as the foundational infrastructure on which we can start to build a whole new economy.”
— Alastair Parvin of WikiHouse

This video outlines how it can be applied to hardware:

And this page lists 10 open hardware projects. If you’ve been around long enough you’ll recognize the Access to Tools theme that was common in the old Whole Earth Catalogue. It was also a theme of R. Buckminster Fuller.
David

World History

March 17, 2014 at 9:16 pm | Posted in Economoney, History, Media, Software | 1 Comment

We’ve all learned something of world history in school, of the empires built up and fallen. But the degree of change over the years, largely though conflict and war, is far greater than the larger conquests. Many an area became organized then collapsed as an entity or was absorbed by a neighbour. Names changed many times. The World Wars brought distant governments dividing communities in non-historical ways, leading to many of the conflicts of more recent years, like Iraq, Eastern Europe and the Crimea.

“The study of history is a powerful antidote to contemporary arrogance.”
– Paul Johnson

Here’s a site with world maps, showing Europe and area around 1 CE (AD). Click up the list on the left to see it evolve. The Historical Maps link up top also has links to Middle East and World History.

If you’d prefer to see this animated, this video shows the evolving map from 1000 BC  – 1000 AD.

And this from 1000 AD to the present time. Evidently its the output from Centennia software but the dates are not properly synced to the maps. Comments also complain about some details in the maps. However, the point is the larger flow of territory and rulership. History is written by the conquerors.

“Those who do not remember the past are condemned to repeat it.”
– George Santayana

I can also note that territory naming often does not represent what that country called itself. Japan, for example, does not call itself that. That’s not even an Anglicized version. Rude, or what?

“That men do not learn very much from the lessons of history is the most important of all the lessons of history.”
– Aldous Huxley

It certainly gives perspective on claims of “historical lands” too. The new trend in searching ancestry via personal genetic testing reveals it’s not your land and my land but our land.
David

First Nations and Vancouver

March 6, 2014 at 5:28 pm | Posted in History, Media | Leave a comment
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The City of Vancouver has produced a Guide for newcomers to aid in establishing roots here. Along with that is an overview of local First Nations (PDF) as it’s often something an immigrant is interested in but not always readily accessible. It’s also a useful general summary of local First Nations for everyone.

As may be obvious from the maps, there is a great deal of overlap in traditional territories. Lands were not owned and thus not formerly defined by fixed boundaries. Rather, they were working territories that included seasonal uses. When finally the provincial government agreed to treaty negotiations, they began by working with individual nations. But until the overlaps had been negotiated and defined, it created an unfair process and problems with individual treaties. Not every nation was as far along in establishing self-government expertise to handle such an important representation. Instead, the nations needed to negotiate amongst themselves and bring that agreement to the provincial government to negotiate their own settlement. This required a common meeting ground as this Chiefs document (PDF) reviews.

We have a rich history, far beyond a one hundred year-old building or a European sailing ship.
David

The Ultimate Mindbomb

January 23, 2014 at 9:43 pm | Posted in Events, History, Internet, Media, Movies | Leave a comment

At a TEDx talk in Victoria, Ian MacKenzie explores the history of the mask that came to be used by Anonymous, then the Occupy movement. Then he looks at the Occupy movement itself. Then how to Occupy the Noosphere with Memes via Mindbombs.

What is the ultimate Mindbomb we could release?

Ian MacKenzie

Ian was also involved in Velcrow Ripper’s film, Occupy Love. While not as far reaching as the 2 previous films in his trilogy, it does better explain the Occupy phenomena than anything else I’ve seen.
David

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