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 The original paternal haplogroup name is no longer current and the tree more complex.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

What3Words Global Addressing

May 14, 2017 at 10:11 pm | Posted in Internet, Online services, Software, Technology, Web Apps | Leave a comment
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You may be familiar with the domain name system for the Internet. By using domain name servers, the human-friendly domain name is converted into the actual numerical IP address of the web server. For example, you can type Google.com into your browser and it will look up the real address of the server, then load the site. This is much easier than remembering something like 216.58.194.78. And this is even more true of the coming IPv6 that will have much longer numbers.

This issue is greater still for mapping the world. Street addressing is somewhat random and in older cities like London or Tokyo, is rather a maze. And what of meeting someone in a large space like a stadium parking lot or a busy monument? And what about all the places that don’t have an address, like a park or forest?

The US Air Force developed the space-based Navstar Global Positioning System (now just called GPS) in 1973. It was fully rolled out by 1995 but only low level resolution was available to the public then. It has been progressively upgraded since and other overlapping systems have been added by other governments. With a GPS receiver, we can locate ourselves quite specifically on the earth. Most modern cell phones include one.

But once again, we have the same issue as with a server IP address. How human-friendly is a latitude & longitude like 49.303371, -123.136826? What about telling someone to meet you at marching.commented.priced instead?

Huh?

This is where What3Words (w3w) comes in. This is a tool that converts the GPS of a 3 sq meter (about 9′ square) space into 3 random words. 57 trillion human-relatable spaces on the globe and each can be addressed with 3 simple dictionary words. The words are randomized to avoid confusing similar words nearby. Thus, unlike street addresses or postal codes that are usually sequential, w3w is not.

Youtube

Where are you now? You can do a search, then drag the map to place the pointer at your exact location. Simple.

You can search by street address or by w3w address. If searching by street address, be careful with mapping accuracy. Google Maps addressing isn’t perfect. I’ve reported errors to them a few times.

In the free smartphone w3w app, Compass will tell you where you are. Its accuracy depends on if you have GPS turned on in your phone. With it off, my cell phone had a 21m radius of accuracy. Surprisingly close but not precise. With GPS on, it dropped to 7-12m – a big improvement but not the 3m accuracy of the grid. To give an exact address, you can drag the marker to the precise location first. And that depends on the quality of the map – w3w does offer several map options.

The key is giving an accurate reference point to the recipient, then it’s easy for them to find it.

There is no intuitive way of cross-checking accuracy if the map is vague or your GPS is imprecise. Also, the location entirely depends on their system as there is no real-world reference points for w3w, like an address on a building. But I can certainly see the advantages for sharing a point when there isn’t good street address references. Or you want someone to come to a side or back door. The above ‘marching.commented.priced‘ example is on a trail in a large park in western Canada. Want to go to Beaver Lake?

As the technology in use gets more refined, this will automatically become more precise.

w3w is an interesting idea that is evidently being used by transport and delivery companies in parts of the world where addressing has been an issue. If you have trouble getting people to the right place, it may be useful for you too.
David

Web Bias

November 14, 2016 at 6:59 pm | Posted in Computers, Economoney, Internet, Online services, Web Apps | 1 Comment
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As people shift more and more to getting news and information from the web, there’s an important detail we might overlook. While we may know a paper is conservative or a station is alternative, the web behaves differently. Many of the larger sites automatically filter content to favour our apparent interests. For example, you’ve probably noticed that if you watch a cat video on YouTube, it will automatically “recommend” more of the same. Many large sites do much the same.

While this may be convenient and help keep us on the site (and seeing ads), it narrows our view of the world by creating a bubble of information. A few years back, I posted a TED talk on the subject.

The recent US election has brought the subject to the fore, along with issues of “fake” news. Facebook is denying it’s news feed had an influence on the election. But the Wall Street Journal has done an interesting mock-up that illustrates the issue in action. You can see how very different the 2 feeds are for a subject. Keep in mind this is not just true of Facebook.

Friends have tested search engines similarly. Test the same search on 2 different computers – one in the financial district and the other in a poor part of town. Completely different results. Multiply this across many sites and it can affect your sense of the world.

The key – diversify your sources and pay attention to reputable international news sites that bring an out-of-country perspective. You can also use a tool like DuckDuckGo to search Google while reducing some of the tracking.

To take this further, what we see of the world will reinforce Cognitive Bias. If you’re unfamiliar, here’s a summary of 12 types. And Facebook has their own page on “Managing Bias“.
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

Temperament

April 20, 2016 at 9:07 pm | Posted in Online services, Psychology | 12 Comments
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Understanding who and how you are and what you have to offer is a big part of finding a fulfilling life and a place in society. Yet we often discover such things by happenstance or difficult experience. Most of what we’re given is generic rules and training that rarely suits us.

Often, we don’t entirely recognize our own abilities and temperament because they’re innate and we assume our experience is similar to others. Yet how we’re distinct points to what we have to offer.

This is where aptitude and related testing can shine a light for us. But testing without temperament can put you on the wrong track. I spent some decades taking pokes at a desired and recommended career goal before I finally realized it required a specific temperament I didn’t have.

The psychologist Carl Jung observed 3 personality polarities in the 1920’s, then his daughter added the 4th. The Myers-Briggs mother-daughter team extrapolated that into the Myers-Briggs test (MBTI). Various versions of mixed quality have shown up over the years and on-line.

Jung went on to develop the Jungian Archetypes from his research, a more symbolic approach to the memes underlying traits.

MBTI is essentially our preferences in how we see the world and make decisions. Some polarities can be quite strong and others less so, though we tend to moderate with age. The results also tend to evolve over time. While not seen as entirely reliable, many find them quite insightful.

MyersBriggsTypes(click the image to see a larger version)
It’s worth noting that the personality types are not evenly distributed in the population.

The full MBTI test is a 6 hour affair where you not only get to know your own type but your contrast with others of each of the opposite polarities. You can also get tested personally by certified testers.

Over the years, I’ve taken the full test and tried a few free on-line tests. One’s I found insightful:

Humanmetrics has a Jungian version.

Keirsey developed a variant based more on behavior and shifted the emphasis a bit. That has a test here.

And recently, I ran into another variant “16 Personalities” that adds a 5th polarity: Assertive/Turbulent.

(I didn’t have any trouble with any of these sites abusing my contact info)

After testing, I’ve also found these profiles useful.

Have fun with it.
David

Stargazing

March 25, 2016 at 2:14 pm | Posted in Online services, Science, Space | 1 Comment
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We’ve developed the bad habit of leaving the lights on all night. On streets, on porches and in yards, on stores and in offices. A world that never sleeps and never sees the Milky Way.

“Stargazing is extinct in cities like New York City and London, but it’s also endangered in places all over the world because of urbanization. We rounded up the most incredible places to see the night sky, and a few places that need to be preserved.”

The Weather Channel has set up images from various low light locations around the world that are ideal for watching the night sky. Does the night sky above you look like this? Best is on New Moon nights, so they offer a calendar too.

Light pollution ruins star gazing but also restful sleep, natural rhythms and thus health. Blackout curtains can help but then you can’t wake with the sun. Motion detectors can make a big difference on your property.
David

Lorem Ipsum

September 30, 2015 at 5:53 pm | Posted in Online services, Software, Writing | Leave a comment
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You may have occasionally run into a web site containing nonsense text that looks sort of Latin. Like this:

“Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.”

This is known as “Lorem Ipsum” or dummy text. It’s used to test page formatting without the distraction of real words with meaning. In fact, it’s been used since the 1500’s when an unknown printer scrambled type to make a type sample book. Remarkably, it has survived throughout the centuries of publishing, into Letraset and on into desktop publishing software and web design tools.

A surprise to me, it’s not completely random text but is actually derived from a Latin work by Cicero from 45 BC – a text on  ethics and good & evil. In other words – it does have Latin roots. However, some of the modern editions have humour and other inappropriate edits mixed in, so be careful of your source.

Here’s is a handy site that discusses the above, shows the original source text, and offers a tool to create randomized dummy text as required. You can choose to start it with the original first sentence but the rest is randomized each time.

Imagine – one could create a large blog, full of articles that contain entirely random text. Ah, the possibilities.  🙂
David

On-line Editors

September 20, 2015 at 3:44 pm | Posted in Books, Internet, Online services, Software, Web Apps | 9 Comments
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Writing a book or other long form project isn’t just the writing. It’s also the editing, the publishing and the marketing. Few who start a book project ever produce a complete manuscript. And fewer of those get through the next hurdles. There’s a good reason why many never get it out there.

In these days of self-publishing and ebooks, many more have the chance to get their works published in some form. But without a publisher, too many are skipping some of the steps. Too many titles have gotten into distribution channels without decent editing. That brings down the whole market.

While word processing software has spell and grammar checking built in, this is not “editing”. It only handles some basic kinds of typos.

Traditional publishers will take a manuscript through 4 or more rounds of editing specialists. But you at least want a Substantive Editor to look at the structure, flow, and the coherence of the work and a Copy Editor to take a closer look at word use and proofread the niggly details. You may also need fact checking.

Recently, more advanced editing software has become available that can help with copy editing. You have to go through each suggested edit to make sure it’s valid, but it can cover a lot of the worst mistakes before you have real eyes on the work. That can make the copy editor’s job much easier.

Most of these tools are web services with a subscription model – you pay annually for access via the web. Sometimes, the tools have Word or other add-ins that bring the interface into your software. Some work only with Word.

A few also offer plagiarism services that check if you’ve copied off outside sources. In other words – a really bad idea. Checking has become easy and cheap so always quote your sources. It can also flag if you have potential sections where you might run into similarity problems later. Plus, the tool may help source your quotes.

I looked at various articles and reviews. Many pointed to a batch of similarly priced tools.

Grammarly often topped the pack but there was sometimes overt advertising influence. Personal reviews were more mixed and there were a lot of reports of unresolved over-billing or being billed for the free trial. Plagiarism checking is included.

WhiteSmoke seemed decent but the setup wasn’t as useful for me. Their web site looks to be infected, so I’m not linking them. One reviewer linked instead to another supplier, suggesting a long term problem.

CorrectEnglish looked decent. But all of these tools are over $100. That can become competitive with a copy editors rates if your primary need is one work.

Then I found a couple of writers blogs like Karen’s that suggested others. Further research showed all where positive about them.

The key one: ProWritingAid – you can actually use their on-line tool for free for a batch of smaller works but you have to manually make the suggested edits in your work. I ran a recently posted article though it and was surprised how many  mistakes it found. Doh! For $35 a year, you can do longer works and edit right in the text, then transfer the updates back. If you use Word or Google Docs, they have an add-in to edit right in the doc. WordPress too. For $5 more you get plagiarism checking.

They also have a decent blog talking about the industry, even inviting comparisons with similar products. And their Twitter feed is full related links, author articles, etc. They’re clearly into it.

Karen’s link above also mentioned the free (in beta) EditMinion. It only does small parts but does catch slightly different things. She suggested you use this first, then ProWritingAid.

She also mentioned a great tool if you’re writing non-fiction. WritingHouse gives you a free tool for assembling a Bibliography in the right format with all the little details.

Note that you have to resist the urge to get into fancy formatting of your work prematurely. That can get butchered by the editing process. Formatting comes after you have a polished draft. Plus the style of formatting will depend on your eventual publishing medium. Default word processing format is usually for 8.5 x 11″ paper. That’s useful for a PDF at best. Book formatting is quite distinct and digital ebooks and web publishing are each their own worlds. A carefully formatted print PDF looks terrible on an ebook reader, for example. Ebooks have to be able to flow into their viewing container.

When you get to this point, I’ve found the book Zero Cost Self Publishing by Stephen Norton useful. It’s a step-by-step how-to for print and the primary ebook distributors. And then there is the exploding world market for ebooks in other languages. Why stick with N. America when you can be a best-seller in China?

Long form writing, whatever the final output, is quite the process. We can all use a little help at different parts of the journey.
David

The Collection

August 26, 2015 at 3:58 pm | Posted in Computers, Media, Movies, Online services, Software | Leave a comment
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Movie Buffs come in many forms. There are those who like movies only in the theatres – perhaps at a favoured cinema or an art house. Others like to manage their own schedule and subscribe to various on-line services like Netflix to stream what and when. And still others like the physical media so they are independent. Or maybe they just like to collect. And of course there are mixtures – those who collect just fav films but go to the cinema for the big screen spectacles and stream others. And so on.

Over time, those collections can get to be large. We can start loosing track of what we have, what we’ve watched, what we’ve loaned and so forth. Myself, I began a simple spreadsheet. When that got too large, I migrated to a simple database. I looked at available free cataloging software like I use for my archive discs but didn’t find what I needed. I also recognized the benefit of storing the data external to the database, something most home office apps don’t do (Access, Base, etc). Good databases store their data externally, so I set up a jdbc database. That worked well for a year and then Java updated in a way that my office software didn’t. Broken.

Time for a new solution. After doing some online research and going over Gizmo and Lifehacker, I narrowed my choices down to 4 programs. DVD collection software has come a long ways. After trying several out, I found Eric’s Movie Database best met my needs.

It took a bit of fiddling to get the data out of the old broken database, then convert to csv format, then to add a couple of custom fields to EMDB (easy). It’s also good to review your old data to make sure its in a standardized format. Some of mine like dates was in shorthand that another database wouldn’t recognize. Then I was able to import a large collection into Eric’s. You can then run a batch update through IMDB and it downloaded a great deal more info than I ever tracked. So much easier than all that typing and now I had visual references too. A quick review allowed me to correct a few identification errors plus load TV episodes for those items.

EMDB is a vast improvement over my little custom database. I just enter the name and a couple of details and it collects all the rest. It’s packed with customization options. It has both manual and automatic backups. You can easily add another database for a different collection and cut and paste those titles over. And you can make the whole thing portable. I’m still discovering features.

If your collection is digital, such as on a NAS or media server, EMDB includes a file Location field. You can index an entire digital collection by file name (if you have good naming habits). And you can also launch the movie from within the software, if that works for your setup. Adding a new file, it will index it without even having to type the movies name.

For a small donation, Eric will send you a file to rename the program in your name.
David

Virtual Coupland

January 30, 2015 at 8:42 pm | Posted in Design, Humor, Internet, Media, Online services | Leave a comment

Douglas Coupland, the GenX author and artist recently had a “wildly popular” art show at Vancouver’s premier gallery, the VAG. It’s full of cultural memes, explored with some humour. This included a giant cast head of himself, onto which the public was invited to stick pieces of gum.

The Artist – from mixhart.ca

(not sure that exactly encourages respect for public art but…)

Google has memorialized it in their “Collections” and sent in a Street View team…  On this site, you can browse some sample images to the right, click Exhibits for more of an explanatory slide show or, on the left, click Street View and browse the galleries themselves. A virtual gallery walk. Keep an eye on the left map to help with directions. I can’t say the directional controls were as intuitive as a usual Street View, but it’s an interesting application of it.

The top menu bar also allows you to browse over 600 other galleries collections, plus some “User Galleries”, apparently assemblies of artwork by users.
David

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