Cavendish Lab at Cambridge University

Posted on February 5, 2014 by Roberta Estes

The old Cavendish Lab at Cambridge University, where Watson and Crick discovered DNA, is kind of like Mecca for people who love genetics. So is the Eagle Pub where they ate lunch daily and announced their discovery. I’m not convinced which is the more important.

Our family tour in September, 2013 was scheduled to visit Cambridge, England, after leaving London. I’ve been truly blessed this trip with the most wonderful coincidences. In London, our hotel was located just across Hyde Park from the Science Museum where Watson and Crick’s original DNA model is housed. In Cambridge, we are staying right around the corner from the Cavendish Lab where Watson and Crick discovered DNA. Talk about literally walking in the footsteps of the masters.

I was pleased when I discovered Cambridge on the itinerary, and I googled to find the Eagle Pub. I was excited to find that it was indeed within walking distance of the Cambridge City Hotel where we were staying. Although I don’t drink, I would visit the pub and raise a non-alcoholic brew for Watson and Crick’s momentous discovery. Problem is, I discovered, that they didn’t have any non-alcoholic brew. In fact, most of England views non-alcoholic brew as “why bother.” While I agree in concept, sometimes it’s not by choice.

Wondering why the Cavendish Lab is important?

The Cavendish Lab at Cambridge University was the birthplace of the discovery of DNA. James Watson and Francis Crick discovered DNA in this lab in 1953. This year of course is the 60^th anniversary of that discovery and James Watson was interviewed in celebration. Crick passed away in 2004.

Before visiting Cambridge, I tried to find the Cavendish Lab on a map and it looked to be entirely across the campus, which is not small. That made no sense to me, since the Eagle Pub was close to the hotel, but I accepted that I might not be able to see the lab. I’d have to be satisfied with the Eagle Pub.

Why is the Eagle Pub important? It’s where Watson and Crick lunched and probably did a lot of brainstorming. Pubs are like that in England.

On our day of arrival, a walking tour of the city with a guide, a retired professor, was scheduled for that afternoon. After we began the tour, around the first corner, on a street that was only wide enough for one car, and then no cars, I remembered to ask the guide about the original Cavendish Lab. Given that he was a retired professor, I figured if anyone knew, he would.

He smiled broadly, and said “I’m so glad you asked…it’s right up ahead.” To say I was thrilled is an understatement. In fact, this is one of the few locations I’m actually IN the photos, um, actually, in most all the photos. My cousins were so excited because I was excited that they took pictures of me. This was definitely “my day” on the trip. This photo of me, taken in front of the Eagle Pub pretty much sets the mood.

The Cavendish Lab, it turns out, was on the right hand side, just about where the road narrowed too much for any vehicle. There was a sign mounted on the wall of the building that this was indeed the old Cavendish Lab. There is a new Cavendish Lab across campus, the one I had seen on the map. So far, my luck on the DNA trail had been remarkably good.

I, of course, was thrilled to be where Watson and Crick began what would be a blooming industry 60 years later with a world of promise. In another 50 years, DNA will be responsible for the cure of many diseases we feel are hopeless or nearly so today. Like at the Science Museum in London, I was very disappointed to see it relegated to not even the footnotes. I tried to find a DNA souvenir, t-shirt, hat, something to purchase and there was not one DNA thing in any store. For shame! Come on – Double Helix Ale anyone???

Cambridge is an ancient medieval city and it’s evident everyplace. The Cavendish Lab is arguably on the oldest “street,” or cartpath, in Cambridge. I say this because the oldest church is right across that cartpath and dates from about the year 1000. At that time, churches were always at the center of the village. Today, that cart-path is not wide enough for a car, and there is no room to expand.

Today, the ancient church is of course physically tied into several other buildings and abuts others, as all buildings here generally are, especially old buildings. This photo shows the oldest church constructed of chocolate brown stones, another very old church as well, and the spires of King’s College Chapel begun by Henry the 6th and finished by Henry the 8th in the distance to the far right. Note that this is a one lane street at this point that shortly narrows to exclude vehicles. To put this in perspective, the Eagle Pub is just about where the trees are on the far right, beside the King’s College Chapel spire.

In most of England, and assuredly in Cambridge, what we consider is the US to be old buildings, a hundred or two years old are considered to be rather new. Their old buildings were constructed before Columbus “discovered” the Americas.

I can only imagine the nurturing quality of studying and working among such history. I suppose one would get used to it, but I hope it would never be taken for granted.

There are two entrances to the lab. One is through this door.

Watson and Crick exited through this door, walked down this cartway every day for lunch and ate at the Eagle Pub, just a short walk away and around the corner in front of the church. It’s here that they fined tuned their DNA research as do both students and professors yet today.

The second entrance to the lab is through this archway which actually forms a tunnel under the building. Half way through the tunnel is an entrance to the buildings on both sides.

Walking a short distance down the cobblestone street, just past the chocolate colored church, you intersect a road and slightly to the left is the Eagle Pub, where Watson and Crick ate lunch most days and discussed their projects. Rest assured that DNA was indeed a hot topic of conversation here. In fact, it’s reported that they were so excited about their discovery that they told everyone in the pub that they had discovered the secret of life, only to have everyone ignore them and just go back to their pint of ale. It had to be an extremely anti-climactic day for them – but if any patron remembers the crazy men in the pub that day that announced the discovery of the recipe of life itself – they indeed were a witness to a momentous discovery.

Inside the pub, in a stairway to the loo (bathroom) we found this sign.

The Pub actually holds more information about the discovery of DNA than the university location does. I find this really unfortunate, as well as ironic, but maybe not as many people as I imagine might be interested in the history of DNA.

I would think they would at least mark the DNA “Double Helix Trail.” It could end, or begin, in London at the Science Museum where the helix model resides today.

The pub itself is in a very historic area, literally in the middle of the “old town”. Here’s a photo of the street itself, the pub, on the right.

Cambridge is a place of thinkers, and obviously, of doers as well. It turns out that DNA was not the only discovery in the Cavendish labs.

I wonder what other discoveries were made in these hallowed halls. Did you know that Mitochondrial DNA was first mapped at Cambridge in 1981, hence, the CRS or Cambridge Reference Sequence? What is it with DNA here? Rosalind Franklin, pioneer molecular biologist and a key contributor to the discovery of DNA studied at Newnham College at Cambridge, but when she made her x-ray diffraction images of DNA, utilized by Watson and Crick, she was at King’s College in London.

Cambridge is steeped in history never more than a few feet away. In the photo of the pub, above, if you turn right when the street ends, you’ll be greeted with this scene, the King’s College Chapel with its rich history of starting and stopping construction through the reigns of 3 kings and the English Civil War. This is the steeple you saw in the distance in the photo of the street where the Cavendish lab is located.

The architecture of this building is utterly stunning.

The first part was built by Henry the 6^th for the 70 professors at Cambridge at the time. The second part to the rear was finished many years later by Henry the 8^th, after the War of the Roses and was very opulent with carvings on all the walls, heraldry, etc. The first part was very simple by comparison. The picture below is of the second part.

One of the most impressive aspects of this chapel, aside from the stunning windows, is the ceiling made of carved stone flying buttresses itself. Because of the ceiling construction and the amount of glass in the windows, it’s actually very light inside and I could take these photos without flash photography which was prohibited.

The church forms part of a 4 building complex that is connected in a square and inside is a courtyard.

I can’t even imagine going to school is this wonderfully nurturing environment. No wonder DNA was discovered here. No one wanted to leave. My university was constructed of concrete blocks, for the most part, and everyone left as soon as possible.

Bachelor degrees at Cambridge are 3 year degrees, not 4, and if you live in Europe, it’s about 9,000 pounds which would be about 14,000 US dollars without lodging and food which is about another 8,000 pounds. If you’re from elsewhere, it’s 18,000 pounds plus lodging. Nurturing and inspiring, yes, but not inexpensive.

Cambridge is a beautiful and inspirational medieval city sprouting seeds for the future. There is a beautiful, ethereal umbilical connection between its past, my present and mankind’s future. It is truly awe-inspiring. As I pondered and reflected upon all of this, I was struck with the weight of responsibility that all of us who work with DNA carry.

DNA is a gift, indeed, a map, of the past, of the present and a cartographic key to the future. We have the responsibility and obligation to work with this Divine gift, ethically, morally and with only the best and most honorable of intentions. We now have the key to the genome, the Holy Grail of humanity. What will we do with it? What does the future in another 60 years, 2073, hold? Everyday in this new field, as we work individually to create a better whole, we are weaving our genetic legacy.

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Charting Companion from Progeny Software

Posted on February 3, 2014 by Roberta Estes

I’ve got to tell you, I love Charting Companion. I’ve used it for many years now with my PAF software, although it is compatible with virtually every genealogy software program on the market, as well as Family Search.

Recently, the owners updated the software to include a wonderful new feature where appropriate on reports. They map and color the X chromosome inheritance path. I did have to upgrade my Charting Companion software, but at $29.95, it certainly won’t break the bank….and it’s worth every penny.

If you’re jumping up and down, doing the happy dance and hollering “WooHoooo,” I certainly understand. I did the same thing.

This option is available for all charts that have ancestors: Ancestor, Fan, Hourglass and Bowtie.

There are several ways to select charts in this software, but the most comprehensive selection in one place is on the menu bar.

Select the type of chart you want to produce. Click through the various options and select the information you want to include on your chart.

To select the X-chromosome option, the user simply selects “X-chromosome” in the Color option tab:

When finished, click preview to be sure it’s what you want. Here are a couple examples of my reports with the X chromosome selected.

X with Fan

This fan chart can’t reasonably be made much larger than this, in terms of generations. If you need more, shift to the Ancestor chart which can span pages. I would suggest providing at least 10 generations when sending information to people you match on autosomal DNA tests. I include 12 generations to at least get every ancestor off of US soil and back into the old country – or as many as I can get off of US soil:)

Ancestor – X Pedigree

I love these X reports. When you match someone on the X, you can send them one of these and they can visually see which of your lines are available for X matching. These, utilized in conjunction with the regular Charting Companion Pedigree Chart report are a powerful combinational tool.

My Favorite Report

I generate a pedigree chart for each “side” of my tree, Moms and my Dad’s. Often, based on my matches, I immediately know which side the new match is from, so I only send them the relevant information. If need be, I just send both files.

I’ve been a long time user of this software. I do have a tree at Ancestry but I hate to refer anyone there. Conversely, I hate receiving links to Ancestry trees. I much prefer Rootsweb/WorldConnect.

All trees have some inherent problems. First, how would a match even begin to know what surname to search for or where to find it on my tree. Secondly, every time I view someone’s tree, Ancestry does me the favor of forever mailing me after that with their updates and such by attaching their tree to my account. I hate that. And yes, I know I can go in and one-by-one, undo Ancestry’s favor, but why should I have to do that? And I certainly don’t want to make anyone else do that either. Sending a pedigree chart provides them with only the relevant information without being invasive, problematic or being a “forever” thing with an attached tree. We’re only looking here, not getting married:)

So, I send a pedigree chart of 12 generations in a pdf file with an index at the end.

If you select 4 generations per page, each item will have the associated location information. 5 generations per page makes the 5^th generation default to only date information, meaning they won’t be able to see locations, so don’t do that.

Select the index option to add the index at the end. This makes it easy for people to skim quickly for surnames that look familiar.

Lastly, when you have your selection in order, you can preview, and then the “publish” button saves this to a file on your system.

Please note that if you include submitter information, it includes everything including your address and phone number in the lower left hand corner. I do not include that information in the pdf file I send to matches. I wish the software had a submitter name/e-mail only option. That’s it though, my only suggestion for this software. I love it!

Chart above, index below.

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Neanderthal Genome Further Defined in Contemporary Eurasians

Posted on January 30, 2014 by Roberta Estes

A new study released by Howard Hughes Medical Institute at Harvard Medical School on January 29^th titled “When Populations Collide” provides some interesting insights about Neanderthal DNA in modern humans. This study compared the full Neanderthal genome to that of 1004 living individuals.

In general, people in East Asia carry more Neanderthal than Europeans who carry 1-3%, and Africans carry none or very little. It appears, according to David Reich, that Neanderthal DNA is not proportionately represented in contemporary humans, meaning that some areas of Neanderthal DNA are commonly found and others not at all. Some Neanderthal genes are carried by more than 60% of Europeans or Asians, most often associated with skin and hair color, or keratin. Reich’s thought is that people exiting Africa assimilated with Neanderthals and selected for these genes that gave them an adaptive and survival advantage in the cooler non-African climate.

One particularly big Neanderthal genetic desert is the X chromosome, a phenomenon called hybrid sterility. Reich suggests that this means that when Neanderthals and humans exiting from Africa interbred, they were on the cusp of being unable to reproduce successfully. Reich explains that “when two populations are distantly related, genes related to fertility inherited on the X chromosome can interact poorly with genes elsewhere in the genome and that interference can render males, who carry only one X, sterile.”

Given the recent discussions about the X chromosome and the possibility that it may be inherited in an all-or-nothing manner more often than the other chromosomes, I had to wonder how they determined that this was hybrid sterility and not an case of absence of recombination.

Reich’s team apparently had the same question, so they evaluated the genes related to the function of the testes, confirming they too had a particularly low inheritance frequency of Neanderthal DNA. These, combined, would eventually cause the X to be present in very small quantities in the genome of descendants since the Neanderthal X could only be inherited from women and then would cause the resulting males to be sterile. So in essence, only females could pass the X on and only their daughters would pass it further. Males carrying that X not only wouldn’t pass the X, they wouldn’t pass anything at all due to sterility.

If, in addition to this, the X has unusual recombination features, that could exacerbate the situation. Conversely, if the X is inherited intact more often than not at all, it could increase the likelihood of the X being brought forward in the population.

Reich says his team is now focused on looking at Neanderthal DNA and human disease genes. He says that his new study revealed that lupus, diabetes and Crohn’s Disease likely originate from Neanderthals.

Another study, published the same day in Science titled “Resurrecting Surviving Neandertal Lineages from Modern Human Genomes,” reaches the same conclusions about the Neanderthal inherited traits related to skin color. This study compared the full genomes of 379 East Asians and 286 Europeans to Neanderthal genomes and discovered that they could map about 20% of the Neanderthal DNA in those individuals today. This, conversely, means that 80% of the Neanderthal genome is missing, so either truly missing or simply missing in the people whose DNA they sequenced. It will be interesting to see what is found as more contemporary genetic sequences are compared against Neanderthal, and as more Neanderthal DNA is found and sequenced.

Fortunately, recent advances in dealing with contaminated ancient DNA hold a great deal of promise in terms of increasing our ability to sequence DNA that was previously thought to be useless. This report is described in the article “Separating endogenous ancient DNA from modern day contamination in a Siberian Neanderthal” and was used in the sequencing and analysis of the Neanderthal toe bone found in Siberia.

To better understand the legacy of Neanderthals, Dr. Reich and his colleagues are collaborating with the UK Biobank, which collects genetic information from hundreds of thousands of volunteers. The scientists will search for Neanderthal genetic markers, and investigate whether Neanderthal genes cause any noticeable differences in anything from weight to blood pressure to scores on memory tests.

“This experiment of nature has been done,” says Dr. Reich, “and we can study it.”

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What If You Die?

Posted on January 28, 2014 by Roberta Estes

Well, it’s not exactly a what-if question, it’s a given. You’re going to. The only real question is when, and will you be prepared?

By prepared, I’m not talking about your will, I’m talking about your DNA.

The unspeakable happened this past weekend. A long time researcher and close friend, Aleda, died, rather unexpectedly. She has been chronically ill for some time, but not critically. On Saturday, she read my blog and worked with her research group on the Autosomal DNA Segment Analyzer. Then, in the afternoon, she said she didn’t feel well and got into her chair to take a nap. Nothing unusual about that. Aleda didn’t feel well a lot, but she persevered anyway, always helping and guiding her research group. But this time was different. Aleda was gone.

Her research group is wandering around like a group of lost souls. It’s like someone shot a hole through the middle of all of us. This isn’t a large well organized group with an official structure, but a small group of closely and not so closely related researchers trying to figure out their DNA and genealogy connections.

If you are a significant contributor, you will be sorely missed. If you are reading this, and have had your DNA tested, you are one of the contributors.

The research group members are already asking, “What next? How do we access the DNA records of the people Aleda had tested?” Good question. Let’s talk about preparing for the inevitable.

Aleda had given the kit passwords to a friend, who is now so upset she can’t find them. As the project administrator of one of the projects that includes one of Aleda’s family member’s kits, I can see some of the information.

E-Mail

I can see that Aleda set up a special DNA e-mail address which I’m presuming she used for all of the kits. Unfortunately, there is no alternate e-mail address.

When Family Tree DNA, and virtually all the companies, do a password reset, they send the password information to the e-mail address on file.

Does anyone, other than Aleda, have the password to that e-mail account?

Project administrators cannot change primary e-mail addresses. Only the kit owner can do that.

If you change your password to your e-mail account, you’ll need to remember to provide the new password to your trusted other as well.

Passwords

If you share your password with someone, that’s fine, but if they can’t find it, or if you change it and don’t tell them, that won’t be helpful. You might want to add their e-mail as an alternate. You might want to provide this information to multiple people, just in case your chosen person predeceases you, or some other unfortunate situation exists, like a fire, system crash or losing the passwords.

At 23andMe, to download a raw data file, a password isn’t enough. You also have to know the answer to the secret question.

Beneficiary Information

Family Tree DNA goes one step further and provides people with a beneficiary form for situations just like this.

Unfortunately, Aleda’s family member’s form is blank, and she protected his information by changing the setting to prevent project administrators from completing this form.

Covering all the Bases

Don’t forget about 3^rd party sites like GedMatch where you may also be registered.

What to do?

1. Family Tree DNA is the only company to provide the option of beneficiary information. Take advantage of this and complete the form. It’s only 3 lines – name, phone and e-mail of your beneficiary. You can find it under the “My Account” tab on the blue/black bar at the top of your personal page.

2. Add an alternate e-mail address.

3. Provide password and e-mail password information to a trusted other, and maybe a few trusted others.

4. Remember to notify password holders when you change passwords to either e-mail or DNA kits.

5. If you are a project administrator, try your best to find a co-administrator and share information, such as genealogy provided by participants.

6. Provide a notification list for your family that includes important genealogy and DNA contacts, including Family Tree DNA if you are a project administrator. Many times I’ve received an e-mail from someone’s account with their name as the subject. I’ve learned to cringe when I see them, because I know what’s coming…but at least the family has taken the trouble to notify those of us who communicate electronically with that person instead of leaving us to wonder forever what happened.

7. Preparing for the inevitable doesn’t just apply to DNA testing, but to all aspects of online life. Think about Facebook, for example. My brother died 2 years ago, today, and no one has his password. We post to his page from time to time, but like a ghost ship, his Facebook account will sail off into the indefinite captainless future.

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Finding Family the New-Fashioned Way

Posted on January 20, 2014 by Roberta Estes

When I first started doing genealogy, I didn’t even realize “it” had a name, or that I was doing “it.” I am truly the accidental genealogist. I simply wanted to find out something about my father’s family. He died in a car accident when I was in grade school and we didn’t live anyplace close to his family. I think the nesting instinct had set in. I was pregnant for my second child.

I did discover some information, but that ended with the memory of older family members. And then, my genealogy endeavors took a decade long holiday while I finished my master’s degree and other life events happened.

One day, I saw an announcement in the newspaper that the local Mormon Church was having a genealogy workshop. They invited you to bring your sticky problem and come on by. I took that same child with me that evening, somewhat apprehensive about the session being a “trap” to get folks into the church. The Mormon people never use genealogy as a way to entrap non-Mormons – so no worry there.

As genealogists have discovered, one discovery leads to two at least more questions. I was hooked that night at the Mormon church. We found the marriage record of my Lazarus Estes and Elizabeth Vannoy on microfiche. I still remember the awe and thrill of that moment, looking at that scratchy old record. Anyone who asks when you’re going to be finished with your genealogy just doesn’t understand the blank noncomprehending stare they receive in reply.

What I expected to find, after my initial foray to find some living relatives, was history. I didn’t expect to find a lifelong obsession. And I had no idea I’d find other, more distant family, that I would become very close to.

My cousin Daryl comes to mind. We met over the internet researching a common family line a decade ago. She has become my sister-of-heart and my travel companion. In fact, here’s a photo we took, trapped inside a cemetery in Tennessee. Thankfully, it WAS fenced and the fence was between us and the bull, even if we were trapped inside. I’m still not sure if that bull was unhappy with our presence in HIS field or hopeful of adding us to his harem. Yep, these are things you only do with very close friends or family! And what great memories we’ve made.

I was thinking this morning about how genealogy has changed. For years, we wrote letters. Remember watching for the mailman to arrive and running to the mailbox? I surely do, especially when you had written someplace for a record and were expecting its arrival. All genealogists knew exactly what time the mail was supposed to arrive!

As time evolved, the advent of e-mail has been a huge boon to genealogy. Now, we very seldom write letters and we interact in the space of minutes or hours with new and old cousins.

I’ve also stopped trying to quantify “cousin.” If we’re related and not a parent/sibling aunt/uncle niece/nephew, then we’re “cousins,” kin, and that’s all that matters. With the advent of DNA testing, I’ve discovered I’m “cousin” to more people than I’m not! My, how the world has both grown and shrank in one fell swoop. I am so very blessed to have so many genealogically discovered cousins, here, as well as many who live in other countries – Marja in Finland who I met in November, David in Australia, Doug in New Zealand who I met up with in England, John in Japan, Yvette in the Netherlands who I’ll meet this year, and the list goes on.

The next big connector was and is Facebook. Now, the first question you ask a new cousin is “are you on Facebook.” While e-mails are personal, directed to you individually, you can get to know your cousins on Facebook in another way, by watching what they do and say. I have a new cousin Loujean, discovered just before Thanksgiving. We are Facebook friends, and I think I know her better than I know my nieces and nephews who are not on Facebook. And yes, I’m dead serious. I have no idea what those nieces and nephews are doing, but I can tell you all about Loujean:)

So, now I’m curious about your experiences with both genealogy and genetic genealogy. Aside from the answers to historical questions, has genealogy or genetic genealogy enhanced your life by adding people to your list of family that you care about? Has it changed your life? If so, how? You can answer the polls below, or leave comments, or both.

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The $1000 Genome? – Not Exactly

Posted on January 17, 2014 by Roberta Estes

You may have seen the headlines and the announcement this week by Illumina, manufacturer of gene sequencing equipment, that the $1000 genome is finally here. Hallelujah – jump for joy – right? Sign me up – where can I order???

Well, not so fast.

It’s a great headline – and depending on how you figure the math – it’s not entirely untrue, but it’s a real struggle to get there. Some marketing maven did some real spreadsheet magic! What is that old saying, “lies, damned lies and statistics”? Maybe that’s a little harsh, but it’s not too far off.

So, is the $1000 genome here or not? Well, kindof. It depends on how you count, and who you are. You see, it’s a math thing.

It’s kind of like a mortgage. How much did your house cost? Let’s say $100,000 – that was the price on the “for sale” sign. But by the time you get the mortgage paid off, 30 years later, the cost of that house is way more than $100,000, probably more than $250,000 and if you add in the cost of taxes, closing costs and maintenance, even more. This will only depress you, so don’t think about, especially when you sell your house for $150,000 and declare that you “made” $50,000. But I digress…

So, let’s translate this to the $1000 genome.

Dr. David Mittleman, Chief Scientific Officer for Gene by Gene, Ltd., parent company of Family Tree DNA, was at the conference this week where the Illumina announcement was made. I asked him several questions about this new technology and if it was ready for prime time yet.

His first comment shed some light on costs.

“The HiSeqX Ten system is actually a ten-pack of new HiSeq instruments, each costing 1 million dollars. So you have to spend $10 million on equipment before you can even get started.”

Ouch. I guess I won’t be buying one anytime soon!

To begin with, without the cost of the kits or processing or staff or software or installation or financing or support contracts or profit, a company would have to sell 10,000 kits at $1000 to even bring the cost of the equipment to $1000 per kit.

So, how did Illumina figure the cost of the $1000 genome? The $1000 is broken down as $800 on reagents, $135 on equipment depreciation over 4 years, and $65 on staff/overheads.

This means that to obtain that $1000 per genome price, you have to run the equipment at full capacity, 24X7, 18,000 kits per year, for 4 full years. And that still doesn’t include everything. You also need service contracts, installation, additional labor, etc. You can read more about the math and cost of ownership here.

And sure enough, when I asked David about who has purchased one so far, there are two buyers and both are institutions. This is an extremely high end product, not something for the DTC consumer marketspace.

Now this isn’t to say this announcement is a bad thing – it’s not – it’s just not exactly what the headlines suggest. It’s the $1000 genome for those with deep pockets who can purchase a $10,000,000 piece of gear and then run 18,000 samples, for 4 years, plus expenses. But yes, it does technically break down to $1000 per test as long as you hit all of those milestones and ignore the rest of the expenses. If you can afford $10 million and have the staff to run it, you probably don’t care about the cost of installation, labor and support contracts. They are just necessary incidentals – like gas for my lawn mower!

In spite of the fancy math, it’s truly amazing how far we’ve come when you consider that a single full genome sequence still cost about 3 million in 2007, and in November 2012 Gene by Gene was the first to offer full sequencing commercially and offered it to their customers for an introductory price of $5495. Of course, with no analysis tools and few testers, I can’t imagine what one would do with those results. This has changed somewhat today. The full genome with some analysis is available today to consumers for $7595, but the question of what is available that is genealogically useful to do with these results still remains, and will, until many more people test and meaningful comparisons are available.

The Illumina announcement also raises the issue of software investment to do something useful with the massive amount of data this new equipment will generate…also nontrivial, and that software does not exist yet today.

There are other issues to be addressed as well, like open access libraries. Will they exist? If so, where? Who cares for them? How are they funded? Who will have access? Will this data be made available in open access libraries, assuming they exist?

Illumina has reported that entire countries have approached them asking for their population to be sequenced, which also begs questions of privacy, security and how exactly to anonymize the samples without them becoming useless to research. This high tech watershed announcement may spur as many questions as answers, but these issues need to be resolved in the academic environment before they trickle down to the consumer marketspace.

This is not to minimize the science and technology that has propelled us to this breakthrough. It is a wonderful scientific and technological advancement because it will allow governments or large institutes to do huge population-wide studies. This is something we desperately need. Think for a minute if our Population Finder ethnicity results were based on tens of thousands of samples instead of selected hundreds.

For genetic genealogists, we are poised to benefit in the future, probably the more distant than the near future. The $1000 genome for consumers not only isn’t here, it’s not even within sniffing distance. So put your checkbooks away or better yet, buy a Big Y or a Family Finder test for a cousin, something that will benefit you in the short term.

This next step in the world of genetic discovery is exciting for research institutes, but it’s not yet ready for consumer prime time. We will be the beneficiaries, but not the direct consumers….yet…unless you want to move to one of those countries who wants their entire population sequenced. Our turn will come. Maybe the next time we see an announcement for the $1000 genome it will be calculated in normal home-owning-human terms.

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Stonehenge

Posted on January 16, 2014 by Roberta Estes

You know, there are just some things in this world that defy words. Some things are stunning in photos, but in person, they are absolutely unspeakable – there are no words adequate to describe them. Overwhelming, majestic, none of those words are “enough.”

Stonehenge is one of those places. Maybe that’s why people have been attracted here for thousands of years. It’s a magnet calling to our human spirit.

This was my second day in London. Jim and I had just spent a rather sleepless night in the Kenner’s Easy Bake Oven, a very small hotel room with no air conditioning, in a heat wave. However, nothing was going to keep us from visiting Stonehenge, so off we went to find the tour company, something much easier said than done, it turns out.

We wanted to sign up for a bus tour, but the company said we had to come down to their office to physically make those arrangements, in person. So, we took a subway tour by accident to get to the bus tour. Thank Heavens we left lots of time. To get to Stonehenge from London, you ride about 2 hours each way on the bus through what I would term nondescript farmland for the hour and a half visit at Stonehenge, but it was worth every minute of that ride and even being lost on the subway too.

But Jim and I had a special treat. Our breakfast was included in our hotel room. It was a real breakfast too, not just cereal and milk. I think it’s because they felt guilty about that Kenner’s Easy Bake Oven thing. In any case, the breakfast was really wonderful. It included several kinds of fresh baked breads, cheeses including brie and freshly made raspberry jelly sitting in little jelly cups in icewater so they would set up quickly.

They also had normal breakfast things like eggs and “bacon” which was really good and not bacon as we know it in the US, and baked beans, which is a breakfast staple in England. This rather unique combination, complete with tomatoes and mushrooms, is known as the English Full Breakfast and you can see some pictures here. And yes, it does include “blood pudding” also known as black pudding which isn’t pudding at all. There is a picture of me trying that…but I won’t publish it. I will try almost anything once, and I did, and guaranteed, there will not be a second time.

I decided that the freshly baked bread was calling to me and so was the cheese. Not only is that my farm upbringing, but it’s also the result of living in Switzerland as a student. It’s all coming back now and I have this indescribable urge to have some wine with my bread and cheese:)

I noticed that the tour description said nothing about food, nor about stopping anyplace, so I presumed we needed to be prepared. Let me translate – go to the bathroom just before leaving and take food or water or anything you’re going to need.

So, I made us a picnic lunch. It was the best lunch ever, with petit pain and brie and jelly (in packets, not the homemade raspberry – no way to transport that) and a banana and a pear and a tomato slice. Yepper, a killer picnic lunch and we had it sitting on the grass at Stonehenge. It was really squishy, but it was really, really good. And yes, we had to lick our fingers. Welcome to our picnic at Stonehenge. After we ate, we took pictures from our picnic site. I mean, how many times in your life do you get to picnic at Stonehenge?

Jim, by the way, refuses to smile in photos. Still, I think this one is very cool. He’s thinking about smiling and trying hard not to! BTW – this photo is now on the cover of Jim’s iphone – a nifty Christmas gift!

There are lots of theories and myths about Stonehenge, the why and how, including aliens and Merlin, but the truth is that no one really knows why it was created, or how, or by whom. However, no culture would invest so much time and labor into something that wasn’t sacred to them in some way.

Below, the oldest known depiction of Stonehenge.

From a manuscript of the Roman de Brut by Wace in the British Library (Egerton 3028), a giant helps Merlin build Stonehenge.

You can’t sit in the beauty and majesty of his incredible monument without pondering and thinking, about Stonehenge itself, and also about the people who created this megalithic structure. And I wondered of course, if I was related to them. Are they my ancestors? I certainly have several British Isles ancestors. Were some of them here then? Did they participate in some way, either in building the monument or whatever form of worship followed? What do we know about Stonehenge?

Stonehenge is a prehistoric monument in Wiltshire, England, about 2 miles (3.2 km) west of Amesbury and 8 miles (13 km) north of Salisbury. One of the most famous sites in the world, Stonehenge is the remains of a ring of standing stones set within earthworks. It is in the middle of the most dense complex of Neolithic and Bronze Age monuments in England, including several hundred burial mounds. It sits simply in the middle of a plain. In fact, while driving through that area, there are little burial mounds everyplace. This is through the bus window, so pardon the glare on the glass. The mounds are to the right and also in the distance mid-photo.

Archaeologists believe Stonehenge was built anywhere from 3000 BC to 2000 BC. Radiocarbon dating in 2008 suggested that the first stones were raised between 2400 and 2200 BC, whilst another theory suggests that the bluestones, from Wales, may have been raised at the site as early as 3000 BC

Stonehenge was built in three phases between 3000 B.C. and 1600 B.C. Archaeologists agree it was a temple — but to what god or gods, and exactly how it was used, remains unclear.

Archaeological evidence found by the Stonehenge Riverside Project in 2008 indicates that Stonehenge could have been a burial ground from its earliest beginnings for elite families. The dating of cremated remains found on the site indicate that deposits contain human bone from as early as 3000 BC, when the ditch and bank were first dug. These burials locations are marked by bluestones. The Stonehenge stones may be the largest headstones ever! Such deposits continued at Stonehenge for at least another 500 years.

Stones for Stonehenge, much of which still stands, were brought from up to 175 miles (280 kilometers) away. Construction continued for centuries, and the site may have been a temple for Druid worship, a giant astronomical calendar, a place of healing, or maybe all of the above.

Evidence suggests large crowds gathered at Stonehenge for the summer and winter solstices, a tradition that continues today.

Senior curator Sara Lunt says there are still major discoveries to be made — more than half the site remains unexcavated. But the original purpose of Stonehenge may remain a mystery.

“We know there was a big idea” behind Stonehenge and other stone circles built across the British Isles in the Neolithic period, she said. But “what the spiritual dimension of this idea is — that is the key, and that is what we can’t get.”

The surrounding circular earth bank and ditch, which constitute the earliest phase of the monument, have been dated to about 3100 BC. The site and its surroundings were added to the UNESCO’s list of World Heritage Sites in 1986 in a co-listing with Avebury Henge. Stonehenge is owned by the Crown and managed by English Heritage, while the surrounding land is owned by the National Trust.

When we were visiting, they were in the process of completing a new visitor’s center. We didn’t see the new center, as it is about a mile and a half away and completely out of view. The then-current center is just out of sight of Stonehenge itself. The idea of the new center is to remove all of the modern day trappings and distractions, including motor noise, so that visitors can enjoy the monument in a more pristine and natural environment. That seemed to be a very volatile subject and not everyone is happy about the changes.

Recently the new facility was opened.

Among the exhibits in the new facility is the reconstructed face of one 5,000-year-old local resident from his skull. Oscar Nilsson, a forensic sculptor, created the bust and says that he had good teeth and handsome features, in a shaggy, prehistoric kind of way. Actually, I think he looks uncannily like my x-husband on a good day….which kind of gives me the creeps and makes me desperately want to know about his haplogroup.

I was very disappointed to discover that they have not, to date, performed DNA testing. My inquiry to English Heritage about DNA testing on these and other remains found in close proximity received the following reply:

Dear Ms Estes,

Many thanks for your email regarding the human remains on display at the new Stonehenge visitor and exhibition centre. I have been asked to respond on behalf of the Project team.

Dr Simon Mays, Senior Osteologist for English Heritage has provided the Interpretation and Curatorial team with some information regarding further testing following the recent sampling carried out on the Winterbourne Stoke 1 human remains that he guided. He advises that analysis of DNA is destructive and we would only consider using such a technique on ancient material if the results would help to answer compelling questions about the human remains that could not be answered in any other way: only then would the destruction of a piece of human bone be ethically justifiable. In this case, DNA analysis was not relevant to the questions that we considered important, which included the man’s place of origin and early development, his mobility and his age at death.

Although a fairly common procedure nowadays for historic and recent material, attempts to extract DNA from ancient skeletons fails in the majority of cases because of, inter alia, poor preservation of the relevant molecule. When DNA does survive from ancient material, it is often in very poor condition, so the information it can supply is strictly limited.

Any destructive analysis that English Heritage might wish to carry out in the future on the human remains in the Visitor Centre would be subject to the agreement of the institutions which have loaned them to English Heritage.

I hope this goes some way to answer your query, but please let me know if you need further information.
Kind regards,

Rebecca Thomas

Stonehenge Programme & Finance Co-ordinator
29 Queen Square | Bristol | BS1 4ND
Tel: 0117 975 1301 (internal 2301)
Rebecca.Thomas@english-heritage.org.uk

Let’s hope they reconsider in the future. If you have feedback for them about how DNA won’t answer questions about the history of this man…their contact information is listed above. I encourage you to share your opinion with them and perhaps ask some pointed questions. I have to wonder if any of the cremains might be a possibility. They are already “destroyed,” so to speak, and the heat of the cremation fire might not have been hot enough to destroy all of the DNA. I know that contemporary cremations are at much higher temperatures and do destroy the DNA. It might be worth having Dr. King or another individual who has successfully extracted ancient DNA do an evaluation. Furthermore, while they are accurate, the process is destructive – it is minimally so. A small piece of bone needs to be drilled – significantly smaller than a tooth. It seems a shame not to utilize the tools available to us.

I have to wonder just who this reconstructed man is, in terms of ancient ancestry and clans. Were these people from Europe or Scandinavia, perhaps? Were they haplogroup R, like about half of Europe is today, or would they carry a different haplotype?

Recent work by Dr. Michael Hammer and first presented at the Family Tree DNA Administrators Conference in November of 2013 indicated that there was no early haplogroup R yet found in early burials. Initially, haplogroup R1b had been thought to have overwintered the ice ace about 12,000 years ago in Anatolia and Iberia, repopulating Europe after the ice melted. However, if that is true, then were are the R1b burials? Instead, we are finding haplogroup G and I and some E, but not any R. The first site to show any haplogroup R is R1b from a German Bell Beaker site dated to the third millennium BCE, or about 5,000 years ago.

The Neolithic timeframe covers the expansion of agriculture from the Middle East across Europe beginning about 10,000 BC and continuing across Europe to about 5,000 BC. Haplogroup R, it appears, did not accompany this expansion, but arrived later, post-Neolithic, potentially with the Bell Beaker Culture between 2,000 and 3,000 BC.

This culture is named after its distinctly shaped drinking vessels.

3,500 years old, 40 cm (16 in) high “Giant Beaker of Pavenstädt”, Gütersloh town museum, Germany. Other Beaker culture items, below.

It’s also believed that mitochondrial haplogroup H spread into Europe with the Bell Beaker culture as well.

Beakers arrived in Britain around 2500 BC, declined in use around 2200-2100 BC with the emergence of food vessels and cinerary urns and finally fell out of use around 1700 BC. The earliest British beakers were similar to those from the Rhine but later styles are most similar to those from Ireland In Britain, domestic assemblages from this period are very rare, making it hard to draw conclusions about many aspects of society. Most British beakers come from funerary contexts.

From Wiki, this map shows the generalized movement of the Bell Baker culture.

The most famous site in Britain from this period is…drum roll please…Stonehenge. Many barrows surround it and an unusual number of ‘rich’ burials can be found nearby, such as the Amesbury Archer who lived contemporarily with the construction of portions of Stonehenge.

The Amesbury Archer is an early Bronze Age man whose grave was discovered during excavations at the site of a new housing development in Amesbury near Stonehenge. The grave was uncovered in May 2002, and the man is believed to date from about 2300 BC. He is nicknamed the “archer” because of the many arrowheads that were among the artifacts buried with him. Had he lived near the Stones, the calibrated radiocarbon dates for his grave and dating of Stonehenge suggest the sarsens and trilithons at Stonehenge may have been raised by the time he was born, although a new bluestone circle may have been raised at the same time as his birth.

In spite of what English Heritage said, DNA testing could help answer many of these questions about who these early people were, where they came from and who they were descended from and related to.

When we visited Stonehenge, the guide suggested that historically there may have been processions from Avesbury, across the Salisbury plain, following the Avon River and then up the hill to Stonehenge. The Avon River, 2 miles distant, and with parallel ditches leading from Stonehenge to the River, is theorized to be how the stones were transported to the Salisbury Plain from their origins in Wales, hundreds of miles distant.

Evidence on the banks of the river of huge fires between two avenues connecting Stonehenge with another nearby Neolithic site, Durrington Walls, shown below, suggests that both sites were linked.

I discovered, with a little googling, that indeed, contemporary visitors have been retracing this exact trail and are attempting to establish a historical walk, of sorts, shown below.

I can’t help but think how wonderful this would be, to retrace the steps of the original people of Avesbury and the Salisbury plains, whoever they were. Hugh Thomson, the author of the “Magic Circles” article hyperlinked above, probably sums it up the best with this commentary:

“I can’t help thinking how much better it is to arrive at Stonehenge on foot. The comparison that comes to mind, and which I know well, is the Inca Trail to Machu Picchu. The experience of trekking to both sites is immeasurably richer, not just because you’ve “earned it”, but because both sets of ruins are only properly understood in the context of the sacred landscape that surrounds them.”

It’s probably much different that arriving on a tour bus after being lost on the subway.

If I ever return to England, I’ll have to come back to Stonehenge. I would very much like to visit at sunrise and now, I’d like to retrace the walk of the original inhabitants, whoever they were. And yes, I’d like to know if I might be distantly related to one of these people buried in these barrows, shown below, surrounding Stonehenge. Think how you’d feel standing here if you knew your ancestors did as well. It could only enhance the visitor experience and the science would, of course, help resolve the many unknowns in the history of Stonehenge. I hope English Heritage gets their curiosity peaked and reconsiders DNA testing, as they seem a bit behind the curve. After all, they have Dr. Turi King, with the University of Leicester, of King Richard fame, quite nearby.

Truly, we had a wonderful day at Stonehenge. The weather was perfect, no rain and sunny. Beautiful photos. Just a few people here, no large crowds, and our lovely picnic.

After our visit, on the bus on the way back to London, I thought, “guess I can check this off of my bucket list,” but then I realized, I really don’t have a bucket list. My life has provided me with so many rich opportunities that I never dreamed that I would have. I never imagined that I would ever have the opportunity to visit Stonehenge, so it actually wasn’t ON my bucket list. However, now that I’ve been here, I’d love to come back.

You know, there’s something wrong with this picture. I thought you visited places to check them off the list, not to add them to the list as a return visit! But Stonehenge, well, it’s a magical place, and it will do that to you…consider this fair warning!

Resources:

http://www.independent.co.uk/news/science/archaeology/before-stonehenge–did-this-man-lord-it-over-wiltshires-sacred-landscape-9008683.html

http://www.theguardian.com/science/2013/mar/09/archaeology-stonehenge-bones-burial-ground

http://finance.yahoo.com/news/ancient-stonehenge-gets-modern-day-092304265.html

http://www.english-heritage.org.uk/daysout/properties/stonehenge/

http://en.wikipedia.org/wiki/Amesbury_Archer

http://en.wikipedia.org/wiki/Beaker_culture

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Second Sleep, the Rodent and Jewelry

Posted on January 4, 2014 by Roberta Estes

Some stories are difficult to tell, well, at least without giving away all of the family scuttlebutt, secrets and airing dirty laundry. But, I’m going to give this one a shot. However, it’s one of those “long way around the block” stories, so here’s the get-your-cup-of-creamed-tea warning.

Oh, yes, and there’s another warning too…this is one of those husband-wife kinds of stories. And believe it or not, there is DNA in here, eventually, but nothing at all like you would ever expect. I guarantee that! And no scrolling ahead either. Just enjoy the story. It’s full of surprises with a couple twists along the way!

Since I’ve invited all of you along on the trip to the British Isles, you all know that Jim, my husband, was along with me. If you recall, our original goal was to visit Lancashire, land of the Speak family, and the trip itself grew from that week into a month. We added a few days onto the front of the trip in London. Jim had never been to London. I had been there, but it was long ago as a student and most of my memories….well…never mind about that.

I actually searched through my old photos to see if there is one of me in London in 1970 to share with you, but unfortunately, I’m not actually in any of my photos from that trip. I’m taking the photos and in retrospect, I wish I had understood photography basics at that time. Let’s just say I have a lot of out of focus pictures of the backs of people in front of buildings that I can’t identify, and pigeons, lots of pigeons.

In any event, before Jim and I left for the British Isles, we scheduled our time and our transportation and pretty much knew what we were going to be doing when, more or less. Neither Jim nor I are strangers to travel, so we know enough to plan generally and to leave enough flexibility to adapt to local circumstances. For example, some years back, we discovered in Vancouver that one city tour picked up at our hotel, where the others didn’t. But we didn’t discover that until we asked at the hotel, so we were glad we hadn’t prebooked and prepaid.

Our London itinerary that we so carefully planned around 2.5 precious days looked like this:

Day 1 – arrival and half day historic tour including the Tower of London and possibly the Science Museum
Day 2 – full day tour of London or Stonehenge, depending on weather
Day 3 – full day tour of whichever one we didn’t do on day 2
Day 4 – leave bright and early with our family group for the Lancashire part of the journey

Please notice that there is no spare time in this schedule, no spare half day, and both day 2 and day 3 are kind of an all or nothing thing. In other words, you either go on the tour or you don’t, there is no half-day option. This will become important in a little bit.

And if you’ll remember, Day 1 did not go well, or at least not as planned. That’s the day I learned to swear in Brit….Bloody Hell….and we wound up staying in a very small, very expensive room in a hotel with no air conditioning, (because we had no reservation in the hotel where we were supposed to be staying) in a heat wave. We not-so-affectionately called this hotel the Kenner’s Easy Bake Oven. Just to set the scene for you.

On the evening of Day 1, after our delightful impromptu afternoon tour with Said, our chauffeur, I fell asleep about 8 PM, which is unheard of for me. I’m a night owl. The red-eye from the night before just wiped me out.

Now, keep in mind we are sleeping in the Kenner’s Easy Bake Oven. It’s hot and very close as the room is very small – like 18 inches of clearance around the bed small. No AC but we have a fan that helps a little. I didn’t care, I was exhausted. Oh, there is also no bedside clock either.

So I fell into a dead sleep and woke up quite refreshed. There is one window, with a light blocking curtain. It appeared to be dark outside. I got up and fumbled around since I didn’t want to wake Jim up by turning on a light. By the time I found my phone, and discovered it was about 1 AM, London time, I was wide awake.

Now my cousin, Elaine, a historian, is probably laughing heartily now, because she identified this concept as that of “second sleep.” It turns out that our ancestors all slept in two shifts. They would sleep for 3 or 4 hours, get up for awhile and do things like write letters, or make babies, and then go back to sleep for 3 or 4 more hours.

So, I had in advertently instituted the concept of second sleep. The problem is, Jim didn’t know about second sleep.

I was also hungry and managed to grope around in the dark and find a bag of trail mix. I was quite proud of myself for not having to turn on one of our two light bulbs in the Kenner Easy Bake Oven.

About 2:30 AM, Jim wakes up. Not entirely, just a little, and hears something.

Crunch, crunch, crunch.

Jim thinks, “Oh Heavens, that’s a huge rodent.”

Crunch, crunch, crunch.

”Really huge.”

Click, click, click.

”The rodent is typing?” ”Huh???”

“Roberta???”

Now mind you, he wasn’t concerned about me – he wanted ME to go and take care of the rodent problem. Sigh.

He was quite startled by the crunching, clicking rodent and by then he was awake too. I explained to him about second sleep but he was a skeptic and gave me “that look.” So, as long as he was up anyway, I asked him to help me upload photos from the camera since I was working on his MAC and not a PC. For some reason, being the middle of the night, he had an issue with this but since we were in the Kenner’s Easy Bake Oven and he couldn’t sleep either, he did help me.

After that, maybe about 4 AM, he starting using words like “crazy” and started singing “lunatic” songs, which made me laugh. No, not just laugh, but laugh like the crazy woman I obviously am. Somehow the sheer lunacy of being in a tiny very hot room in London wide awake in the middle of the night and Jim’s large rodent seemed utterly hilarious. His last words to me before we finally fell asleep after laughing ourselves into hysterical tears was “If you tell me you’re tired tomorrow I’m going to beat you with an organic carrot.”

The next morning, he woke me up about 8:30 to get ready to go on the Stonehenge tour, and I really didn’t want to get up, so I groaned, rolled over, and said “I’m tired” and the peals of laughter began all over again…..

I will share the very special story of Stonehenge with you in a few days.

On the way back from Stonehenge, a 2 hour ride on the bus, we started to discuss the itinerary for Day 3, and then Jim started to do “the husband thing.”

Yes, that husband thing. They all do it, but each one has their own style.

It’s what they do when they know they are about to be in trouble, that’s Big Trouble or maybe even BIG TROUBLE. When they are at the point where they have to fess up. In Jim’s case, he generally mutters and pretends that he told me something already, and then acts offended that I didn’t remember.

Now keep in mind that we had very carefully discussed and planned our 2.5 days in London…for weeks…and that after arrival, on Day 1, we decided on which day to visit Stonehenge and which day to do the London city tour.

So, here’s how the conversation went.

Jim – “I think we should leave for the tour tomorrow a little later.”

Roberta – “What do you mean by ‘a little later?’”

Jim – “Like late morning, around lunch time.”

Roberta – “Why would we do that and how can we? The tour leaves in the morning.”

Jim, barely audible – “Because I have that appointment in the morning.”

Roberta – “What appointment?”

An appointment? What appointment? Jim doesn’t know anyone in London. How the Bloody Hell can he have an appointment? And it just came up in the last day, while he’s been on vacation, since we last discussed this? I’ll just leave the conversation above, at this point, for the sake of decency. Let’s just say, it was headed in a downward spiral and I’ll leave you to fill in the blanks.

It seems that one of Jim’s international customers had an office in London, or so he claims, and Jim saw the opportunity to be a hero by “sacrificing” one of his vacation days and calling on said customer to “explain something.” Well, of course, that’s not how Jim phrased it. His version included the words “had to” and “salary continuation plan,” but I know Jim.

Did I mention that I was doing a daily family blog, for the kids, my quilt sisters and cousins to keep up with our great adventure? I also find that blogging, which is really, in the case of my “Journeys” blog, shared journaling, makes it much easier to organize photos later too, as we upload them daily to a file folder and I select from them as I write the blog. The biggest challenge is getting a signal and bandwidth to post the blog as we travel, but I digress.

Let me share with you the family blog from Night 2. It was a little different that the one from the night before which included the hysterical laughter episode. Let’s just say that the only people laughing about Night 2 were the readers…

“Hmmm, Jim is asleep and I’m obviously not. Now Jim is also in trouble.

Jim made a customer appointment for tomorrow morning. I can hear you now….”he didn’t!” Yes, he did…and yes, without talking to me about it. We only had 2 full days here and he took the morning of one of the days so that means we can’t do a full day tour tomorrow. Well, I could, but the problem is that because of the hotel booking screw-up, we have to move hotels in the AM and I am NOT dragging all of his luggage plus mine to another hotel several blocks away. I mean, his main suitcase alone is over 50 pounds, and full of electronic gadgets. It would take me several trips like a Mama cat moving her litter to move all this luggage. So, he’ll just have to come back here and retrieve his mad-as-a-wet-hen wife in the lobby sitting and waiting with all of the luggage because it’s after checkout, even after late checkout. No, the appointment was NOT first thing in the AM. Yes he’s in a lot of hot water which makes this Kenner Easy Bake room seem cool by comparison.

So, all things considered, would it be terribly evil of me to turn off the light, get the trail mix, sit down on the floor beside the bed where he is sleeping….and crunch??????”

Suffice it to say that Jim was lucky that he wasn’t sleeping on the only couch in the place which was located in the lobby. But regardless, I was really steamed, and not just because I was sleeping in the Kenner’s Easy Bake Oven.

Now, if you’re a female, right about now, you’re probably shrieking, “He WHAT?????” and if you’re a male, you’ve just dropped your head into your hands and you’re shaking your head and groaning, “Oh no,” because you know what’s coming.

Now in Jim’s guy-brain, it would just all be OK because I would just stay in the hotel, with the luggage, and wait for him and we’d go on the tour later. No problem.

Well, we have two huge problems, aside from the mad-as-a-wet-hen wife problem.

Problem one is that you can’t just leave later on the tour, so in essence he was going to ruin the entire day for both of us, more than one third of our time in London. I would have gone without him, except I couldn’t because of problem two.

Problem two is that this was the day we had to check out of the Kenner’s Easy Bake Oven by 11 AM and return to the hotel where we were supposed to be staying and where we were meeting the rest of our tour group. Unfortunately, check-in there wasn’t until 3:30. I told the gal at the front desk the situation, and after she stopped laughing, she said that I could extend the checkout until noon, but beyond that, I’d just have to bring my stuff to the lobby and sit there and wait, or haul all of our luggage, a month’s worth for 2 people, by myself, to the other hotel, where I could sit in their lobby and wait until check-in time.

Now, the good news….the lobby was air conditioned.

The bad news….Jim didn’t know what time he was actually going to be back.

The morning of Day 3 wasn’t fun no matter how you paint it. Jim left early to deal with transportation issues. I got up and packed both of our luggage, ate breakfast and then moved to the lobby and made myself a nest on the couch.

When I was arranging for late checkout and then checking out, I had to explain to the gal on the desk about why – especially when I had the same credit card but a different name entirely. When I explained the situation, she said, “Well Honey, you have his credit card. You just put your luggage back here behind the counter and I’ll keep it safe until he gets back. I’ll call you a taxi and I know a wonderful jewelry store. You can shop until time to check in at the other hotel.”

I thought about this, then asked, “But how would I know when Jim got back?” and she said, “I’ll call you….no better yet…I’ll just call the taxi driver….and I’ll tell your husband exactly where you are and what you are doing.” And she smiled a very big smile. I really, really like this gal. I’m sure that back somewhere in time, we’re related! We obviously share the jewelry gene.

Now for a minute, I did consider that. I seems like SUCH a good idea. I even considered just faking it to see Jim’s face. Seemed like a Kodak moment just waiting to happen. But in the end I just went and sat on the couch. I really did not want to escalate this little “tiff” into a war….so I waited, and waited, and waited….and I thought about calling Said but then I would have had to admit to Said what boneheaded thing Jim had done….and then Said would have had to deal with all of that luggage…if he was even available. Plus, Jim had, inadvertently I think, taken most of the British cash. So instead, I stood outside within sight of the luggage and took a picture of the tile sidewalk that looked like a quilt, and then I sat in the lobby, feeling quite abandoned, and stewed…and read a book…and waited. At least it was air conditioned and it was a good book.

When Jim finally returned, late, sometime after lunch, which he had eaten and I hadn’t because I couldn’t leave the %#@*^ luggage, we moved to the hotel where we were supposed to be originally. After we checked in, we then verified that it was too late to do the Hop-On-Hop-Off tour, and that’s when we decided to walk to the Science Museum. We enjoyed the Science Museum, especially seeing the double helix model. I’ve already shared that with you…but you didn’t know the back story then.

But just for good measure, obviously in a moment of fleeting insanity, Jim immortalized the non-event and took a picture of me pointing to the tour at the Hop-On location that we walked right past, but were too late to take! Yep, that’s the red bus we weren’t on, right on that poster!

That evening, we met the tour group that included my cousins and went to the tavern and ate fish and chips…what else, and spotted dick. I was almost over being mad at Jim, almost, when I discovered two things as he visited with my cousins.

First, he had showed his customers my family blog entry about him being in trouble. I guess he was, or maybe he wasn’t, amused. I don’t know which and it didn’t matter. I’m not sure whether he was trying to engender sympathy or show his corporate dedication, but suffice it to say that the female account rep offered to give me the addresses of “good” London jewelry stores. Unfortunately, or maybe fortunately for Jim, we were headed out of London.

Second, and this is what sealed his fate…he replied to my family blog with a comment….and this is what he said, waxing philosophic.

“It would be impossible to plead my case here, so I will not even make any attempt to. Perhaps it is best to simply say that sometimes the most difficult of situations makes for the best of possibilities overall.

I am also confident that jewelry may salve the wounds of a few lost hours of vacation time.

Life is an unscripted journey, and without a few detours or speed bumps, where would the fun be?”

I was so mad I was making up my own swear words…kind of like Bill Cosby who got so exasperated in his old “Himself” series of stand-up comedy videos that he couldn’t even talk without stammering and sputtering.

By now, both men and women are probably groaning and saying, “Oh no. Someone take that man’s shovel away from him cause the hole he’s digging is just getting deeper and deeper.”

Well, yes and no.

You see, as it turns out, Jim was, um….er… r, i, g, h, t. This is probably the only time I’ll ever say that, and publicly, no less, but it turned out that he was right. Yes, seriously. Hey, when you’ve got a lemon this big you have no choice but to make lemonade cause it’s too sour to eat and too heavy to carry around!

Well, truth be told, by now Jim is probably regretting being right, because, you see, it led to innovation, reinvention, metamorphosis and of course…you know what’s coming… jewelry.

I spent the entire rest of the trip looking for jewelry….because he, most assuredly owed me, big time, and being a wife, I had a certain wifely obligation to not let that opportunity go unfulfilled. Kind of like the time he accidentally spent a bunch of money in the casino on a cruise, way more than he intended….he came back to the room with jewelry. He may be a guy…but he is not dumb. That jewelry made me forget entirely about his casino tab!!! I mean at that point, there is nothing you can do about the tab so might as well enjoy the jewelry!

I told Jim this was my DNA trip so my new jewelry was going to be my DNA jewelry. But I never found any jewelry that I liked, and I certainly found nothing that reminded me in any way of DNA. I was disappointed, to say the least. Free ticket to jewelry and I can’t even find any to purchase.

So, I told Jim, I’m just going to have to design it myself. A look of horror shot across his face.

By this time, Jim was actually actively encouraging me to buy something, anything, to settle the debt.

“Here, don’t’ you like this? Look, a Claddaugh ring with a green stone. How about this?”

“No!”

“How about this red bus charm? Reminds me of the London busses.”

“No, not that one either! Reminds me of the tour we didn’t get to go on.”

And so it went. I think he was getting frightened. I think maybe he realized, all too late, just how much trouble he was really in. Ah, the cost of being right.

But I found no jewelry. This jewelry had to be special jewelry. Really special jewelry. Worth-a-day-in-London and being-abandoned-in-the-Kenner’s-Easy-Bake-Oven-hotel-lobby special jewelry. The more I thought about it, I really did want DNA jewelry. What started as a half-joke meant to be a cute throw-away comment became an inspiration and grew on me. So I googled, and nothing…no DNA jewelry, or none that I wanted.

So, I came home and set about designing my own, with my long-time trusty family jeweler, Al Hummer of Ore Creek Custom Jewelry. He made our wedding set years ago, and since then, those of several friends and family members too. And better yet, I took some older jewelry I had and rebirthed it, kind of like DNA, recombined it and gave it some mutations. Oh, no, not my wedding set. I wasn’t THAT mad at Jim. The new DNA ring was ready the week before Christmas. Amazing, the timing of that…and the necklace and earrings will be finished after New Year’s.

It’s actually going to be a new custom jewelry line, called the Helix line, and it’s beautiful….stunning…fitting of the DNA legacy and helix name. We’ve already designed a second helix inspired set too that will be available in the spring of 2014. Maybe by Valentine’s Day! What timing!

So yes, this will be available for everyone, not just me.

But I can’t tell you any more until the line is finished, the before and after pictures of the rebirthed jewelry taken and the professional photography of the Helix pieces completed.

What, you want a sneak peek? Well, OK, but just one, and don’t tell Al that I let you peek, because he wants the new line to be just perfect and make a splash in the jewelry and DNA world. He’d be mortified at my own “DNA ring selfie” picture.

See the helix? I’ll tell you all about the process later. It’s been wonderfully fun and it’s full of personal significance, just like our DNA!

Oh, and what about Jim you ask? I bet he’ll never say anything like that again. I mean, the man in essence gave me a blank check, obviously in a fit of macho bravado…in writing…with witnesses. I mean, how does it get better than that? I’d have to get Judy Russell’s opinion of course, but IMHO, that was a binding contract. I guess that is the price of being right! And he was. Jewelry is salving the wound, every single day. Right this minute in fact. That “hiccup” led to the birth a wonderfully innovative and transformative jewelry line. Who knew? Sometimes opportunity knocks in mysterious ways, wearing work clothes, or maybe in the forsaken lobby of the Kenner’s Easy Bake Oven hotel in London.

After all, as Jim said, life is an unscripted journey, and without a few detours or speed bumps, where would the fun be?” Sometimes the blessings and the successes are in the detours. I’m always reminded that Thomas Edison’s first 99 light bulbs were “failures,” or experiments, or as I’d prefer to call them, “learning experiences,” but no one knows about those. Number 100 couldn’t have happened without 1-99, but it’s only number 100 that counts and is remembered today!

So now, when we announce the Helix line sometime in early 2014, you’ll know at least part of the rest of the story. And yes, of course, there’s more…;)

______________________________________________________________

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Chromosome Parody Video

Posted on December 31, 2013 by Roberta Estes

I love this science video. Creative and innovative. Great job ladies and gents. We need more of these to show that science really is fun.

Oh, and I want one of those hats for the next conference!!! How cool is that!

Enjoy, smile and Happy New Year to everyone!

The lyrics are shown below the video on YouTube, but here they are as well:

Hello? Hello? Baby, you called. I can’t hear a thing.
I have got not service in the laboratory.
I have got no time for talking. Baby, can’t you see?
I am trying to study some biochemistry.

When the chromosomes condense then we call it prophase.
And when they line up then it is called metaphase.
When they pull apart then we call it anaphase.
And when they divide into two cells that is telophase.

Stop calling. Stop calling. I don’t wanna talk anymore.
I have a test that I am studying for.

GTACCCGTAGT
Neucleotides are
CATGGGATCA
They go
TACATGTCT
Neucleotides are
ACTTCGGAATA

DNA wrapped around histones.
It’s all in the chromosome.
Everything in your genome:
It’s all in the chromosome.

And when those cells explode they call it apoptosis.
Different than necrosis. Not caused by osmosis.
It’s dangerous when the cell begin undergoing anoikis.
Then there’s metastasis. Cell death is so tasteless.

DNA is simple if at first you only think,
That you have a purine paired with a pyrimidine.
The sugar-phosphate backbone holds all the bases
Which is twisted around like a spiral staircase.

Copying, copying like in vivo but much faster.
I got my genes from the lab thermocycler.

______________________________________________________________

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Promethease – Genetic Health Information Alternative

Posted on December 30, 2013 by Roberta Estes

People are beginning to ask about how they can obtain some of the health information that they were previously receiving from 23andMe. For $5, at Promethease, you can upload any of the autosomal files from either Family Tree DNA, 23andMe or Ancestry.com. They will process your raw data and provide you with a report that is available to download from their server for 45 days. They also e-mail you a copy.

At Promethease, your raw data file is deleted within 24 hours of completion of your report, and your report file will be deleted after 45 days, so be sure to download your report for future reference. Currently they process about 20,000 genotypes, or SNPs. They do note that they update their data base regularly from SNPedia, fed from PubMed publications. Therefore your report in the future will include SNPs that won’t be in your report today and what we’ve learned about those SNPs may differ as well.

They have also noted that you receive different items in your report based on which vendor’s full data file you submit. That’s true. I uploaded all 3 of my raw data files, from Ancestry, 23andMe and Family Tree DNA and ran Promethease against each of them. While 23andMe optimized their chip for medical and health results, Family Tree DNA intentionally removed some medically relevant data in order to avoid any FDA type of issues. It’s unknown how Ancestry treats medically significant SNPs, but I’m running all 3 vendor’s files to view differences.

The Promethease report utilizing the 23andMe raw data file reported on 20,080 genotypes.

The Promethease report utilizing the Family Tree DNA raw data file reported on 8179 genotypes.

The Promethease report utilizing the Ancestry raw data file reported on 10,498 genotypes.

To start the process of uploading your file and running your report, visit:

https://promethease.com/ondemand

Of course, you’ll need to take care of housekeeping, sign up and pay.

You will then be asked to select an ethnicity. I always hate this question, because I’m more than one and the categories never fit. If you don’t fit any category well, select the closest. Promethease says it only affects the sort order. That was a relief to me, as I always wonder what I’m missing by making one selection over another.

While the report actually runs, which takes about 15-20 minutes, amuse yourself by watching the video about how to download, read and understand your results. Or you could write a blog, like me!

You can review this video at any time by visiting the original link. It does make more sense after you have your report in hand.

My report only took 8 minutes to run, and according to the front page of my report, they analyzed over 20,000 SNPs or known mutation locations. I’m excited to see what my report holds.

One of the reasons I’ve been interested in this type of DNA reporting is that my mother was “diagnosed” with Parkinson’s Disease. I put diagnosed in quotes, because Parkinson’s is a diagnosis of exclusion, for which there is no specific diagnostic test, meaning the diagnosis is one made after other alternative diseases for which there are tests, are excluded. However, she never had some of the traditional symptoms, like the specific walking gait typical in Parkinson’s patients, nor some of the other symptoms, nor were the Parkinson’s medications effective in controlling her hand tremors. Her father also had the same tremors, which I’ve always suspected was Familial Tremor, not Parkinson’s. I wanted to see if Mom or I carried elevated risk for Parkinson’s. Mom’s DNA was archived at Family Tree DNA, so I could run the Family Finder test even though she had passed away by the time autosomal testing was available. So I uploaded and ran her file at Promethease too, and compared with my own.

So, let’s look at my report based on the 23andMe raw data file.

At this point, you have to choose to click on “Bad News” or “Good News” first. Someone should do a study about whether you select bad or good is genetically influenced.

In my case, I was interested to see if my “bad news” was the same “bad news” that 23andMe provided. My top “bad news” item is indeed the same item that is reported at 23andMe. Having said that, there are a lot more and different items here that were not reported at 23andMe. After looking at the varied results from Promethease, I suspect that 23andMe was trying to distill data on my behalf.

However, Promethease does not attempt to analyze your results. Some mutations are known to be connected to multiple conditions, so they simply tell you that. In some cases, you will have some negative and some positive mutations for the same disease. Again, they simply inform you, complete with a reference. It’s worth noting that for one disease I’m particularly interested in, Parkinson’s, I have a lot of conflicting data, pages worth. This just goes to show how complex interpreting this information really is, and shows that genetic predisposition, positive or negative, with only a few exceptions, is not genetic predetermination.

My good news made me feel really good. I’m at decreased risk of frontotemporal dementia or Alzheimer’s and Parkinson’s. I’m optimistic and empathetic. I wonder if this has anything to do with selecting the bad news option first – I knew I had the good news to look forward to. Get the bad stuff over with and get on with it…

Ironically, some of my good news items are in direct conflict with some of my bad news items. And yes, some are Parkinson’s, which has apparently been more heavily studied that some other diseases. Hopefully, the decreased and elevated risks will cancel each other out and I’ll just be average.

However, when running my Ancestry data file at Promethease, one of my elevated risks was Parkinson’s, based on the SNPs discovered in the 23andMe research, which conflicts directly with the information provided based on the 23andMe raw data file. Searching further, different SNPs have been reported to either be associated with increased or decreased incidence of the disease – and I carry some of each – but none are extremely elevated.

So where does this leave me in terms of whether Mom had Parkinson’s, or not? There is nothing to indicate an extremely high risk of Parkinson’s. Some indicators are for elevated risk, some for reduced risk. Compared to the one condition I know she had, which has a very highly elevated risk in all 3 reports, the Parkinson’s risk is simply unremarkable and doesn’t stand out. Bottom line – I still don’t know for sure, but I still don’t think she had Parkinson’s. Had I found highly elevated risk factors, I would have rethought my opinion.

Many diseases have multiple genetic components along with other external factors. Of course, not all studies report the same findings, and this report is based on academic medical studies.

Rarely are genetic predispositions more than just that, a slightly increased or decreased probability. Few are fatal and some are more of a life sentence than a death sentence. Having said this, there are notable exceptions, and if you really don’t want to know a worst case scenario, or aren’t prepared to deal with the results, don’t participate in DNA testing or reporting for medical or health information. If you have reason to suspect your family may carry one of the genetic terminal illnesses, visit your doctor for advice.

And speaking of physicians, much of this information, such as the information about how certain medications are metabolized could be critically important. In my case, I’m actually taking one of the mediations that is referenced where I have a decreased sensitivity. Yep, I knew that, but now I can provide this information to my physician.

For those who tend to worry and borrow trouble they don’t yet have, running this type of report might not be a good idea. It’s certainly not for hypochondriacs – IMHO. It’s a personal choice, and a very inexpensive one at that, so financially available to everyone. If what it contains is going to worry you, don’t do it. I noticed that there are several anxiety categories in these reports – but then you have to run the report to see if you carry them – kind of a catch 22 if you tend to be anxious and worry.

My personal perspective is that there may be information here that is valuable to me, or to my physicians, or to my children. The worst “bad news” item I already knew about through 23andMe, but I also anticipated that condition, without genetic testing, because my mother had this same disease in old age. I’m not referring now to the Parkinson’s, but a vision related condition that she definitely did have. This item was also consistently reported at a high degree of risk utilizing the data files of 23andMe, Family Tree DNA and Ancestry. Thankfully, it is an old age problem and one that can be treated, if not cured today. The Promethease reports, along with 23andMe’s report, have simply reinforced that I need to be proactive and vigilant and to eat lots of veggies. The good news is that many items include preventative measures in the verbiage or associated studies that your Promethease report links to at SNPedia.

How does this report compare to the 23andMe experience, assuming 23andMe was still an option or might be again in the future for health information? The 23andMe customer interface is much smoother and more user friendly. It seems to be focused on more “fun” and less “worry.” The Promethease report is that, a report, although they do a great job making it interactive. There is no sugar coating – just the facts Ma’am. And I think it’s actually much easier to use. You can easily search by disease, by category, and the searches actually work.

Promethease differs in another way too. Personally I like the idea that my data is mine, I’m in complete control of it, and it’s not being sold by Promethease out the back door for studies or purposes I might not be too thrilled about. I don’t want my DNA to be used to patent genes that cause the tests for the condition to be restricted to the patentee at dramatically inflated prices. While the Supreme Court determined that genes can’t be patented in the case of the BRCA breast cancer genes, the fight continues with lawsuits being filed, and 23andMe holds a Parkinson’s patent that was obtained by utilizing customer data. Nor do I want my data to be used to patent the technology for “designer babies.” If my DNA is going to be utilized for research, I want the ability to authorize that use, specifically.

Therefore, I feel much better about uploading a raw data file from an autosomal test at a firm like Family Tree DNA, who NEVER sells or otherwise divulges my data without first requesting permission. I thereby maintain complete control over my genetic results, rather than utilizing companies who either sell (or otherwise utilize) my results or reserve the right to do so. This is the case with both 23andMe and Ancestry.com, and to be clear, they have never claimed otherwise.