Some people eat, sleep and chew gum, I do genealogy and write...

Wednesday, June 5, 2019

The History of the Development of Genealogical DNA: Part Eight: Discovering DNA


Many of the important scientific discoveries of the 19th and 20th Centuries were inexorably dependent on technological advances. The first "discovery" of what we now call DNA was made in 1869, by the Swiss physiological chemist Friedrich Miescher. first isolated various phosphate-rich chemicals, which he called nuclein (now nucleic acids), from the nuclei of white blood cells. However, it took more than 50 years for the technology to develop to the point where a further discovery the importance of what he had found was possible. Miescher isolated various phosphate-rich chemicals, which he called nuclein (now nucleic acids), from the nuclei of white blood cells.

During the period 1885 to 1901, Ludwig Karl Martin Leonhard Albrecht Kossel, a German biochemist was able to isolate and name its five constituent organic compounds: adenine, cytosine, guanine, thymine, and uracil. These compounds are now known collectively as nucleobases, and they provide the molecular structure necessary in the formation of stable DNA and RNA molecules. See Wikipedia: Albrecht Kossel.

The term "deoxyribonucleic acid (DNA)" began to evolve when Richard Altmann, who was a German pathologist and histologist from Deutsch Eylau in the Province of Prussia, coined the term, "nucleic acid" in 1889. See Wikipedia: Richard Altmann.

The missing link was making a connection between identifying the presence of the organic compounds and determining their function in the reproductive and inheritance process. One more step towards acquiring this understanding came in 1902 when Sir Archibald Edward Garrod, an English physician, was the first to associate a disease with inheritance. For a detailed history of the discovery, see Wikipedia: Archibald Garrod.

What is remarkable is that so much of the technology necessary for the identification and utilization DNA for forensic, genealogical, and medical purposes has been developed only in the last 100 years with major developments only in the last 75 years or so.

DNA finally came center stage in 1944 with the discoveries of Oswald Avery, an immunochemist at the Hospital of the Rockefeller Institute for Medical Research. He is best known for the experiment, published in 1944 in conjunction with his co-workers Colin MacLeod and Maclyn McCarty, that isolated DNA as the material of which genes and chromosomes are made. See Wikipedia: Avery-MacLeod-McCarty experiment. Here is a citation to the original published article.

Avery OT, Macleod CM, McCarty M. STUDIES ON THE CHEMICAL NATURE OF THE SUBSTANCE INDUCING TRANSFORMATION OF PNEUMOCOCCAL TYPES : INDUCTION OF TRANSFORMATION BY A DESOXYRIBONUCLEIC ACID FRACTION ISOLATED FROM PNEUMOCOCCUS TYPE III. J Exp Med. 1944;79(2):137–158. doi:10.1084/jem.79.2.137. Further see https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2135445/

The next step in the process occurred in 1950 when Erwin Chargaff, an Austro-Hungarian biochemist who immigrated to the United States during the German Nazi era and was a professor of biochemistry at Columbia University medical school, discovered two rules that helped lead to the discovery of the double helix structure of DNA. See Wikipedia: Erwin Chargaff. Here is a quote from that Wikipedia article that explains how that occurred.
Erwin Chargaff proposed two main rules in his lifetime which were appropriately named Chargaff's rules. The first and best known achievement was to show that in natural DNA the number of guanine units equals the number of cytosine units and the number of adenine units equals the number of thymine units. In human DNA, for example, the four bases are present in these percentages: A=30.9% and T=29.4%; G=19.9% and C=19.8%. This strongly hinted towards the base pair makeup of the DNA, although Chargaff did not explicitly state this connection himself. For this research, Chargaff is credited with disproving the tetranucleotide hypothesis (Phoebus Levene's widely accepted hypothesis that DNA was composed of a large number of repeats of GACT). Most researchers had previously assumed that deviations from equimolar base ratios (G = A = C = T) were due to experimental error, but Chargaff documented that the variation was real, with [C + G] typically being slightly less abundant. He was able to do this with the newly developed paper chromatography and ultraviolet spectrophotometer. Chargaff met Francis Crick and James D. Watson at Cambridge in 1952, and, despite not getting along with them personally, he explained his findings to them. Chargaff's research would later help the Watson and Crick laboratory team to deduce the double helical structure of DNA.
The second of Chargaff's rules is that the composition of DNA varies from one species to another, in particular in the relative amounts of A, G, T, and C bases. Such evidence of molecular diversity, which had been presumed absent from DNA, made DNA a more credible candidate for the genetic material than protein.
The formulation of the structure of DNA in the now ubiquitous double-helix is often so completely condensed into a single discovery that the contributions of many scientists working on different aspects of the problem are almost completely ignored. A key factor in the discovery is attributed to Rosalind Franklin, an English chemist and X-ray crystallographer whose work was central to the understanding of the molecular structures of DNA (deoxyribonucleic acid), RNA (ribonucleic acid), viruses, coal, and graphite. See Wikipedia: Rosalind Franklin.  Although all the recognition for the discovery went to James Watson and Francis Crick, the actual discovery was based on a crucial X-ray diffraction image of DNA labeled as "Photo 51", from Rosalind Franklin in 1952. See Wikipedia: Nucleic acid double helix. While Watson and Crick went on to receive the Nobel Prize in Physiology or Medicine in 1962 with Maurice Hugh Frederick Wilkins, Rosalind Franklin's crucial part in the discovery process was ignored because she died in 1958 of bronchopneumonia, secondary carcinomatosis, and ovarian cancer. Exposure to X-ray radiation is sometimes considered to be a possible factor in her illness. See Wikipedia: Rosalind Franklin.

Who was Maurice Hough Frederick Wilkins? Here is a short summary of him and his work from Wikipedia: Maurice Wilkins.
Maurice Hugh Frederick Wilkins CBE FRS (15 December 1916 – 5 October 2004) was a New Zealand-born British physicist and molecular biologist, and Nobel laureate whose research contributed to the scientific understanding of phosphorescence, isotope separation, optical microscopy and X-ray diffraction, and to the development of radar. He is best known for his work at King's College London on the structure of DNA. 
Wilkins' work on DNA falls into two distinct phases. The first was in 1948–50, when his initial studies produced the first clear X-ray images of DNA, which he presented at a conference in Naples in 1951 attended by James Watson. During the second phase, 1951–52, Wilkins produced clear "B form" "X" shaped images from squid sperm, images he sent to James Watson and Francis Crick, causing Watson to write "Wilkins... has obtained extremely excellent X-ray diffraction photographs" [of DNA]. 
In 1953 Wilkins' colleague Rosalind Franklin instructed Raymond Gosling to hand over to Wilkins a high quality image of "B" form DNA (Photo 51), which she had made in 1952 but had “put it aside” as she was leaving King's College London. Wilkins showed it to Watson. This image, along with the knowledge that Linus Pauling had proposed an incorrect structure of DNA, “mobilised” Watson and Crick to restart model building. With additional information from research reports of Wilkins and Franklin, obtained via Max Perutz, Watson and Crick correctly described the double-helix structure of DNA in 1953.
What did Crick and Wason do to become famous? It is somewhat difficult to find an accurate description of the work done because most accounts leave out the contributions of Wilkins and Franklin. At least Wilkins got recognition in the award of 1/3 of the Nobel Prize. Scientific advancement is the accumulation of the contributions of many small advancements. That we choose to recognize and award some is sometimes tragic and patently unfair. Here is the citation to the 1953 article:

Watson, James D., and Francis Crick. 1953. "Molecular structure of nucleic acids: a structure for deoxyribose nucleic acid". Nature. 171 (4356): 737-738.

It is surprisingly difficult to find an online copy of the original article. Here is a link to a copy.
See http://www.sns.ias.edu/~tlusty/courses/landmark/WatsonCrick1953.pdf.

Notwithstanding the emphasis on Crick and Watson, the entire contribution was monumental in beginning an understanding of the processes involved in genetic inheritance.

Stay tuned.

See these previous posts:

Part One: https://genealogysstar.blogspot.com/2019/04/the-history-of-development-of.html
Part Two: https://genealogysstar.blogspot.com/2019/05/the-history-of-development-of.html
Part Three: https://genealogysstar.blogspot.com/2019/05/the-history-of-development-of_5.html
Part Four: https://genealogysstar.blogspot.com/2019/05/the-history-of-development-of_7.html
Part Five: https://genealogysstar.blogspot.com/2019/05/the-history-of-development-of_10.html
Part Six:  https://genealogysstar.blogspot.com/2019/05/the-history-of-development-of_14.html
Part Seven: https://genealogysstar.blogspot.com/2019/05/the-history-of-development-of_19.html

Monday, June 3, 2019

Introducing The Family History Guide -- Exploring Genealogy Series #12


Introduction to The Family History Guide Exploring Genealogy Series #12

This is #12 in the Exploring Genealogy Series on my YouTube Channel. Although I have had the channel for many years, I have just recently been adding more videos. The idea behind adding new videos is to explore websites, apps, and programs that help genealogists. I have been adding new videos now for about a month and have 12 in the series so that is about 3 a week. I may not keep up that pace this summer because I will be traveling a lot, but stay tuned for new videos on this blog and on my Rejoice, and be exceeding glad... blog.

It amazes me that so few genealogists know about The Family History Guide.

thefhguide.com
The Family History Guide has been online for about five years and it is just now getting some serious traction. Here is a link to The Family History Guide Facebook page.

https://www.facebook.com/TheFamilyHistoryGuide/
Here is a link to The Family History Guide YouTube Channel.

https://www.youtube.com/channel/UCSdEueFFI669fDBwILOCDvw

And here is a link to my own YouTube Channel.

https://www.youtube.com/channel/UC4cT2_EjTMVVJgaF5Gdwl1Q?view_as=subscriber

Sunday, June 2, 2019

Developments in Genealogical DNA Testing

https://kstp.com/national/wisconsin-cold-case-dna-solved-raymand-vannieuwenhoven/5373922/
Recently there has been a constant stream of news stories about the use of genealogical DNA testing, primarily from using GEDmatch.com, to solve "cold cases" or criminal investigations that have previously gone unsolved. Here is a quote from the above news article,
Last year, detectives contacted Virginia-based Parabon NanoLabs, a DNA technology company whose work with genetic genealogy analysis has helped police identify 55 suspects in cold cases nationwide since May 2018, according to the company. Parabon uploads DNA from crime scenes to GEDmatch, a free, public genealogy database with about 1.2 million profiles, all voluntarily submitted by people who've used consumer genealogy sites like Ancestry.com and 23andMe.
 However, DNA test results are not only helping to solve cold cases, but new technology also has increased the speed at which DNA test results can be used in current investigations. Here is a quote from a Utah news article dated May 30, 2019, entitled, "New DNA technology helped police get quick results in Elizabeth Shelley case."
Rapid DNA machines allow police officers to test a DNA sample from a suspect or victim right at the crime scene. This helps them get more timely results. 
But while Rapid DNA tests are good enough to establish probable cause, the test results will have to be verified before they could be presented as evidence in court.
You might have missed the fact that the U.S. Legislature passed the Rapid DNA Act of 2017 last year. Here is a link to a summary of the provisions of the Act. See "H.R. 510 (115th): Rapid DNA Act of 2017" Here is a quote from the summary.
Labelled S. 139 in the Senate and H.R. 510 in the House, the legislation was introduced by Sen. Orrin Hatch (R-UT) and Rep. James Sensenbrenner (R-WI5). 
Former FBI Director James Comey cited a real-life example of how the technology could be used effectively. “[It will] allow us, in booking stations around the country, if someone’s arrested, to know instantly — or near instantly — whether that person is the rapist who’s been on the loose in a particular community before they’re released on bail and get away or to clear somebody, to show that they’re not the person,” Comey said in testimony. 
Rapid DNA was used for the first time ever in a criminal investigation in 2013, to nab burglars who stole more than $30,000 worth of items from an Air Force Member’s Florida home while they were serving in Afghanistan. Presumably more such cases would be solved and quickly with expanded use of rapid DNA.
What does all this mean for genealogists? What is happening in the world of criminal investigation will have a direct impact on the procedures and availability to genealogical DNA testing. It is very likely, as has already happened with some websites, that the use of DNA testing for genealogical purposes will start changing and may likely become more complicated. For example, read this article.

https://dna-explained.com/2019/05/19/gedmatch-implements-required-opt-in-for-law-enforcement-matching/
What this means is that if one of your relatives is involved in criminal activity, it is possible that the investigative agency could use your family tree information to match DNA obtained from the investigation. There will undoubtedly be some further legal developments in this area.

Friday, May 31, 2019

Getting the Rest of the Gold out of the Google Goldmine for Genealogists Part Seven

https://chrome.google.com/webstore/category/extensions
  • Google Help
  • Google Search
  • Google Newspapers Archive
  • Google Drive
  • Google Docs including Sheets, Slides, Forms, Draw and more
  • Google Keep
  • Google Trips
  • Chrome Web Store
  • Chrome Extensions
Overwhelming is a word that applies to most of my interaction with the internet. I am always finding more resources and spending time learning about new programs and new websites. If you have an Apple device, you are probably familiar with the Apple App Store with its about 1.8 million apps. If you are an Android user, you are likely familiar with Google Play and its more than 2.1 million apps. Of course, some apps work on both formats and so the numbers actually overlap but there are still millions of options. It is inconceivable that anyone could know about even a measurable percentage of all these possible apps. Of course, as genealogists, we can skip over games and a lot of other categories, but that still leaves a huge number of options. 

OK, So I decided to ignore both app stores and focus on Chrome extensions from the Chrome Web Store.  However, you should also know that the Chrome Web Store has themes for Chrome. Oh, but you don't use Chrome. Well, that puts you into a rather small minority. Chrome usage continues to increase and the latest statistics at the time of this post showed Chrome with 62.8% of the total world market for browsers with Safari as a distant second with 15.83% and with Firefox at 4.86% and the rest below 4%. See StatCounter.com "Browser Market Share Worldwide." You will get different numbers from different websites but the ranking is about the same. 

You may simply use the browser that came with your computer. So, if you bought a PC computer recently, you might be using Microsoft Edge and if you bought an Apple computer, you may be using Safari, but the issue goes not just to the browser, but also to the search engine. Over the past few years, I have been consistently comparing search engines using some common genealogical searches. Google's search engine was and is so much better than any of the others that there was really no contest. 

Yes, there are some Safari extensions, but the ones I find most useful for genealogy are primarily and exclusively for Chrome. The useful extensions are one reason to consider Chrome and why it is so widely used. 

Here are a few of the extensions I use frequently for purposes related to genealogy. I am ranking them in the order that I use them. 

#1 Zotero

Zotero is a free stand-alone, open source project that helps you collect, organize, cite, and share research. It is most valuable to me because it works as a Chrome extension. With this extension and the program on my computer, I can create bibliographies, annotate documents and organize my own book collection. You need to investigate this product if you have anything to do with research or writing. Here is the link: https://www.zotero.org/


I have a love/hate relationship with Grammarly. It works as a Chrome extension, but also works with other software products. It has a free component but also has a subscription component. I like it because it corrects my grammar sort of. It is most useful in making my use of comas consistent. I dislike it because it is so limited in its word structure that it gives error messages when the grammar is perfectly acceptable. It is also a good spelling checker. The worst conflict comes from my use of collective nouns and their interaction with number. (In the preceding sentence, the word "number" is used as a collective noun referring to the concept of "number" i.e. singular, plural etc. I could make the error message go away by changing my wording, but I usually just ignore the error message.) But all in all, it is helpful. 


Whenever I think my computer has slowed down, I run a speed test to see if I am just getting anxious or if there is really a problem. Mostly it is anxiety. 


I agree, I am getting a lit bit far out of the idea of genealogy, but I save my blog posts to my genealogy album on Pinterest. 


Technically a browser app which is different than an extension, but it works just the same. It loads into your browser and captures citations from different websites. RecordSeek automatically creates an MLA format source citation for you, so you get the benefit of an official citation, without the frustration. If you aren't using this extension, you should be. 

I suggest you look around and see if there are any extensions you might like. You never know until you look. 






Wednesday, May 29, 2019

Getting the Rest of the Gold out of the Google Goldmine for Genealogists Part Six

https://support.google.com/a/users/answer/9282960\
  • Google Help
  • Google Search
  • Google Newspapers Archive
  • Google Drive
  • Google Docs including Sheets, Slides, Forms, Draw and more
  • Google Keep
  • Google Trips
  • Chrome Web Store
  • Chrome Extensions
There are so many online apps and programs that it is impossible to even become aware of all of them. In some categories of programs, there are dozens or hundreds of near duplicates. I often learn about an interesting program and try it out for a time and then never seem to get back to using it again. Really useful programs need to fit into your lifestyle and justify the time it takes to learn a new program. Obviously, there are many people who learn a few programs and then never move on or learn new ones. My purpose in adding these Google programs to my previous list of golden Google programs is to let you know that there are options and encourage all of us to look for better and more accommodating ways to do our genealogical work. 

Google Keep plays a role as a program for taking notes, creating task lists, and creating reminders. You can get a quick overview of the program from the "Keep cheat sheet." The advantage of using a program like this is that it synchronizes across all your devices. As with any new app, it helps to view a video or read the instructions. Here is a link to one of the many videos about Keep.



The second app in this particular post is Google Trips. We have several trips planned and found out how useful Google Trips can be. Basically, it keeps reservations and itinerary and is set up to work offline if needed. It also works with your Google Gmail account to give you valuable notifications. Using Google Keep and the Google Trips app together will add a significant amount of organization to a genealogy research trip, a business trip, or even a family vacation. 

https://get.google.com/trips/
Google Trips works only on iPhones and Android phones. As is almost always the case, there are several YouTube videos that introduce the program. Here is one of them.


Introducing Google Trips

Stay tuned for the last segment in this series.

See the other posts in this series:

Tuesday, May 28, 2019

Getting the Rest of the Gold out of the Google Goldmine for Genealogists Part Five

docs.google.com
  • Google Help
  • Google Search
  • Google Newspapers Archive
  • Google Drive
  • Google Docs including Sheets, Slides, Forms, Draw and more
  • Google Keep
  • Google Trips
  • Chrome Web Store
  • Chrome Extensions
Genealogists have a significant challenge in transitioning from paper to digital records. We only have to consider the tremendous effort that FamilySearch.org has gone through over the past few years to digitize its 2.4 million rolls of microfilm to see that the process is ongoing and far from complete. All of us also find ourselves somewhere along the transitional process from paper to digital. A significant number of genealogists still reject the majority of genealogists still reject the transition altogether.

Part of my idea in focusing on Google and its online programs and apps is to show the advantages of using digital methodology over paper-based systems. Because, for the most part, the programs I highlight are "free" in the sense that they have no additional charges other than the standard costs of obtaining online digital access, I can suggest them without feeling that I am trying to convince genealogists to spend money which is an even more difficult issue to confront than the transition from paper to digital.

The highlighted apps or programs in the list above are crucial but not unique to a transition away from an entirely paper-based system. Apple has a set of similar programs that come pre-loaded on Apple's computers and devices. Microsoft has another similar set of programs that are tied to an online subscription. There are also free open source sets of the same programs that can be downloaded to your computer. However, if you investigate each of these systems, you will see that they all, including Google, have "hidden" costs usually based on the amount of usage and online storage you want to utilize. Since I am currently in the process of replacing an external hard drive that is failing, I am painfully aware of the time and cost of moving Terabytes of information around on my current high-speed computer system. Ultimately, all of these programs make money by selling online storage capacity unless they do not offer storage as part of the package such as LibreOffice.

Google system revolves around the Google Drive program. Google Drive is an online data storage system that provides 15 GB of "free" storage. Google Photos is handled differently than the document programs. To see the options for Google Photos, look at this link: https://www.google.com/photos/about/

Google Drive is directly connected to the suite of programs that are usually referred to as "Google Docs." If you have a Google account, i.e. a Gmail account or have signed in to Chrome, you automatically already have Google Drive and Google Docs accounts. All you have to do is log in with your account. Any documents you create in any of the Google Docs programs are automatically stored in your Google Drive account. You can find a huge number of videos about Google Drive and Google Docs on YouTube.com. You can also start by looking at Google Help.

https://support.google.com/drive/?hl=en#topic=14940
Google Docs includes the following basic apps or programs but the connections between other programs is extensive and there are more programs that can be added.
  • Google Docs is also a word processing program. It is not a complete substitute for an extensive program such as Microsoft Word, but it has sufficient features for most of the day to day word processing needs. 
  • Google Sheets is a spreadsheet program. When you start comparing these programs to other spreadsheets such as Microsoft's Excel, depending on your level of expertise and needs, you might not think much of the program. But if your needs are modest and you don't need extensive programming functions, the Sheets program works well. 
  • Google Slides is the presentation program. Some presenters like it because it is easy to access and free. Again, it is not fair to compare it to Microsoft's PowerPoint. There is a reason why people pay a significant subscription price for these other programs. 
  • Google Forms is a useful alternative to other forms programs and the fact that it is integrated into Google Drive and the other programs is helpful. 
The suite of programs also includes some that are not commonly listed such as Google Drawings. There are also programs such as Google Sketchup, Google Sketchpad, Google Doodle, and Google IO. I don't use any of these specifically for genealogical purposes but it always helps to know that they are there. 

Let me give some examples of how I use these programs. 

Many genealogists use Research Logs. I don't do paper, so I use Google Docs for my research logs. This is an advantage because as I add research information it is instantly available on all my devices; iPhone, iPads, laptop computers, and any desktop computer I happen to be using at a library or the home of a relative. The information I keep includes the regular items you would want to know about the status of an individual research project. 

I use Google Drive to move documents from my iPhone to my desktop computer. I can take a photo of a document in a library (if allowed) and immediately make it available to my computer at home or my laptop or whatever. 

I use Sheets to organize trips. We can share the individual sheets with family members and coordinate complex trips, family reunions, and other events. 

Since I can export a Google Doc to Microsoft Word, I do the majority of my initial writing outside of blogs in Docs. I even compose email messages and letters in Docs so that I have a ready reference for those emails and letters that are part of my genealogical research. 

This list could go on and on. Once you begin to use Google Docs or some other online-based system, you will probably wonder how you ever go anything done on paper. 

See the other posts in this series:

Monday, May 27, 2019

Exploring Genealogy Series #11 Exploring MyHeritage.com


Exploring Genealogy Series #11 Exploring MyHeritage com

This is #11 in the Exploring Genealogy Series. In this particular segment, I am exploring the MyHeritage.com website. In the previous video, #10, I provided an introduction to the website and this episode continues that exploration.

This series is intended to cover apps, websites, and other resources used by genealogists. In my blog posts, I am posting some of the videos on this blog, Genealogy's Star and some videos on my other blog, Rejoice, and be exceeding glad...

My Exploring Genealogy Series is hosted on my YouTube Channel. Here is the link to the Channel.

https://www.youtube.com/channel/UC4cT2_EjTMVVJgaF5Gdwl1Q?view_as=subscriber
Please take a moment to subscribe. You can find the YouTube channel by searching for my name as follows: "james tanner" Channel.  You will have to pick out my name from the other people with the same name.