Computational Chemistry

TL;DR -- Machine learning and its use of physics was the focus for the Nobel award. This was followed up with the chemistry award being given to protein research. This is a step forward for various reasons. Ultimate consequences are not really known at this time. Research deals with the future.  

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Yesterday, we noted that the Nobel Prize for Physics in 2024 was given for work in machine learning. ML which is usually known as AI (artificial intelligence) deals with the technology of a computer systems taking as input huge streams of data and reducing these through various techniques into information that people can understand and use. But, this information can feed back into the computer model itself. 

The emphasis is on modeling which is accomplished through computational techniques. "computational" goes along with "theoretic" which deals with analytic and quantitative means applied to a field of study in order to effect desirable effects such as design, prediction and continuing analysis, generally in support of scientific endeavors. If one surveys the STEM discplines, one sees a huge influence of computational modes. With respect to some of the harder problems such as life and intelligence, one could very well suggest that theoretical chemistry will play a huge role. So, this is a necessary step; but, we have huge problems yet to resolve. 

Along with that of Physics, the Prize for Chemistry in 2024 was given to researchers who used a variant of ML from Google (AlpaFold). This work portends to future benefits that have been elusive using other means. Needless to say, the success is heavily dependent upon the researchers who are working now as well as the continually developing frameworks of their disciplines. 

A technical paper explains some of the details: COMPUTATIONAL PROTEIN DESIGN AND PROTEIN STRUCTURE PREDICTION. The following is a quote from the paper:

In summary, the achievements of David Baker, Demis Hassabis and John Jumper in the fields of computational protein design and protein structure prediction are truly profound. Their work has opened up a new era of biochemical and biological research, where we can now predict and design protein structures in ways that had not been possible before. Hence, a long-standing goal has finally been met, and the impact of this will have far-reaching consequences. 

As it says, this is research and applies to the future. We will look at some recent applications of the techniques and discuss the matters that relate. 

The use of AI is somewhat unfortunate. The work is an example of applied mathematics, computational modeling of such, people who are in the position to exploit the facilities in their work, and long years of work captured various ways as science has been doing for the past 200 years or so. 

AI deals with intelligence which we know is mostly associated with living forms. Now, we can look more closely at modeling these by using improved protein analysis plus a whole lot of other information. Like with physics which is strongly using normals in order to reduce problems to a proper scope, we will see this with other scientific domains. 

At we see with GenAI, what are the costs of this research in comparison with other work that is necessary, in terms of the resources used (say power), or the potential for misuse given our proclivity to not know how to manage complexity? 

Congratulations to the Laureates. Looking forward to watching things unfold. 

Remarks: Modified: 04/04/2025

10/09/2024 --  

Nobel, Physics, 2024

TL;DR -- Good old mathematics behind machine learning gets some respect. That is good news. 

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New directions pend. We have talked AIn't for a while. There's no critter in the buckets of bits. There may be patterns. Now, the Nobel Prize folks say that this is physics and a result of its mathematics. 

Okay, that's great. We argued anyway that the focus ought not be intelligence which goes with life, and its study - biology, as far as we know. We stressed the mathematical connectsions, but having physics now in the game improves the chance of lifting awareness to things that matter. 

So, this post goes with our technology focus which we are trying to define and foster.   

Remarks: Modified: 11/18/2024

11/13/2024 --  Added Nobel Prize, to the name. 

11/18/2024 -- So, we now have Physics, Chemistry and Medicine, connected. Expect further discussions. 

Birthplace of the US Navy

TL;DR -- Where was the U.S. Navy born? Several sites have reason to make the claim. there was a discussion this year about the topic. Turns out, though, that the U.S. Navy has decided. It was not in New England, proper, though Philapelphia is close enough. 

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In 2015, there was continued discussion of a controversy in New Hamphsire history, who was first? That is, which site could claim the earliest settler? This question might have been resolved for the 2023 commemoration that did not get the attention given to the arrival of Cape Ann's crew (Gloucester 400). 

• Rev. Hubbard (2 May 2015): In the Remarks for 4 May 2015, we mentioned that Dover and Portsmouth were candidates. 
• Evidently, Portsmouth came into the lead. 

Coming up is the 250th of the U.S., so comparative themes of this sort will continue. This year, in May, discussion of a "great debate" was sponsored by the Essex Heritage Society pertaining to who could be touted as the birthplace of the Navy. This graphic shows some detail about the occasion. 

We can use the Navy's opinion for the answer: Birthplace of the U.S. Navy. The official answer is Philadelphia, PA since that is where the Continental Congress was in session, making decsions, and providing for funds. In their write up, the Navy diplomatically mentions the other towns and their contributions. 

Early on, while looking different categories of descendants of Thomas and Margaret (Fryer) Gardner, we considered the Sarah Balch family (see post, See Descendants of Sarah). Her descendants were Chaplains of both the Continental Navy and the U.S. Navy.  

Remarks: Modified: 09/30/2024

09/30/2024 --  

Past and present

TL;DR -- The 250th of the U.S. will allow lots of research to get some air, as the attention goes to the history of the country. We will follow that thread several ways, including a deep look at technology of computing with respect all aspects that we know, to date. We can compare different areas. One of these one-up looks will be NYC and LA, in order by age. LA is comparatively a youngster. The dynamisms of the two difer quit a bit, too. 

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Some locations kept good records via photographs of their change through time. At the same time, we have temporal issues such as Los Angeles being younger than New York City. Then we have technology bringing in abilities that can be pinpointed in time. For instance, we know that Gardner, the photographer, was active during the Civil War. We posted several photos from his era, including one from Lawrence, KS. We called the post with the photo "Frontier century" (April 2021); its themes were several: the great expansion in the middle after the revolution (deed done primarily by the 5th generation); families being lost in time as they escaped the heavy hand of documentation; and modern efforts at recovering evidence of their existence). 

We will continue to focus on the middle of the country but have, of late, been looking at Los Angeles and its Bunker Hill (west, we call it) that mainly appeared in the late 1800s and went away a century later to be replaced by high-climbing things that cast a long shadow. We have had lots of photos of the LA area and can be more intimate as we find older photos to match up with something recent. 

LA and NY City
across time

In this photo, the left side shows part of the train yard in LA at two different times. Reminder, LA was Old Spain and Mexico until the latter part of the 1830s. LA claims a start in the early 1780s which is associated with New Spain. The area settled is known, now, as Down Town LA (we'll use DTLA). A church built in the area in 1784 later burned. At that site, the Old Plaza Church (still standing) was built built in 1814.  

On the right of the photo, we have snaps of NYC's Manhattan starting with a photo from 1876. This an old area and was part of the colonies prior to the U.S. Revolution. With the 250th of that event coming up, we will have time to cover stories about all areas of the U.S. 

One of our themes will deal with the long reach (Mirror building; Settlements, temporary and otherwise; NEHGS events) of New England. There will be others, such as technology. 

Before moving on, we know that NY City has tall builidngs. Lots of them. The tallest now is the One World Trade Center at almost 1,800 feet. Wikipedia has a list of buildings taller than 600 feet (110 buildings). 

In DTLA, the tallest building is only 1,100 feet). The LA City Hall is 454 feet (it's shown on the left in photo) and is the 42nd largest building. The smallest (53rd in the Wikipedia list) stands at 352 feet. 

We mentioned Bunker Hill west. It got its name, of course, from the site of a Revolutionary battle. We will be looking more at that area in DTLA as it represents changes over time, as influx of population changes the dynamics of a location. With a great collection of photos from different periods, we find people taking photos from that same area and focus of direction. 

Related to Bunker Hill west is this one that show 101 early on and then later. In the meantime, St. Vibiana's was closed as a church (became an event's center) and moved up the hill from Main Street to the summit. Parts of that area had been lowered early. Houses and dirt were taken away to have proper foundation for buildings. One story to look at is the Central Library which experienced two fires by arson. During the time of recovery, maneuverings got the building limit raised from that related to the height of the City Center. So, the first one went up to cast a shadow over the library. The library sold its "air rights" as one means to fund getting back to its work. They had to replace $Ms in burnt books, for instance. 

LA Central Libray with its
"twin" (to the right)
U.S. Bank Tower

On the list of tallest, the "library tower" now is #2. 

Reminder: with respect to photos (such as we see from Water and Power Associates of CA), provenance needs to have special attention, always. How all of this influence from Gen AI plays out will be a thing to watch. The ease with which fakes can be generated will make the problems more diffficult to resolve, albeit there are known ways to attempt to obtain stable and safe environments. Technology will provide the means many times for its managment; a key choice concerns human involvement. Yes, we humans can handle the complexity. Unfortunately, we could have known more; that is to be discussed.  

Remarks: Modified: 09/27/2024

09/27/2024 --  

HD Thoreau, Minnesota

TL;DR -- One persistent theme will be Native Americans and the future of the U.S. We will start a series in New England and follow its long arm across the country. Too, we look at Concord which brings up Thoreau and his friend, Emerson. The latter has appeared here more than once; let's take time to know more about HD. 

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One obvious theme that the TGS must pursue is nature versus technology. It has been a theme of increasing complexity over the past two decades. Though lots of subjects pertain to this theme, we merely touch upon a couple of major aspects in this post. One in particular will be "intelligence" as it has been associated with life (not with buckets of bits or whatever configuration we might conceive). 

Last time, we mentioned one of the native tribes (Nipmuc) of the New England region where the European culture of the U.S. got its start some 400 years ago. Although there are tribes over the entire continent, we will start in New England and learn about Native American culture with respect to the U.S., its past and its future. 

In the map shown in the prior post, the region of the Nipmuc tribe included an area called Concord where the English settled. We have several families under study who were associated with the middle and western parts of Massachusetts. We'll pick HDT who was friends with our cousin (Ralph Waldo Emerson) who spent his years after his father died in the environs of Harvard. RW Emerson has been mentioned in several posts. 

Today, we consider Henry David Thoreau (Wikipedia, WikiTree). HD was influenced by RW's little tract on Nature. Two of our favorite sources provide the full text of this RW take on matters: Transcendental web; archive[.]org   

Venturing further, we can quote a Harvard study published during the time of HD's 200th memorial. The study found this quote of HD, who BTW was a graduate of the Institution. 

Instead of helping Harvard, he said, men should consider giving money to their towns to preserve and protect a huckleberry patch.

The “commercial spirit” of the day, he said, rested on a love of wealth that made people selfish and greedy. The world would be a better place, he said, if people “made riches the means and not the end of existence.”

For the most part, HD was in New England. Later, in poor health, he ventured out to Minnesota to look for a better climate in which to live. He had struggled with TB. During his time in the St. Paul region (1861 timeframe), HDT was impressed. 

To be brief, we provide links to material on DT and his life. 

• HDT's Final Journey: Minnesota - Mayo took note of HDT. They provide this quote: “For my part, I could easily do without the post-office. I think that there are very few important communications made through it. To speak critically, I never received more than one or two letters in my life — I wrote this some years ago — that were worth the postage.” 
• Thoreau and the Minnesota River - being a naturalist, HD would have wandered under the MN skies. 
• The Life of HDT - one bit of activity by HD was forming a school with his brother. HD had taught at Harvard and wanted to spread the good joy of learning. We will be looking at this type of thing in depth, as New England, from its start, emphasized universal education. 

Information on his supporters.

Samuel Hoar (Wikipedia, WikiTree) 

Nathan Brooks (Papers, WikiTree)

John Keyes (Autobio, WikiTree - brother George)

R. W. Emerson (our post)

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Back to Harvard, we see that they recently performed an experiment with GenAI and classwork. The topic was Physics so that provides a wonderful grounding affect due to the empirical nature of the study. Reminder, back in HD's time, this field of study would have been (actually, was) known as Natural Philosophy. 

• Professor tailors AI tutor for Physics - one encouraging result is that this effort followed the theme of increasing human insight using the tool of the artificial tutor. Test results indicate that those in the study who used the AI mode scored better. There is a lot to look at, but this work has to consider psychological and social factors with respect to the tutor experience. 

Remarks: Modified: 09/17/2024

09/17/2024 --  

The Nipmuc's influence

TL;DR -- Technology is only part of our focus. People are prime. Technology will learn that people in the loop is the key to truth maintenance. 

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We have mentioned technology as a focus a few times. In doing so, we were not forgetting people and their 400 years of  history. Of late, technocrats have run after the idea that people are not important. What John calls AIn't and its hype are an example. 2024 has found the experience with GenAI over the past two years as motivation for managers (executives) of many companies to bring AI whole-hog into their processes. 

Okay, John has been mostly silent on this for the past two years are he re-evaluated everything that he knew with respect to emerging information from the machine learning work, including the technical aspects of applying mathematics as was enabled with the advancement of computing. Too, he reviewed robotics as it has been seen as an opportunity to web sensors with smarts and thereby create some creature worthy of our attention beyond our usual reaction to technological marvels of bowing to their developers. Language has become the domain of the artificial; John's put to that is the mindless/meaningless pursuit of optimatiztion of rules never was what language was about. Tsk, on the English departments of Universities. So much to research and discuss. 

Okay, backing up, technology is how mathematics finds its game It has not been properly attuned, yet, to what humans are about. That will change. We will discuss how to pay attention. 

Aside: for the past few years, as AI can to be more known (okay?, doubt that?, let's just take IBM and Google's winning of games in a very public atmosphere - with the ultimate being Go (so what?, never played it nor most of the other games), John has watched. Quality? Declining. Mood? Becoming more mean-spirited and stupid with respect to the culture that the US has been trying to put into place with regard to justice and equity. Look around, computers driving people like the computer is the master of we humans who have to slave to its/their owners. 

Back on track. Mathematics is the key here. So, that will be an important discussion. 

Too, toys have always been a focus. Now, we have adult toys of note. I don't have any, myself, except for some computational types. Puritan? Perhaps. It fits. 

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With the 400th of Plymouth (that off-course vessel - Mayflower), there was an effort to know more of the native populations that were here prior to the arrival of the Europeans. That's today's message. 

• In conversation with Cheryll Toney Holley - she is of the Nipmuc tribe. One factor that we see with respect to taming the ill-begotten aspects of technology is to know people and their history. 
• Nipmuc - mentioned in 1631 by Dudley, this group led the efforts to establish an awareness of their existence, generally. 

Tribal territories, 

southern New England

This review starts in the northeastern regions of the U.S., but it will cover the areas of the large interior of the country over the time of the expansion. Too, we will look at the extreme west (arrived at by land and sea) and the southwest. 

Remarks: Modified: 09/17/2024

09/17/2024 --  Nipmuc cultural area included the Concord region. We stop to look at one influencer from that region: HDThoreau.  

Restart, somewhat

TL;DR -- Two events in 2023 were seminal; these carried over into 2024 which is 8 months old. The two relate to each other. And, pending changes to our material has been pending. Time to start that process. 

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In 2023, Gloucester has its 400th. Some felt that it would be 2024. We will look more into that as the closes out. 

Since early 2023, we have adapted to two things: possibly, there are two Thomases; GenAI came on the scene and changed the world in ways that can be taken positively or negatively. Let's look at these two.

• The first was the result of research that the TGS has been doing. In March of 2023, we were looking to have Margaret Fryer Gardner as a focus. But, on looking at WikiTree, we saw that in February of 2023, we saw that research had identified birth records of the children in the records of Sherborne, Dorset, England. Those who discussed the findings decided to split the Thomas Gardner profile into two with the first Thomas being here for the start of the effort by Dorchester Company while the second Thomas was the husband of Margaret and father of the kids. See the post (New not old planter). After a little more reading, we decided that we see these two as one. However, we will make the demarcation (two profiles) now, in our records and websites. Further research then will be documented. At some future point, the hope is to have sufficient information to make a decision. In the meantime, we can discuss why we think it's one guy. 
• In November of 2022, OpenAI released ChatGPT to extreme acclaim and got millions of people to sign on. We missed that event for several reasons that might be of interest. It was not until February of 2023 that we became aware of ChatGPT. In our first session, we told ChatGPT about Thomas Gardner and Roger Conant (at the same time, the research at WikiTree was progressing). Since then, we have interfaced with various GenAI systems (we like Bard and still are using Gemini for testing), reviewed the mathematical basis for the claims, discussed means to get maturity brought to the action, and a lot more. Basically, this goes along with our decision to focus on technology.  
  
  
  

So, now, we will restructure. Per usual, we will continue to have the FAQ which will be brought up to date. Also, we will release issues of Gardner's Beacon periodically, hopefully with more of a regularity. 

Remarks: Modified: 12/28/2024

09/15/2024 -- People will always be the focus, rather than technology. 

12/28/2024 -- See updates in GB, XIV, 1 for 2024 updates.