Posts by Jim Logajan

    Assuming anyone is still checking in here - I wonder what keeps people from posting. Here's what has kept me from posting:

    After I exercised some stock options in the client company that I've done work for the last 10 years and become part owner, I've found an extra incentive to make sure things go well there. We have had a major development project underway for the last year that has sucked my time. So work has kept me busy.

    The closest I've come to nanotechnology lately is that I started studying the Kindle edition of Molecular Biology of the Cell, 6th edition, by Alberts et al (MBoC) from beginning to end. I've had a copy of the third edition for about 15 years but had only ever used it as a reference; never tried to read it all the way through. As I started reading the 6th edition (to fill in gaps in my knowledge and get more up to date info) I became curious about the history of molecular biology, so I went looking for recommendations on books on the subject. Based on reviews, I bought a copy of Operators and Promoters: The Story of Molecular Biology and Its Creators, by Echols and Gross. Early on it said if I wanted to know more about the period it didn't cover, I should read The Double Helix by Watson and The Eighth Day of Creation: Makers of the Revolution in Biology, by Judson. (There is a commemorative edition of the latter that I only discovered later.)

    So I read Double Helix, then The Eighth Day, and am just now finishing Operators and Promoters. Once done I'll get back to finishing MBoC. Except I can't help it, I got curious about the history of chemistry, so a copy of The Development of Modern Chemistry by Ihde will be arriving soon.

    Lastly, not sure why it took me so long, but bought a 3D printer and downloaded a free copy of DesignSpark Mechanical so I could design the types of things I wanted to print. Fun stuff - if I had more time I'd be designing and building some nanotech related tools. It's amazing sometimes how much time one expends on the allegedly "trivial" aspect of mounting and arranging parts in some apparatus. Sure, it may take hours to print the needed parts, but it can take that long or even longer to do the same using the tools in a garage workshop.

    So the Set described in the there discussed tooltip paper ( ) is not reversible in the bond-topology-state.

    Since the goal of the study did not include the additional burden of that requirement, I am not surprised. Efficient reversibility would see a longer-term goal.

    I made a 3D model for visualizing the qualitative progression of the energy wells that is necessary for a energetically reversible mechanosynthetic operation. This model is quantitatively disconnect from any particular physical process like e.g. hydrogen abstraction.…nosynthesis_principle.jpg

    I'm afraid I don't know what the image is supposed to be showing me. None of the axis are labeled - do you have some additional context or discussion somewhere?

    I'm probably missing something, but I don't see how one can draw any inference about future tools from the first set of invented tools for molecular carbon mechanical synthesis. I skimmed sections 13.3.7, 13.3.8, and 8.5.2 of Nanosystems and it does not look to me like there are any dangers. Even if none of the released binding energy were stored for later re-use, the universe is awash in thermonuclear energy. I think it is something of a technical oddity that so much of it is temporarily inaccessible. Energetically inefficient nanotech production would still be, on a relative scale, far more efficient than current tech production.

    Many thanks for migrating all the posts from the beehive forum to wotlab forum for better maintainability. All the posts seem well preserved :) - perfect job.
    Also I'm delighted to see that you've implemented my suggestions for sub-forum topics.

    Now everything is ready for a great year 2016 :)

    I paid the firm to migrate the posts - it was very inexpensive. So low that I later offered more money to expedite things (but they didn't take it.) I believe the fellow that actually did the work was in Armenia, based on the source of the emails. They probably have developers scattered around the globe.

    Anyway, your sub-forum topics did seem good once I found time to give it some thought. All that is needed now is to attract posters. Over the next week or so I'll try to respond to some of your older posts.

    Welcome to the Sci-Nanotech Forum

    • IMPORTANT NOTE: Login usernames and passwords had to be changed when the forum software was changed form Beehive to WoltLab Burning Board. If you had an account and did not get an email with new login information (sent December 25, 2015) please email me at and I will assist in getting you back on. In the worst case you would need to create a new account.
    • Sci-Nanotech is an ad-free forum primarily intended for discussions about atomically precise manufacturing (APM) nanotechnology. The forum is financially and operationally independent of any commercial, educational, or government entities.
    • This forum was created to replace the moderated Usenet newsgroup sci.nanotech (hence the choice of the domain name.) That newsgroup has seen almost no activity in recent years partly because moderation slowed dialog and partly due to technical limits of Usenet that lead to its general decline.
    • The rules that community members are expected to follow are fairly simple: remain civil, try to stay relevant (or at least not distracting,) keep calm, and avoid crowding. Off-topic posts and threads will generally be allowed, though we reserve the right to suppress any that become too distracting to the core focus of the forum. The owner and any delegated moderators are lazy and will intervene only if seriously provoked by a horde of member complaints or our computer network resources are abused. The forum software that was chosen has a number of features that should allow members to self-police, or at least mostly avoid, other members they discover are too disagreeable to converse with.

    - Jim Logajan

    Images attribution: Walterdenkens

    While I think functional programming (declarative) should be considered for implementing higher level nanomachine operations (such as long term planning) my understanding is that it is difficult to get predictable performance from existing implementations. For operations requiring real-time responses, such as nano-systems operating in-situ, imperative programming may still be the only realistic choice. Also, the underlying hardware operates imperatively (it has state that changes with time) so there is a mismatch between the declarative notation and what is actually occurring on the machine.

    I first used a declarative language about 25 years ago. I had been writing code in imperative languages the previous 18 years (yes, I'm an old coder,) so while I understood the concept, it was not easy to figure out how to express the same program declaratively. That project lasted about a year, after which I did not encounter any use of declarative languages.

    Quote from Lukas (LSUESS)

    Any news?

    I would like to switch to Wotlab Burning Board. It should be pretty straightforward to get the software up and running, but the problem that has kept me from switching is deciding how to handle transfer of user accounts and posts from the Beehive software to Burning Board.

    One choice is to simply not do any transfers - instead, keep this board running for a while at a different URL (e.g. ) and alert existing users of the change to the new software and tell them they will need to re-create their accounts on the new forum. Users like yourself could re-post (hopefully via something as simple as copy-and-paste) messages you wanted to preserve from the old forum to the new one. After a couple months I'd then close access to the old forum. You have made the most posts of greatest value and interest - would you be OK reentering them on a new forum?

    The other choice is for me to do the transfer of accounts and posts. But if I do such a transfer (there are companies that specialize in that sort of thing that I'd rather hire than spend time myself - it is a non-trivial cost in either my time or money) the two forums use different one-way hash functions, so I'd still have to reset user passwords and send users the new passwords.


    Quote from JimL (JIMLOGAJAN)

    I've also played with demos of UBB.Threads and Xenforo, both of which are commercial offerings. In terms of features that I think are useful, Xenforo seems to have the edge.

    I kept coming across comparisons of Xenforo to Wotlab Burning Board ( So I looked more closely into it - they provide a way for one to create a demo and play with it. After a couple hours of playing around with it, I'm impressed. Cost doesn't appear to be too bad. I may choose that product and purchase it this weekend.

    I'm not entirely sure that FUDforum is a good choice. Not a bad choice, but there are some other options I'm considering.

    I've also played with demos of UBB.Threads and Xenforo, both of which are commercial offerings. In terms of features that I think are useful, Xenforo seems to have the edge. Two things I would like that seemed to be missing in part from FUDforum are:

    Being able to get emailed alerts on selectable forum events (new posts, new threads, new users, etc.)

    A quick summary list of all the unread threads or posts that exist, regardless of subforum, in either a chronological or reverse chronolgical order.

    Just an update to anyone interested:
    After further research where I took another look at many of the possibilities, my list has narrowed to one of these:


    My preference is now slightly toward FUDForum.

    Development of UBB.Threads appears to have slowed in the past few years. I played with its sample forum. Editing of posts seemed OK enough but felt a tad limited and unhelpful. Creating and editing posts in the two finalists felt much more natural. I also read some of the public interactions between prospects/customers and UBB.Threads company personnel. The company doesn't doesn't seem to interact with prospects much - existing customers seem to provide most of the marketing muscle. In the end it just didn't seem to have enough going for it relative to the other options and extra cost, so I dropped it from consideration.

    While phpBB was another contender, it didn't seem to be different enough from the final two choices to add to the list. It didn't help that the developers of phpBB appear to have got strong feelings against indented threaded views; so much so that they will not even make it a user-selectable option. I'm neutral on the issue, but I think users should have that option. It does help that FUDForum can allegedly be integrated with Usenet and email lists, while it isn't clear whether phpBB can be (not that there is any value these days in integrating with Usenet.)

    >> I personally prefer open source software mainly out of those reasons:
    >> * problems in the closed source parts -> tell them and pray

    Problems in open source -> tell them and pray or solve the problem yourself.

    >> * company goes out of business -> you're forced to leave the sinking ship

    Unless the last release is broken there should be no reason to switch software. I frequent two piloting forums that use vBulletin that stopped upgrading to the latest release of vBulletin years ago - the company may as well have gone out of business. They seem to have survived OK.

    >> So if you see major technical advantages (excluding experimental features) in UBB.Threads maybe this is the better solution.

    I haven't come to any decision yet about what will replace Beehive. UBB.Threads is only better than Beehive in some aspects; it remains to be seen if it is optimal. I do know that when I try to use a browser on an iPad with Beehive, it can't handle quoting (in fact the quoting mechanism isn't very good in general.) I need to do further research.

    I think the most important things are
    A.) lots of usage which forces the (big) user community to keep it working and documented
    B.) the possibility of easy backup and migration

    Beehive appears to have only a modest user community and they don't talk much about how to do backup and restore. So it doesn't rate very well on those important points.

    1.) Among the forums I regularely visit the software I most often encountered was phpBB  -- open source with friendly homepage

    That is certainly high on my list.

    2.) vBulletin -- this one is proprietary though

    I've never liked the vBulletin software and the company appears to have had some past internal problems. Commercial or proprietary aren't an issue so long as support is available and competent without costing great amounts of money.

    Might Inyoka be an option ?? -- I'm always amazed about the quality of documentation for ubuntu.
    It seems to be a multi purpouse CMS (wiki + forum + blog ?)
    I just found this and haven't looked into it in any detail.

    First I've heard of Inyoka - looks intriguing but the German I learned in school is rusty, so if there is no English version of the documentation I'm afraid I'll have to pass. I think I would, however, consider Burning Board ( which does provide English documentation.

    I guess you know this page already:…f_Internet_forum_software

    Yes. Another site that I also found useful is this one:

    I've concluded that while the Beehive forum software has interesting aspects, I'm finding it difficult to use and am equally surprised as other users by some of its behavior. It appealed to me because the threads panel was always visible, so there is no need to constantly navigate back to a main threads window when one is finished reading a thread to move on to the next thread of interest. I consider such navigation reduction important enough to lose some screen real estate. (The better Usenet readers worked this way and it has a lot to commend it in my humble opinion. Certainly the Beehive authors thought so too.)

    I haven't ruled anything in or out, but I'm currently considering porting the forum to UBB.Threads (
    It has the advantage of longevity, widespread usage, and commercial support while not costing very much.
    A password reset will need to be done for all existing users regardless of which system this forum gets ported to, so there is that (hopefully minor) annoyance to reckon with.

    Anyone with objections, recommendations, or suggestions one way or another please let me know as soon as possible. I'd like to start the migration process within a week or two.

    Quote from LSUESS

    Some thoughts:

    • Is it easy to make make backups with this forum SW?
    • Since this seems to be not a mainstream forum software migrating might become difficult in the future.
    • With AI cracking captchas spam protection becomes a nightmare - my website was attacked pretty soon - worry ...
    • (Where do you host it?)
    • I've contacted ~30 people (austria) which might be interested checking out this forum.
    • ... I might PM you about the last point sometime but not now ...
    • I realized that the search function could be made less stringent. I quickly ran in a 30sec timeout.
    • The list on the left is hard to read - lack of spaces makes it difficult to see whether its just a second line or the next topic.
    • the quoting button doesn't always work
    • (are sticky notes possible?)

    I'm finally back from my travels (a long planned tour of Scotland) and somewhat caught back up at work (to the extent that is possible) and I started to look into responding to some of the posts of yours, such as the one above, and have belatedly concluded that my choice of the Beehive forum software was a mistake.

    The user documentation is almost non-existent - I have to actually examine the source code or experiment myself to learn how to do things. Sometimes very simple things. I'm not sure, for example, if there is an easy way to quote a message and insert replies after each paragraph that I want to address.

    I'm going to start a new thread on the subject of migrating the forum posts to different forum software.

    By the way, this web site is currently hosted on

    I can certainly create those folders and move existing threads to them, but it has been found by others (and my own observations) that it is actually counterproductive to create folders too soon in the life of a forum. As categories become evident threads may be created.

    I happen to think discussion of applications cannot occur without also their impacts being brought up even when an author of a post tries to avoid it, and vice versa.

    Which of the existing threads do you feel should be placed into the folders you have proposed?

    quote: Lukas (LSUESS)

    IIRC I once heard something along the lines that: "one cannot focus a particle beam (in position space) below what it was at the point of origin because of Liouville's theorem of constant phase space volume (of closed systems?)"**

    You bring up many interesting points that I will try to respond to later, but I'll address just the one I quoted:

    The system isn't closed because, classically at least, a charged particle moving through the focussing fields will experience acceleration and thus radiate energy away. If it weren't for quantum mechanics the nuclei would most likely first settle into an ever tighter beam line and then eventually slow to a stop, since there are field potentials along every axis.

    >>>> ... a belated welcome ...
    >> Don't sweat it, I'm actually pleasantly surprised since I was expecting to wait at least half a month.

    Unfortunately you indeed will have to wait a half month for any half-way intelligent responses (at least from me) since I am currently traveling for the next couple weeks. I've only a few spare hours a day to check things online - and composing posts on an iPad seems to cut my IQ in half.

    But in regards to your post about Drexler's Abundance book - I agree that he did a good job of instilling intuition in readers of the physics and mechanics of atomic and molecular scale structures and dynamics. It would be even better with appropriate visuals.

    Wish I had time now to respond in more depth to your posts, but in the mean time hopefully some of the other members will pop in at some point and give their thoughts.

    First, a belated welcome to sci-nanotech!

    I liked the idea you used to make the size of an atom comprehensible.

    Since you asked for comments on your new text, these are my thoughts:

    I did not understand why you say that biological products cannot be produced because a very different technology is needed to produce them. Since you don't explain any details of the technology you are talking about in the product materials paragraph I can't begin to guess what is possible and impossible. My first thought was "wait - why can't I make biological materials? Is making a protein molecule not possible? What would be possible?" I think you may need to at least tell the viewer that later videos will explain the origin of the limitations of nano-factories.

    I don't have any further comments at this time on your introduction video.

    A couple months ago I did search Youtube for videos where the word "nanotechnology" appeared and while there were more videos than I could possibly view or even sample, I did review several hundred, sorted first by view count, then by viewer ratings, and lastly by most recently uploaded. I found very few of any educational value. The closest I thought that came to having useful material of use to scientists, engineers, and technologically literate audience is this one by Ralph Merkle:

    But it is too long for one sitting and is a recording of a lecture, which wastes the potential offered by videos.