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<p class="MsoNormal">Hi Nick,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I\u2019m attempting to identify another use of the word <i>evolve</i> that you will accept as valid, nothing more.<o:p></o:p></p>
<p class="MsoNormal">In computational phylogenetics, one typically uses an error distribution (which arises from biochemistry) to estimate
<i>distance </i>between different DNA sequences. The probabilities of adenine changing into guanine, to cytosine, or to thymine, of guanine changing into cytosine or thymine, and of cytosine changing into thymine. This symmetrical matrix serves as a sort
of clock.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">One assumes that it is the exception, not the rule, that mutations arise from environmental pressure. With these assumptions (and sufficiently long sequences), one can place some individual contemporary organisms as closer and others
as farther away in <i>evolution distance</i>, or time. The task is to find the most likely ancestral sequences. The
<i>evolution </i>of which I speak is process of iterating a probabilistic model such that one sequence of inferred ancestral DNA iteratively morphs (<i>evolves</i>), site-by-site, into an observed sequence of DNA. This definition has nothing to do with adaptation,
other than it can be used to quantify when unusual things happen.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Marcus<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><b><span style="font-size:12.0pt;color:black">From: </span></b><span style="font-size:12.0pt;color:black">Friam <friam-bounces@redfish.com> on behalf of "thompnickson2@gmail.com" <thompnickson2@gmail.com><br>
<b>Reply-To: </b>The Friday Morning Applied Complexity Coffee Group <friam@redfish.com><br>
<b>Date: </b>Sunday, July 5, 2020 at 2:03 PM<br>
<b>To: </b>'The Friday Morning Applied Complexity Coffee Group' <friam@redfish.com><br>
<b>Subject: </b>Re: [FRIAM] The theory of everything<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<p class="MsoNormal">Sorry. I may not be worth your effort, here. I just don\u2019t understand what you said.<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">Let it be the case that as we examine the history of species, there are repeated (and therefore predictable) pathways through which they pass. A lineage of any sort, entering the water at some historical stage becomes more streamlined,
let\u2019s say. Because streamlining is characteristic of creatures that move through water, we say that any such lineage has adapted to life in water. Thus, in my way of thinking, to evolve [phylogenetically]in this case is to become more like creatures that
move through water. I have never been entirely clear what this additional constraint, ADAPTED phyletic descent, constitutes. I have been writing for many years, and I have been challenged on many points, but nobody has challenged me on this one, To put
the question baldly, wtf is natural design, anyway, as a descriptive property. Please don\u2019t answer that design is, whatever designers produce, because that is an example of a tethered description, and leaves us with nothing to say about the good that \u2018designers\u201d
produce in the world. <o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">Nick <o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<div>
<p class="MsoNormal">Nicholas Thompson<o:p></o:p></p>
<p class="MsoNormal">Emeritus Professor of Ethology and Psychology
<o:p></o:p></p>
<p class="MsoNormal">Clark University<o:p></o:p></p>
<p class="MsoNormal"><a href="mailto:ThompNickSon2@gmail.com">ThompNickSon2@gmail.com</a><o:p></o:p></p>
<p class="MsoNormal"><a href="https://wordpress.clarku.edu/nthompson/">https://wordpress.clarku.edu/nthompson/</a><o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
<p class="MsoNormal"> <o:p></o:p></p>
<div>
<div style="border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal"><b>From:</b> Friam <friam-bounces@redfish.com> <b>On Behalf Of
</b>Marcus Daniels<br>
<b>Sent:</b> Sunday, July 5, 2020 2:49 PM<br>
<b>To:</b> The Friday Morning Applied Complexity Coffee Group <friam@redfish.com><br>
<b>Subject:</b> Re: [FRIAM] The theory of everything<o:p></o:p></p>
</div>
</div>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">A matrix exponential proceeds toward an equilibrium state.
<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"><b><span style="font-size:12.0pt;color:black">From: </span></b><span style="font-size:12.0pt;color:black">Friam <<a href="mailto:friam-bounces@redfish.com">friam-bounces@redfish.com</a>> on behalf of "<a href="mailto:thompnickson2@gmail.com">thompnickson2@gmail.com</a>"
<<a href="mailto:thompnickson2@gmail.com">thompnickson2@gmail.com</a>><br>
<b>Reply-To: </b>The Friday Morning Applied Complexity Coffee Group <<a href="mailto:friam@redfish.com">friam@redfish.com</a>><br>
<b>Date: </b>Sunday, July 5, 2020 at 1:47 PM<br>
<b>To: </b>'The Friday Morning Applied Complexity Coffee Group' <<a href="mailto:friam@redfish.com">friam@redfish.com</a>><br>
<b>Subject: </b>Re: [FRIAM] The theory of everything</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
<p class="MsoNormal">So, phylogenetic evolution is evolution that proceeds toward adaptation. How would a state theorist characterize that constraint?
<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">n<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<div>
<p class="MsoNormal">Nicholas Thompson<o:p></o:p></p>
<p class="MsoNormal">Emeritus Professor of Ethology and Psychology<o:p></o:p></p>
<p class="MsoNormal">Clark University<o:p></o:p></p>
<p class="MsoNormal"><a href="mailto:ThompNickSon2@gmail.com">ThompNickSon2@gmail.com</a><o:p></o:p></p>
<p class="MsoNormal"><a href="https://wordpress.clarku.edu/nthompson/">https://wordpress.clarku.edu/nthompson/</a><o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
<p class="MsoNormal"> <o:p></o:p></p>
<div>
<div style="border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal"><b>From:</b> Friam <<a href="mailto:friam-bounces@redfish.com">friam-bounces@redfish.com</a>>
<b>On Behalf Of </b>Marcus Daniels<br>
<b>Sent:</b> Sunday, July 5, 2020 2:37 PM<br>
<b>To:</b> The Friday Morning Applied Complexity Coffee Group <<a href="mailto:friam@redfish.com">friam@redfish.com</a>><br>
<b>Subject:</b> Re: [FRIAM] The theory of everything<o:p></o:p></p>
</div>
</div>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">Yes, phylogenetic evolution is often modeled using a matrix exponential.<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal"><b><span style="font-size:12.0pt;color:black">From: </span></b><span style="font-size:12.0pt;color:black">Friam <<a href="mailto:friam-bounces@redfish.com">friam-bounces@redfish.com</a>> on behalf of "<a href="mailto:thompnickson2@gmail.com">thompnickson2@gmail.com</a>"
<<a href="mailto:thompnickson2@gmail.com">thompnickson2@gmail.com</a>><br>
<b>Reply-To: </b>The Friday Morning Applied Complexity Coffee Group <<a href="mailto:friam@redfish.com">friam@redfish.com</a>><br>
<b>Date: </b>Sunday, July 5, 2020 at 1:35 PM<br>
<b>To: </b>'The Friday Morning Applied Complexity Coffee Group' <<a href="mailto:friam@redfish.com">friam@redfish.com</a>><br>
<b>Subject: </b>Re: [FRIAM] The theory of everything</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
<p class="MsoNormal">Marcus, <o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">So in your sense, a system evolves if it passes along a predictable pathway from state to state. I wonder if phylogenetic evolution is a special case of yours.
<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">Nick <o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<div>
<p class="MsoNormal">Nicholas Thompson<o:p></o:p></p>
<p class="MsoNormal">Emeritus Professor of Ethology and Psychology<o:p></o:p></p>
<p class="MsoNormal">Clark University<o:p></o:p></p>
<p class="MsoNormal"><a href="mailto:ThompNickSon2@gmail.com">ThompNickSon2@gmail.com</a><o:p></o:p></p>
<p class="MsoNormal"><a href="https://wordpress.clarku.edu/nthompson/">https://wordpress.clarku.edu/nthompson/</a><o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
<p class="MsoNormal"> <o:p></o:p></p>
<div>
<div style="border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal"><b>From:</b> Friam <<a href="mailto:friam-bounces@redfish.com">friam-bounces@redfish.com</a>>
<b>On Behalf Of </b>Marcus Daniels<br>
<b>Sent:</b> Sunday, July 5, 2020 1:19 PM<br>
<b>To:</b> The Friday Morning Applied Complexity Coffee Group <<a href="mailto:friam@redfish.com">friam@redfish.com</a>><br>
<b>Subject:</b> Re: [FRIAM] The theory of everything<o:p></o:p></p>
</div>
</div>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">\u201cEvolve\u201d in this sense: <a href="https://en.wikipedia.org/wiki/Dynamical_system">
https://en.wikipedia.org/wiki/Dynamical_system</a><o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal"><b><span style="font-size:12.0pt;color:black">From: </span></b><span style="font-size:12.0pt;color:black">Friam <<a href="mailto:friam-bounces@redfish.com">friam-bounces@redfish.com</a>> on behalf of "<a href="mailto:thompnickson2@gmail.com">thompnickson2@gmail.com</a>"
<<a href="mailto:thompnickson2@gmail.com">thompnickson2@gmail.com</a>><br>
<b>Reply-To: </b>The Friday Morning Applied Complexity Coffee Group <<a href="mailto:friam@redfish.com">friam@redfish.com</a>><br>
<b>Date: </b>Sunday, July 5, 2020 at 9:47 AM<br>
<b>To: </b>'The Friday Morning Applied Complexity Coffee Group' <<a href="mailto:friam@redfish.com">friam@redfish.com</a>><br>
<b>Subject: </b>Re: [FRIAM] The theory of everything</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
<p class="MsoNormal">Jochen, <o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">FOOD FIGHT! FOOD FIGHT! I absolutely and totally disagree that \u201ceverything evolves\u201d [while agreeing that anything that is everything is nothing]. Rocks and tornadoes do not evolve. They change, but the don\u2019t evolve. Evolution (to me)
is a very specific pattern of design arising through phylogenetic descent \u2013 lineages being bent through time to match their circumstances. I am not entirely sure that some inanimate things don\u2019t evolve. I would have a hard time arguing ferociously that the
sorting of pebbles on a beach is not the result of some sort of evolution. I certainly don\u2019t want to define evolution as something that only organisms can do, if only because that turns the assertion, \u201conly organisms evolve\u201d into a nothing, or an everything,
depending on how you care to look at it <o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">In this matter, as in all matters, Eric will correct me. <o:p>
</o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">Nick <o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<div>
<p class="MsoNormal">Nicholas Thompson<o:p></o:p></p>
<p class="MsoNormal">Emeritus Professor of Ethology and Psychology<o:p></o:p></p>
<p class="MsoNormal">Clark University<o:p></o:p></p>
<p class="MsoNormal"><a href="mailto:ThompNickSon2@gmail.com">ThompNickSon2@gmail.com</a><o:p></o:p></p>
<p class="MsoNormal"><a href="https://wordpress.clarku.edu/nthompson/">https://wordpress.clarku.edu/nthompson/</a><o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
<p class="MsoNormal"> <o:p></o:p></p>
<div>
<div style="border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal"><b>From:</b> Friam <<a href="mailto:friam-bounces@redfish.com">friam-bounces@redfish.com</a>>
<b>On Behalf Of </b>Jochen Fromm<br>
<b>Sent:</b> Sunday, July 5, 2020 4:47 AM<br>
<b>To:</b> The Friday Morning Applied Complexity Coffee Group <<a href="mailto:friam@redfish.com">friam@redfish.com</a>><br>
<b>Subject:</b> Re: [FRIAM] The theory of everything<o:p></o:p></p>
</div>
</div>
<p class="MsoNormal"> <o:p></o:p></p>
<div>
<p class="MsoNormal">Russ, I agree. Maybe we found it already, the theory of everything & nothing: Darwin's theory of evolution. It is a theory of everything because everything evolves. It doesn't say anything how fish, insects, dinosaurs, mammals, birds, religions,
civilizations, companies, parties or states look like, though. Therefore it is also a theory of nothing. I have to reread your book.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><a href="https://www.hpcoders.com.au/nothing.html">https://www.hpcoders.com.au/nothing.html</a><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">-J.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
<div>
<div>
<p class="MsoNormal"><span style="color:black">-------- Original message --------</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span style="color:black">From: Russell Standish <<a href="mailto:lists@hpcoders.com.au">lists@hpcoders.com.au</a>>
</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span style="color:black">Date: 7/5/20 11:49 (GMT+01:00) </span>
<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span style="color:black">To: The Friday Morning Applied Complexity Coffee Group <<a href="mailto:friam@redfish.com">friam@redfish.com</a>>
</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span style="color:black">Subject: Re: [FRIAM] Book publishing advice needed
</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span style="color:black"> </span><o:p></o:p></p>
</div>
</div>
<p class="MsoNormal">Being self-published hasn't stopped my book "Theory of Nothing" from<br>
being cited. According to Google Scholar, it has 22 citations, 9th on<br>
my list in terms of citation count, just after "Why Occams Razor", a<br>
peer reviewed paper on similar topics. It got a bit of a boost from<br>
Max Tegmark's book, as he singled it out as inspiration, kind of ironic when it<br>
was one of Max's "crazy papers" that inspired me to write "Why Occams<br>
Razor" and then "Theory of Nothing".<br>
<br>
I think you need to have a reason to publish a book. Making money is<br>
not one them - almost nobody makes money from writing books. Vanity<br>
publications ("it looks good on the CV") is another one to avoid. Best<br>
bet is if you have a story or a topic that needs telling, and you<br>
think would be interesting to other people, then go for it. Marketing <br>
then becomes telling other people about it, advancing arguments from<br>
it in fora like this. With a bit of luck, it goes viral.<br>
<br>
One good reason for writing academic books is that it gives you<br>
expanded scope to explain your ideas more fully, and in less<br>
technically forbidding terms. Allows you to expand your readership<br>
beyond the narrow circle reading your peer revieed articles. But you<br>
probably want those peer reviewed articles to back up/draw upon your<br>
book work. That's probably the reason why old academics write books,<br>
and young ones write papers.<br>
<br>
In my case, I've self-published 3 books so far: "Theory of Nothing",<br>
which has sold over 1000 copies, and perhaps 2-3 times as many free<br>
downloads from my website and the usual pirate websites, but in no way<br>
does the royalties cover the time I put into it (unless being paid<br>
less than a Calcutta rickshaw driver was a career ambition); "Amoeba's<br>
Secret", a translation of a semi-autobiography by Bruno Marchal, which<br>
was about the clearest exposition he gave of his ideas, and "Magic<br>
Cottage", an Anthology of my son's writing, which was quite exquisite,<br>
and sadly something he's not really doing now. Magic Cottage proved to<br>
be more of a vanity publication than I thought it would be - but<br>
partly because he never took up my suggestion of leaving a copy around<br>
his college room, now apartment, where it could act as a conversation<br>
starter. I also envisaged him using the book when going for jobs that<br>
might require writing skills, but it seems he hasn't needed to do that<br>
to date.<br>
<br>
<br>
Cheers<br>
<br>
On Sat, Jul 04, 2020 at 10:25:03PM +0200, Jochen Fromm wrote:<br>
> Thanks. Yes, self-publishing is an option. I am looking for an official<br>
> publisher mainly for one reason, namely that other scientists and researchers<br>
> can cite it, since I still cling to the illusion that someone would actually do<br>
> it. Normally self-published texts are not considered as reliable or trustworthy<br>
> sources. I didn't expect that finding a decent publisher would be so<br>
> difficult. <br>
> <br>
> -J.<br>
> <br>
> <br>
> -------- Original message --------<br>
> From: Tom Johnson <<a href="mailto:tom@jtjohnson.com">tom@jtjohnson.com</a>><br>
> Date: 7/4/20 20:10 (GMT+01:00)<br>
> To: The Friday Morning Applied Complexity Coffee Group <<a href="mailto:friam@redfish.com">friam@redfish.com</a>><br>
> Subject: Re: [FRIAM] Book publishing advice needed<br>
> <br>
> Jochen:<br>
> The deal being offered strikes me as a bad deal.<br>
> <br>
> Background: I have been practicing and teaching about "Be Your Own Publisher"<br>
> for nearly 15 years. There are, in my opinion, some major problems with all<br>
> publishers today. It starts with control of the copyright. I think YOU should<br>
> want to maintain control of the copyright to your work. It will depend on the<br>
> contract, but many or most publishers will try to lock down the copyright in<br>
> their favor for all -- ALL -- forms of your work in perpetuity and throughout<br>
> the universe. Sometimes quite literally.<br>
> <br>
> Second, you should assume -- especially with a small publisher and you, not<br>
> being as well known as Stephen King or Daniel Steele -- the publisher will do<br>
> little if anything to promote your book beyond a mention in its catalog and,<br>
> maybe, some promotional links on Amazon. Given that, a 5 percent royalty<br>
> should be seen as a con.<br>
> <br>
> Third, given your computing experience, you should find it easy to format and<br>
> produce the book yourself. I have used Lulu.com for years. It is especially<br>
> good if you want to have both hardback, paperback and PDF editions. Again the<br>
> advantages: you keep the copyright, you can set (and change) the prices and to<br>
> a degree the royalties. Also, Lulu and Amazon handle all the backend financial<br>
> arrangements and administration and pay directly and quickly. I also use a<br>
> very good, high quality digital printer in Albuquerque for paperback editions. <br>
> It is Lithexcel. It handles all the printing (one copy to any number) quickly,<br>
> along with all the fulfillment and accounting. The folks there will also, for<br>
> only $25, set up your book in the Amazon inventory search engine. Finally,<br>
> there is Amazon's self-publishing arm. While Amazon might take a bigger slice,<br>
> the control over all aspects is in your hands.<br>
> <br>
> Here's the problem/challenge with all of these. YOU have to do the marketing/<br>
> publicity/promotion. But so what? If you today sign with any publisher of any<br>
> size you will have to do the same thing.<br>
> <br>
> Hope this helps. Feel free to contact me with questions. Also you might want<br>
> to see <a href="https://bit.ly/2ZvihKc">https://bit.ly/2ZvihKc</a> <br>
> Tom<br>
> <br>
> ============================================<br>
> Tom Johnson - <a href="mailto:tom@jtjohnson.com">tom@jtjohnson.com</a><br>
> Institute for Analytic Journalism -- Santa Fe, NM USA<br>
> 505.577.6482(c) 505.473.9646(h)<br>
> NM Foundation for Open Government<br>
> Check out It's The People's Data <br>
> ============================================<br>
> <br>
> <br>
> <br>
> [icon-] Virus-free. <a href="http://www.avast.com">www.avast.com</a><br>
> <br>
> <br>
> <br>
> On Fri, Jul 3, 2020 at 1:29 AM Jochen Fromm <<a href="mailto:jofr@cas-group.net">jofr@cas-group.net</a>> wrote:<br>
> <br>
> At one end of the spectrum there are the 5 big commercial publishers<br>
> Hachette, HarperCollins, Macmillan, Penguin Random House and Simon &<br>
> Schuster. They only publish stuff their agents select to make a lot of<br>
> money. There are also the big academic publishers like OUP, CUP, HUP and<br>
> MIT Press, which preferably publish strictly peer-reviewed content from<br>
> professors at Ivy League universities who made their PhD at the age of 20.<br>
> <br>
> At the other end of the spectrum there are "predatory publishers" who<br>
> publish anything you submit as long as you pay enough money for it. Open<br>
> access books can also be very expensive. Publishing an "open access book"<br>
> at De Gruyter for example costs up to 8000 $. You pay for it so that other<br>
> people read it. It is basically some kind of advertising of your own work.<br>
> <br>
> For my own new book I finally have an offer from a small publisher in<br>
> Washington D.C. who is somewhere in the middle of the spectrum. They are<br>
> really small and offer 5% royalties. Should I accept this offer or wait for<br>
> a better one? It is the only one from more than 25 publishers I have asked,<br>
> and the publishers at the moment are flooded with submissions. :-/<br>
> <a href="https://www.theguardian.com/books/booksblog/2020/mar/26/">https://www.theguardian.com/books/booksblog/2020/mar/26/</a><br>
> novel-writing-during-coronavirus-crisis-outbreak<br>
> <br>
> -J.<br>
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