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Clasp: Common Lisp using LLVM and C++ for Designing Molecules

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Youtube Summary
Google Tech Talk
August 3, 2015
(click show more for more info)
Presented by Christian Schafmeister

ABSTRACT

I will show you what you can do with CANDO/Clasp to design molecules.

Here are some of the things that CANDO can do.

- Automatic atom type assignment and partial charge estimation.
- Force field energy calculations and fast energy minimization is built in (steepest descent, conjugate-gradients and truncated Newton-Raphson; the minimizers automatically switch from one approach to the other as you get closer to the energy minimum).
- The energy function has a chiral restraint, and several other restraint functions built in. You can also add new energy terms and analytical first and second derivatives will be automatically generated and lowered to efficient code for energy minimizations.
- It builds three-dimensional models of molecules using geometric construction (is that a term?) from a library of fragments (like rotamers).
- Expose and drive OpenMM or Amber or any other molecular dynamics package written in C++, C or Fortran DIRECTLY from CANDO.
- It has a built in compiled scripting language (Common Lisp) that generates LLVM-IR and native code that interoperates with C++. This is the big deal, it’s not just a scripting language. It will be fast enough that you can write ANYTHING that the chemistry problem needs in Common Lisp or in C++/C/Fortran and hook it in.
- Builtin Message Passing Interface (MPI) library for running on hundreds of thousands of CPUs.
- A built in serialization facility to save and load any type of object built within CANDO. Molecules, force fields, parameter files etc. Everything, including code, can be written to files, loaded or sent between processors via MPI.
- Built in SMARTS for doing chem-informatics and pattern recognition on molecules.
- It reads Chemdraw files, so you can sketch molecules and it will build 3D models from them.

If you are doing computational drug screening, then you can do everything in CANDO.

This is what I designed CANDO for: Molecular Lego represent an infinite universe of highly pre-organized molecules with programmable shapes and functional group display that are all synthetically accessible. CANDO is the engine that will rapidly build starting molecules, assign atom types and charges and then do conformational searching, docking, scoring and analysis to identify functional molecules. By tightly coupling all of these capabilities as part of a compiled language it will enable molecular design like it has never been done before.

CANDO is general, it can work with any kind of molecule.
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More presentations!

I think two are almost the same presentation:

https://www.youtube.com/watch?v=PQDwvatwjD8 (July 2010) 10S6P4 Christian Schafmeister 2010 UNTT 3rd Annual Conference Session 6 Presentation 4

https://www.youtube.com/watch?v=8X69_42Mj-g (July 2015) Clasp: Common Lisp using LLVM and C++ for Molecular Metaprogramming

https://www.youtube.com/watch?v=0rSMt1pAlbE (Aug 2015) Clasp: Common Lisp using LLVM and C++ for Designing Molecules

https://www.youtube.com/watch?v=9HXfvT85EFE (Oct 2018) Modular Polymer Catalysts - Chris Schafmeister

https://www.youtube.com/watch?v=mbdXeRBbgDM (Nov 2018) LLVM Developers Meeting: C. Schafmeister lessons Learned Implementing Common Lisp with LLVM

Ah, related to #clasp:

https://www.youtube.com/watch?v=8X69_42Mj-g Clasp: Common Lisp using LLVM and C++ for Molecular Metaprogramming

https://www.youtube.com/watch?v=mbdXeRBbgDM 2018 LLVM Developers Meeting: C. Schafmeister lessons Learned Implementing Common Lisp with LLVM

https://www.youtube.com/watch?v=0rSMt1pAlbE Clasp: Common Lisp using LLVM and C++ for Designing Molecules

https://www.youtube.com/watch?v=9HXfvT85EFE Modular Polymer Catalysts - Chris Schafmeister

https://www.youtube.com/watch?v=PQDwvatwjD8 10S6P4 Christian Schafmeister 2010 UNTT 3rd Annual Conference Session 6 Presentation 4

kristjansson
In that they're both implementations of Common Lisp, but is there a deep connection between the two than that? Not that directing more attention to clasp is a bad thing!
fiddlerwoaroof
SICL is being developed in a modular fashion: I believe clasp uses SICL’s compiler framework Cleavir for its own compiler. (I’ve also heard that ABCL and ECL have considered reimplementing their compilers with Cleavir)
drmeister
Clasp author here - Clasp uses SICL's Cleavir compiler.
Checkout https://github.com/clasp-developers/clasp

"Clasp: Common Lisp using LLVM and C++ for Designing Molecules": https://www.youtube.com/watch?v=0rSMt1pAlbE

Your Google talk was one of my top 10 ever, it blew me away.

It's not uncommon in the tech industry to build some mad scientist solution - pardon the expression - because we're trying to do something pedestrian but have painted ourselves in to a corner, eg HipHop VM.

Doing it to help with cutting edge science is genuinely exciting.

https://www.youtube.com/watch?v=0rSMt1pAlbE

drmeister
Thank you!
"How the strengths of Lisp-family languages facilitate building complex and flexible bioinformatics applications."

https://www.ncbi.nlm.nih.gov/pubmed/28040748

-- US National Library of Medicine National Institutes of Health

"Clasp: Common Lisp using LLVM and C++ for Designing Molecules"

https://www.youtube.com/watch?v=0rSMt1pAlbE

-- GoogleTechTalks

oblio
That's nowhere near something like medical clinical trials, though.

Think of studies where you:

a) have statistically representative sample size (100+ developers)

b) actual numbers and compare them (the average development time needed for the Java/C++/etc. applications was Y and the average development time needed for Lisp applications was Y - Z, where Z > 0, etc.; the average execution time for Java/C++/etc. applications, etc., you get the idea)

Computer Science studies are still in their infancy.

All this Lisp hype is just hype and gut feelings.

Yesterday I was on the European Lisp Symposium, listening to the talk about Clasp and CANDO. Christian Schafmeister, who is a chemist, basically wrote his own Common Lisp implementation with focus on speed and C++ interop to have a base to run a molecule design tool on - because no available software was up to the task he's doing (designing stuff like water filters out of molecules)[0].

What it made me realize is that... I need to find myself something else to do than programming. Something else to learn about in greater detail. There are many, many interesting problems out there to solve, but you have to know about them first. Programming is great as a support speciality, if you have another one to support it. Right now the only thing I'm specialized in is making better tools for developers. Which we're in need of, true, but even more so are other domains.

[0] - Yesterday's talk should be up soon; in the meantime, here's his talk from last year at Google: https://www.youtube.com/watch?v=0rSMt1pAlbE.

hnal943
reminds me of what Donald Knuth had to say about academic specialization in Things a Computer Scientist Rarely Talks About:

  There might be some light on the horizon, however.  I predict that in the not too distant
  future, people in acamedmic life are going to define themselves not by one specialty
  area, but by two sub-specialties that belong to two rather different main specialties.
  This means that we'll have a web of interests, in which each person will serve as a
  bridge between different parts of the overall structure.  You can see that this is much
  better than having a tree hierarchy that branches out further and further, with nobody
  able to talk to the people on other sub-branches.  We'll have people that each belong to
  two areas, in two different parts of the overall structure.  Then we'll be able to have
  some hope of coping with new knowledge as it comes along.
Johnny_Brahms
"C++ templates are to common lisp macros, what IRS tax forms are to poetry."

This is a new favourite quote of mine.

None
None
vijayr
Is there a list of real world, expert vetted list of problems that can be solved with software? Problems like the one you mentioned (not yet another project management app). It would be awesome if someone can curate a list like this and act as a bridge between experts from other fields and programmers who want to work on such problems.
snerbles
Such information is valuable and often guarded while products are under development.
vijayr
Why would someone guard such information unless they themselves are making a product solving the problem? If I am a Chemist (or whatever other field) and I have some problems to solve and I am not a programmer, isn't it in my own interest to publicize the problems so someone else can make software for it?
CJefferson
I have a range of such problems. On major issue is that learning what the problem is, and exactly how to solve it, is a fairly major undertaking.

Also, because I'm in research, no-one is going to pay you for your work (or if you get paid, it will be embarrassingly small)

I'm not sure how many people there are who would be willing to invest a couple of weeks learning a new topic, to then write a program in that topic without pay. Oh of course, and probably useful to provide some minimal support going forwards as well.

vijayr
What kind of problems are they? What field?

I understand what you are saying about pay. But here is the counter argument for it - say you have 3 problems to solve, that can be solved with software. You don't have time or patience to code it yourself, but you know your peers and friends also have the same 3 problems. If you can clearly write down the requirements, I think there will be programmers who will be willing to work on the problem - especially if they know there are people who want the problems solved and there is a possibility of turning it into a side project or a business.

Maybe you could pick a handful of the problems, post them here and see if there is any interest?

CJefferson
I won't do it in this post, but I'll aim to write up a blog post, and see if it gets any interest.
swah
Ideally we should just work together with those people, share the profits...
cossatot
Ideally there would be profits...
pizza
That lecture is very interesting, thanks.
lumberjack
I had the same realisation a few years ago. I switched from CS to math and physics. It is definitely more challenging but I do not regret the switch. Plus I discovered math can be quite fun.

Most of the most challenging software requires domain knowledge that CS/software devs do not have. Ultimately it is easier to go from a math/physics background to CS/software development than the other way round.

Feb 25, 2016 · nabla9 on The Lisp Curse (2011)
Lisp is programmable programming language, especially Common Lisp. It works as programmer amplifier. Better you are, more you benefit from it.

I challenge anyone to watch this lecture from Christian Schafmeister and say they are not impressed: https://www.youtube.com/watch?v=8X69_42Mj-g and https://www.youtube.com/watch?v=0rSMt1pAlbE

robohamburger
Only part way through the first video but this is very inspiring.

"C++ templates are to common lisp macros as IRS tax forms are to poetry" so true.

tosseraccount
What popular programs are written in Lisp?
stray
The software I produce at work is Ruby. I don't know that it's popular -- but it is central to a large company's operations.

But I generate and validate that Ruby code with Common Lisp -- in other words, I write Lisp that writes correct, idiomatic Ruby.

I would be very surprised if I were the only person doing this.

giancarlostoro
Is it possible that you can share some information on this, if allowed by your company / employer? This is a first I've heard of this, sounds quite interesting.
copperx
I understand why you might want to do that, but why are your reasons for doing it?
eudox
Have you written about this somewhere? I've love to read more about it.
nabla9
Popularity is not the correct measure stick.

Lisp is more like research language than implementation language for bean counting apps. Better question is what bleeding edge things have originated, are being done or have been done in Lisp.

John Carmak is doing VR research with Racket.

Christian Schafmeister doing molecular metaprogramming.

Raytheon implemented a signal processing analysis pipeline for missile defense in Lisp

Commercial Lisp vendors keep lists of some of their customers. Specialized Cad programs like Bentley PlantWise are not popular but they are very complex.

http://franz.com/success/

http://www.lispworks.com/success-stories/

eudox
Maxima and pgloader

http://maxima.sourceforge.net/

http://pgloader.io/

defgeneric
pgloader (Dimitri Fontaine) is a great piece of software.

There's also cl-abnf from the same author and project which is another great example of the expressive power of common lisp.

Also, everything Fernando Boretti does is awesome ;)

https://github.com/eudoxia0 http://eudoxia.me/article/common-lisp-sotu-2015/ https://github.com/dimitri/cl-abnf

ronjouch
I'm regularly hearing about web applications written in ClojureScript, a.k.a. Clojure (a dialect of Lisp, [1]) compiled to JavaScript. Recently I've heard of:

- https://github.com/asciinema/asciinema-player

- https://precursorapp.com/ (not open-source)

[1] http://www.clojure.org/

dopamean
Clojurescript is not "also known as" Clojure.
dctoedt
> Clojurescript is not "also known as" Clojure.

The GP says "ClojureScript, a.k.a. Clojure ... compiled to Javascript, which (I believe) is accurate.

betenoire
That's not what he said:

aka. Clojure (...) compiled to JavaScript

You stopped reading a few words too soon :)

dopamean
Ha. I misread. Thanks for the correction.
zubairq
There are also others, such as Appshare which I have built
vmorgulis
Emacs?

Edit: Urbit has a Lisp (http://urbit.org/)

defgeneric
Urbit is deeply reactionary.
vmorgulis
Curtis Yarvin, yes.

Brendan Eich is a bit too.

kruhft
The underlying 'functional assembly' VM language of Urbit (Nock) is a lisp that works on arbitrarily large integers. Here's a compiler for it I wrote a while ago, written in Common Lisp:

https://gist.github.com/burtonsamograd/29103c2dfaa67f4fd344

vmorgulis
Interesting.

The music on your home page reminds me a bit Utopia soundtrack (like the sound of the frog).

https://www.youtube.com/watch?v=_ZYVb8Q5i9w

kruhft
Thanks. I wrote it myself. I just put out a new album yesterday:

    http://kruhft.bandcamp.com/album/listener
ZenoArrow
If you count dynamic websites as programs then you're using one right now. ;-)
xrange
A better question: "What impressive programs are written in Lisp?". Or "Why isn't there a Squeak-like Lisp machine environment, where 'compatibility' doesn't have to matter?". If a language is incredibly productive and programmable, why don't we already have a VPRI-like STEPS environment in 20,000 lines?

http://www.vpri.org/pdf/tr2011004_steps11.pdf

delish
> What impressive programs are written in Lisp?

I'd only call this anecdote, but one or more benchmarks assert that cl-ppcre, common lisp's perl-compatible regex implementation, is faster than any other, include perl's.

The larger question I'm intuiting from your post, "Why doesn't language power make a difference in practice?" I don't have an answer to.

AnimalMuppet
> Why doesn't language power make a difference in practice?

Depends on your definition of "make a difference in practice". If you mean "make the language become one of the dominant ones", yeah, that doesn't seem to have happened. Either Lisp is less effective in the large than one would expect from its power, or it's less powerful in practice than people think, or power has almost no relation to language dominance.

But if you mean "make a difference to the user", well, it lets the user more easily write the program that the user wants to write. In practice, that makes a difference - to that user.

None
None
ianmcgowan
This is covered in the article. You might say it's the central point of the article - lisp attracts "lone wolf" programmers who want to build perfect abstractions closely mapped to the real-world problem; as opposed to projects that require many man-years of effort run by MBA's who want fungible "resources" to do their tiny-bite-sized pieces according to spec. The philosophy is different.
vmorgulis
There is OpenGenera (but more than 20k sloc):

https://github.com/ynniv/opengenera

defgeneric
State of the Common Lisp Ecosystem, 2015

http://eudoxia.me/article/common-lisp-sotu-2015

jdblair
AutoCAD uses AutoLISP for scripting and extension. Its been a significant part of AutoCAD since 1986.

http://ronleigh.com/autolisp/ahistory.htm

kruhft
emacs (mostly)
mkramlich
Signpost.com's backend was Lisp. Originally, when the company was named Postabon.

I know because I worked directly with their cofounding CTO, Shaneal Manek, during the early buildout phase. I wrote their launch iPhone app, and it talked to a web service Shaneal made, in Lisp. Our app was featured on live TV during some morning business news segment, major network. It was pretty exciting. Anyway they later shifted the feature set and, I believe, rewrote the backend in Java, after Shaneal went to Greplin. Pure speculation for the rewrite was because it was considered as being easier or "cheaper" to find Java devs. Though I'd argue a sharp/solid engineer can work in any language, and Shaneal was definitely that.

I'd suggest also that perhaps the biggest strategic win was that the combination of our slick iPhone app and the Lisp backend with the CxO's pedigrees all helped them to eventually land investment from Google Ventures. Runway and eyeballs are king.

I also worked at Orbitz as a senior engineer back when they used ITA and ITA had not yet been bought by Google. So I can +1 confirm on what is probably the most famous commercial application of Lisp.

incepted
Not many, but even so, this is never the right question to ask.

That question would be: what programs are written in <LANGUAGE> that couldn't benefit from being rewritten in another language?

And most often, the answer to that question is none.

Because languages matter a lot less than language fanatics want you to think.

As for Lisp, I used to be a total fan until I realize the importance of a sound static type system, and now I will never go back. Lisp will never go anywhere because this is the 21st century and we know now that static type systems are an absolute requirement for modern programming.

lokedhs
Right. That's why no one seriously consider Javascript for any new project, and no one would propose the idea of using it on a server.

I am not saying that you are wrong in liking static typing, but arguing that dynamically typed languages are non-starters in this decade is a statement that is easily disproven by the existence of Javascript.

dmbaggett
For one, the service that performs the vast majority of airfare searches -- formerly ITA Software, now Google Flights.

Having spent time at the MIT AI Lab and having co-founded a company whose principal product was a Lisp/C hybrid, I think the challenge with mainstream adoption of both Lisp-like and functional languages is the syntax. There's an element of "don't use a programming language that's hard to hire for" but I think that's secondary as it never bothered us or posed a real problem.

Naughty Dog's Crash Bandicoot games (which I also worked on) used Lisp for all the character control logic.

kruhft
> I think the challenge with mainstream adoption of both Lisp-like and functional languages is the syntax

Ironic(?) considering there is almost no syntax to Lisp.

defgeneric
It's really such a simple syntax change from f(x) to (f x) yet it makes an enormous difference and opens up a whole new world of possibilities. Sure, there are homoiconic languages in which you can write macros that aren't lisps but the expressive power and ease of use suffers. Take for example macros in Julia (itself heavily lisp-inspired), they're possible but ugly and not nearly as seamless as macros in lisp.
dmbaggett
That's exactly the problem: until you're used to it, it looks nothing like psuedocode. Contrast with Python. I'm not saying it's right, I just think this is the issue.
kruhft
Really, the major difference syntactically is:

   (f x)
vs.

   f(x)
I've never really understood why people seem to have such a hard time with that.
xrange

    c = sqrt(a*a + b*b)
    
    (set! c (sqrt (+ (* a a) (* b b))))
klibertp

    (define c
      (sqrt
       (sum (sqr a)
            (sqr b))))
Which you read out loud like this: "c is a square root of a sum of two values, squared".

Easy to read as you see and easy to understand. This:

    c = sqrt(a*a+b*b)
is way harder to read.
mahyarm
I think the thing about lisp isn't the fact that it's functions start with a paren. It's the fact it uses function composition to write everything that makes it harder to keep track of. Most languages don't define their functions like this:

  c = sqrt(a^2+b^2)
  vs.
  define(c, sqrt(sum(sqr(a),sqr(b))))

  def getMaxValue(numbers):
		answer = numbers.first()
		for (i in xrange(numbers.length)):
			if (numbers[i] > answer):
				answer = numbers[i]
		return answer

  vs.
  (defun get-max-value (list)
	  (let ((answer (first list)))
	    (do ((i 1 (1+ i)))
	        ((>= i (length list)) answer)
	      (when (> (nth i list) answer)
	        (setf answer (nth i list))))))

  if you could only use python functions:
  defun(get-max-value, [list], 
		let(answer,first(list)),
		 do( (i,1,(1+ i)), 
		 	(>=(i, length(list)), ans), 
		 when( >(nth(i,list),answer), 
		 	setf(answer,nth(i,list)))))

  defun(get-max-value, [list], let(answer,first(list)), do( (i,1,(1+ i)), (>=(i, length(list)), ans), when( >(nth(i,list),answer), setf(answer,nth(i,list)))))
klibertp
> if you could only use python functions

I'm not sure if this is what you're talking about but there actually is a Lisp where you can call Python functions. It's called Hy[1] and I encourage you to take a look, it borrows some good solutions from Clojure, but generally is quite an acceptable Lisp :)

[1] http://hylang.org

lispm
The actual Lisp version is:

    (defun get-max-value (list)
      (reduce #'max list))
or even

    (defun get-max-value (list)
       (loop for element in list maximize element))
mahyarm
Not really. We are demonstrating how multiline statements become hard to read in lisp because in practice you can only use function calls to write everything.

Any language where you write an entire function as a huge one liner expression with functionality in nested function calls is hard to read. It's the behavior, not the syntax per say.

What the actual behavior is doesn't matter as much, even if you can reduce both of them to one liners in many languages.

ex:

  def get-max-value(list)
    reduce(:max, list)
  end
klibertp
I already mentioned sweet-expressions in another comment. And also, there's one important thing we're forgetting when discussing syntaxes, which is the fact that we very rarely read the code without syntax highlighting, so the examples you posted actually look like this: http://pygments.org/demo/3781004/

This does change the situation somewhat.

lispm
Not really, since Lisp does not only have function calls, but special forms and macros.

In actual Lisp practice, one uses macros, special forms and function calls.

You seem to have failed to understand the difference.

There are two REAL reasons why Lisp is harder to read than some other languages:

* the syntax looks and works slightly different and most programmers have been trained to other programmning language syntax. With training, this is less a problem.

* Lisp uses a data syntax as the base layer of the programming languages and encodes programs as data. So the syntax of Lisp comes on top of s-expressions. Very few other programming languages are doing that and as a consequence it complicates a few things. The user of Lisp has to understand the effects of code as data. This is something you don't have to understand in Java or Python. It can be learned, but it has to be learned.

At the same time, this code as data principle of Lisp gives a lot of power, flexibility and new capabilities. It makes Lisp different and in some way more powerful than Java or Python. The added power comes from easy syntactic meta programming in Lisp, which neither Java nor Python provide. This has also consequences for interactive programming, since programs can be written and manipulated by programs under user control.

jstimpfle
No.

Why do mathematicians not use s-exps but syntax that is much more similar to C? Reading "sum" "mul" etc. takes longer than if you have visual anchors like * +. And infix is an advantage for simple expressions, because they split arguments, where as with sexps you have to parse from left to right and count parens.

vlasev
As a mathematician, sum(whatever) or product(whatever), reads just fine. There are in fact, a lot of uses of sums and products, so after a while, they are pretty naturally.
jstimpfle
Yes, sum(whatever) is fine. What is "whatever"? If it's the common case of two operands, then I don't think you're making a point against a + b.

And you don't think (sum (mul a (minus b c)) d), or (+ (* a (- b c)) d) for that matter, is more readable than a * (b-c) + d, do you?

> There are in fact, a lot of uses of sums and products, so after a while, they are pretty naturally.

I think you are talking about summing up a collection (like, an array, a matrix, etc.) as opposed to building an expression tree. Of course, sum(myIntList) is just fine. That's a whole different story.

There are also the rare cases where you have to sum, like 6 integers. (sum a b c d e f) might not be worse than a + b + c + d + e + f. But that's by far not the common case in most problem domains. The common case is like a*(b-c) + d.

klibertp
> Why do mathematicians not use

Please tell me why should I care. No, really - I'm a programmer, not a mathematician.

> Reading "sum" "mul" etc. takes longer than if you have visual anchors like * +.

Citation for this?

IMO it's exactly the opposite, but I may be wrong. Some kind of reference would be nice.

> And infix is an advantage for simple expressions, because they split arguments, where as with sexps you have to parse from left to right and count parens.

Ok, so 2 ("sum" vs. "+", 3 vs. 1 char) additional characters are bad, because they take longer to read, but for example 3 additional characters here:

    (+ a b c d)
    vs.
    a + b + c + d
are good, because they take longer to read. That's interesting.
jstimpfle
>> Reading "sum" "mul" etc. takes longer than if you have visual anchors like * +.

> Citation for this? IMO it's exactly the opposite, but I may be wrong. Some kind of reference would be nice.

I know it from myself and don't think I have to to provide evidence that by large most people work like this. Reading and interpreting text is just WAY more complex a process and thus much slower than associating a shape with a meaning.

For example, application designers have known for a long time that it's important to build a symbolic language (icons etc) because that's just way faster (once you have learned what the symbol means, for example with the help of a tooltip).

There's another guy who explained this at length

http://c2.com/cgi/wiki?LispLacksVisualCues

Search for "top" throughout the page.

> (+ a b c d) vs. a + b + c + d

Yes. But as explained in my other comment, that's not optimizing for the common case.

klibertp
> I know it from myself and don't think I have to to provide evidence that by large most people work like this. Reading and interpreting text is just WAY more complex a process and thus much slower than associating a shape with a meaning.

I don't think there is a difference in speed between reading "sum" and "+". You don't read the word "sum" letter by letter: you see it as a whole token and your brain recognizes it instantly.

> For example, application designers have known for a long time that it's important to build a symbolic language (icons etc) because that's just way faster (once you have learned what the symbol means, for example with the help of a tooltip).

You're talking GUI, which is different than writing and reading code. There are, for instance, much less GUI elements visible on the screen than there are identifiers even in a short snippet of code and there is much more context available for deduction in the code than in the GUI. I don't think the two situations - recognizing GUI features and recognizing and understanding identifiers in the code - are comparable.

jstimpfle
Come on. It's totally obvious that the shapes of * and + are much simpler and much more distinct than "sum" and "mul" (which by the way are relatively short and simple examples for words).

Humans have excellent shape recognition -- recognizing (and differentiating) a tree and a person happens subconsciously, effortlessly. Interpreting the words "person" and "tree" takes way more effort.

Similarly, humans have usually very good spatial sense. If there are persons to the left and to the right of a tree, it is effortless to recognize that they are "separated".

> You're talking GUI, which is different than writing and reading code.

No. I'm talking perception.

> There are, for instance, much less GUI elements visible on the screen than there are identifiers

That depends. There are very complex GUIs out there. But let's assume it for a moment. (By the way that typically that means the code is not good (weak cohesion)).

> there is much more context available for deduction in the code than in the GUI.

That is not supportive of your previous argument: The more identifiers, the less context per identifier.

> I don't think the two situations - recognizing GUI features and recognizing and understanding identifiers in the code - are comparable.

It's both about perception. It's very, very important that programmers can focus on their work instead of wasting energy building parse trees in their minds, incurring severe "cache misses". Again, take this simple commonplace example:

  (sum (mul a (minus (b c)) d)
  a*(b-c) + d
If you don't think there's a huge difference I can't help you. I'm sure I need about three seconds to parse the sexp as a tree and figure out what goes with what. Then I have to go back and interpret the operators.

Conversely, the infix/symbol operators example I can map out with minimal, and linear, movement of the eyes. In most cases I don't even need to parse it as a tree -- it's almost a sequence. On a good day, it costs me maybe a second to parse the thing and extract the information I need.

Another advantage of symbols for arithmetic is that they give a sense of security, because one can intuitively infer that they have "static" meaning. While usually words are reserved for things that change, i.e. mutable variables. Being able to infer non-mutability based on shape alone gives a huge advantage.

klibertp
> Come on. It's totally obvious that the shapes of * and + are much simpler and much more distinct than "sum" and "mul"

I disagree that it's obvious. Moreover, I don't believe there is a measurable difference between the speed of recognizing "sum" and "+", once you're equally familiar with both.

> The more identifiers, the less context per identifier.

I don't believe it's that simple, but we're starting to go into semantics (which are part of comprehensibility of code, but not part of it's readability I think).

> If you don't think there's a huge difference I can't help you.

I think you can help yourself: just go and train yourself in reading prefix notation, like I did. Then get back to this example and then tell me again that there is a huge difference.

> I'm sure I need about three seconds to parse the sexp

I don't even know how to measure the time I needed to read the sexp, it was that short. And I even instantly realized that you've put parens around "b c" in the "minus" call, which would cause an error in most lisps.

> Conversely, the infix/symbol operators example I can map out with minimal, and linear, movement of the eyes.

That's why I used newlines and indentation in my example above. To take your example:

    (sum (mul a (minus b c))
         d)
This also reads linearly, just in a different order than you expect. This doesn't make it objectively harder or slower to read, it's just unfamiliar to you.

Also see my other comment on familiarity: https://news.ycombinator.com/item?id=11180682

jstimpfle
I'm not interested in differentiating between readability and comprehensability. If I want to work on some code I need to comprehend it. That starts "in the small" with the mechanical aspects of "readability", if you will. Where to draw lines is not relevant. Every aspect to the process of comprehension is important. The "small" aspects are more important than you might think: Because they affect every line of code. Whereas there are fewer instances of the more global aspects to comprehension.

Like in a binary tree, where half of the elements are in the lowest level.

> you've put parens around "b c" in the "minus" call

You have a point. One pair of Irritating Superfluous Parentheses less.

    > (sum (mul a (minus b c))
    >      d)
Even the consideration to sprinkle such a trivial expression over multiple lines hints at the superiority of a * (b-c) + d. It's just the most straightforward thing to do. No far-fetched argument can change that.

I'd love to see eye-tracking data which show the tradeoffs between various syntaxes.

The regularity and the simplicty of sexps is of course good for computers, because these can barely associate. Because they can't learn new tricks (they have fixed wiring). But humans have streamlined their languages (which also includes syntax; again, I'm not differentiating here) to their environments since forever.

Sexps are also good for abstraction and meta programming. But as we all know abstraction has a cost and there is no point in abstracting an arithmetic expression. And most code, for that matter.

klibertp
> I'm not interested in differentiating between readability and comprehensability.

Fair enough, but then please stop using single letter variable names, add type annotations where applicable, provide docstrings and contracts for functions. Comprehensibility is so much more than syntax that I think mixing the two will make for even more interesting, but even less fact-based discussion.

> I'd love to see eye-tracking data which show the tradeoffs between various syntaxes.

Yeah, that would be very interesting. The thing is, there is no such data available, but you still are convinced that one kind of syntax is better than the other. I'm not - from where I stand the differences and tradeoffs in readability of syntaxes, once you know them equally well, seem too minor to measure.

> Even the consideration to sprinkle such a trivial expression over multiple lines

No. It's just different way of getting to the same effect. I don't see why would one be worse than the other (splitting things using infix operators vs. splitting things using horizontal and vertical whitespace).

Other than that, you completely avoided the familiarity issue. Do you think that we're genetically programmed for reading infix syntax? If not, then it means we need to learn infix syntax just like any other. My question was, would someone not yet exposed to infix propaganda have a harder time learning infix (with precedence rules and resolving ambiguities) or prefix?

You also ignored my question about the difference in readability when you are equally well trained in both syntaxes. You can't compare readability of two syntaxes fairly unless you have about equal amount of skill in both. And the fact that readability is influenced by skill is undeniable. So, in other words, are you sure you're as skilled with sexps - that you wrote comparable amount of code - as with infix? Honestly asking.

jstimpfle
> Comprehensibility is so much more than syntax

Absolutely. It's a tender flower.

> No. It's just different way of getting to the same effect. I don't see why would one be worse than the other (splitting things using infix operators vs. splitting things using horizontal and vertical whitespace).

It's very important since size matters. Efficiency of encoding and cost of decoding (~ perception) matters. But if you don't think it makes a difference -- fine, you are free to read braille instead of plain text even if you have perfect eyesight. You can also add three layers of parens around each expression if you think that's more regular.

> Do you think that we're genetically programmed for reading infix syntax?

No. There's this fact that all combinations of basic grammar are represented in natural languages: SVO, SOV, VSO, VOS, OSV, OVS. And then there are some programming languages which don't differentiate between subjects and objects, but go for (OVO), VO, VOO, VOOO... (or concatenative style OV, OOV, OOOV...). Which is great since the goal of formalism is to be "objective". (Note that Object-oriented programming is actually subject-oriented programming from this standpoint. It's not "objective")

Instead I say that it is more efficient if syntax is optimized for the common cases. Shorter is better, if the decoding won't produce more cache misses. Infix and symbols don't produce cache misses for the vast majority of humans, in the case of arithmetic (read: mostly sequential, barely tree-shaped) expressions.

Sexps are inherently unoptimized for the common cases. They are "optimized for abstraction": for regularity. It is an explicit design goal to not differentiate things which are different "only" on a very concrete level. Instead of content, form is accentuated. This is not suitable for the > 95% of real life software that is just super-concrete and where abstraction has no benefits.

I'm sure I have now given 5 to 10 quite plausible examples which support the standpoint that symbols-and-infix arithmetics is good for humans, based on how their mind works. You haven't provided any counter-arguments but just shrunk off everything. But thanks anyway for that. I think I'm satisfied now with the examples that came out.

> are you sure you're as skilled with sexps [..] as with infix?

No. Never will be.

Are you? Show me a Lisp program with more than casual usage of arithmetics and tell my why you consider it readable. By the way, the first google hit I just got for "lisp arithmetic readability" is http://www.dwheeler.com/readable/

lispm
> Infix and symbols don't produce cache misses for the vast majority of humans

You tried to prove your theory by finding positive evidence. But the evidence is very weak and far fetched.

> which support the standpoint that symbols-and-infix arithmetics is good for humans, based on how their mind works.

Given that we largely don't know how the mind 'works', that's a weak argument.

> Show me a Lisp program with more than casual usage of arithmetics and tell my why you consider it readable.

Given that a lot math code is expressed in low-level Fortran, I'll take Lisp every day.

From a statistics system in Lisp:

    (defgeneric gaussian-probability-density (x params)
      (:documentation "general gaussian density method.")
      (:method ((x number)
                (params gaussian-probability-univariate-parameters))
        (\ (exp (* -1.0 (/ (- x (mean params))
                           (standard-deviation params)))
           (sqrt (* 2.0 pi (variance params))))))
I find that perfectly readable.
AnimalMuppet
If my cup hadn't been empty, you would owe me a new keyboard.

What? You were serious? Um, no. Just no. Your way is not easier to read - at least, not for (I would guess) 95% of programmers, and 99% of humans.

klibertp
How do you know? Any proof/any scientific source, or is it just lore and how you personally feel about this?
AnimalMuppet
I already admitted that it was a guess. But I still think I can defend it.

Starting in elementary school, everyone learns to read math notation. By high school, everyone knows what

  c = sqrt(a*a + b*b)
means. The Lisp version may be easier to read for those who have spent enough time using Lisp. That's not the majority of programmers, though, and it's only a tiny minority of the general population.

Do you think that, to a non-Lisp programmer, the Lisp version is easier to read? Do you think it is easier to read to a non-programmer who has had high school math? Or is it just easier to read for you?

terminalcommand
Learning lisp syntax requires just a very short introduction. In SICP, it is said that they never formally taught lisp at class. The students just pick Lisp up in a matter of weeks.
klibertp
> Starting in elementary school, everyone learns to read math notation. By high school, everyone knows what

We're either talking about objective readability or personal familiarity. What you say is that, after extensive training for many years, it is easier for people to read notation they were trained to read. This is both true and utterly uninteresting.

What is interesting, though, is how much training you need to read prefix and how much training you need to read infix. It's obvious that infix takes more time to learn: operator precedence and things like using "-" in both infix and prefix forms make it objectively more complex than prefix notation. You just forgot how much time you spent learning it.

> Do you think that, to a non-Lisp programmer, the Lisp version is easier to read? Do you think it is easier to read to a non-programmer who has had high school math?

Again, this is not interesting at all. You're talking familiarity, not readability. Of course, it's easier to read something you've been taught to read. To make this more objective, take an elementary school kid - who wasn't exposed to years long infix propaganda - and check both notations' readability with them.

Personally, I learned to read just about any kind of notation used in programming. From my observations, there are only minor differences between the speed of comprehension when using different notations - once you've trained enough. The difference is how much training you need. I can tell you that reading J - an infix language, it's an APL descendant - took me much, much longer to master than reading Lisp.

Houshalter
Imagine you removed a parenthesis at the end. Would you even notice? It's not compact at all, and there are fewer visual cues.

Infix notation works better when it is applicable. Limiting the number of parentheses is also best when possible.

You can add parentheses and make it less compact if you want. You could theoretically write c=sqrt(axa+bxb) as:

    c =
        sqrt(
            ((a *
                a) + 
                (b *
                    b)))
But that's just ridiculous.
klibertp
> It's not compact at all,

You are now arguing against parens. You can have mostly prefix syntax without parens, with blocks delimited with indentation only. Scheme's sweet-expressions[1] are one such example. Anyway, please take my example, remove the parens and check if your argument still applies.

If it does, then it's down to the function names and your (common) misconception that "+" or "^" is somehow more readable, easier to understand or something than "sum" or "sqr". Where I simply disagree. BTW: why do you insist on using infix syntax for a couple of operators, while you use every other possible operator in a prefix notation and are happy with it? What is the difference between "sqrt" and "-" which makes it ok to use sqrt in prefix form?

> Limiting the number of parentheses is also best when possible.

No. It's only best if it aids readability. This is something that Lisp does rather well actually - there are many examples of equivalent Java and Clojure expressions where Clojure version has half as many parens. Getting rid of parens for the sake of getting rid of parens is counterproductive.

[1] http://srfi.schemers.org/srfi-110/srfi-110.html

Houshalter
Because your version takes up 6 lines! A simple one line expression!

And yes you can remove the parentheses, but not only does no one do that, it still takes up 6 lines. And then you have significant whitespace too.

>why do you insist on using infix syntax for a couple of operators, while you use every other possible operator in a prefix notation and are happy with it? What is the difference between "sqrt" and "-" which makes it ok to use sqrt in prefix form?

Because that's universal and standard for math notation. But also sqrt only takes one argument. If it took two arguments, then it would be perfectly reasonable to add an infix operator for it too. Many languages do add infix operators for everything from combining strings to ANDing booleans, etc, because they are so much more readable.

knughit
Yes, whichever ever one you have seen a million times before looks more readable. So?
AnimalMuppet
Something nobody has mentioned yet is that, in the C-style version, the precedence rules are eliminating some parentheses. You can't do that in Lisp (except maybe with a macro). But then, in Lisp, you don't have to remember precedence rules.

In this example, the advantage is on the C side, because pretty much everybody who knows any math knows that multiplication has precedence, and they can just read that syntax. If you have to go look at the precedence chart in K&R or Stroustrup before you know how to parse the expression correctly, well, then the Lisp approach is probably more efficient...

21
Can you understand why most have a hard time with

  (* (+ a b) (+ c d))
instead of

  (a + b) * (c + d)
Hint: if the first notation is so superior, why don't math papers use it.
Jtsummers
I do understand, but I'll also point out that that first expression will often (with longer variables or expressions in particular) be broken out like:

  (* (+ a b)
     (+ c d))
Which is readable, though not necessarily compact.

Also, * and + in the former, aren't strictly the same as in the latter. * and + take an arbitrary number of parameters in CL. From [0], `(* )` => `1`. I can't test, but I believe `(* 2)` => `2` (the spec doesn't describe the case of a single parameter, unless I'm missing it). `+` is the same, but `(+)` => `0` instead, it's identity value.

Order of operations is made more explicit, and, I've found, it's more useful to think of `+` and `*` as `sum` and `product` rather than `plus` and `times`.

[0] http://www.lispworks.com/documentation/HyperSpec/Body/f_st.h...

[1] http://www.lispworks.com/documentation/HyperSpec/Body/f_pl.h...

rol
If you have Quicklisp[1] installed you can install the "infix" package and get infix notation in Common Lisp[2]:

    $ sbcl
    This is SBCL 1.2.4.debian, an implementation of ANSI Common Lisp.
    More information about SBCL is available at <http://www.sbcl.org/>.
    
    > (ql:quickload 'infix)
    ; Loading package
    (INFIX)
    > #i(1 + 1)            ; addition
    
    2
    > #i(2^^128)           ; exponentiation
    
    340282366920938463463374607431768211456
    > (defun factorial (x)
         #i(if x == 0 then
              1
            else
              x * factorial(x-1)))       ; infix function call
    
    FACTORIAL
    > (factorial 5)
    
    120
    > #i(factorial(5) / factorial(6))
    
    1/6
    > '#i((a + b) * (c + d))      ; Put a ' before the #i() to see what code is generated
    
    (* (+ A B)
       (+ C D))
--

[1] - https://www.quicklisp.org/beta/ [2] - Don't know if there is a similar package for Scheme.

adwf
I wouldn't recommend using infix libraries if you really want to get into Common Lisp though. They're a bit of a crutch for people coming from other languages, but that's it.

Pretty much the whole language is based on Polish notation. The sooner you realise that + - * / are just function names like any other, the better you'll do.

For example:

  (+ 1 2 3)

  in plain symbols is just:

  (function parameter parameter parameter)
  
  But if I were to write my own addition function:

  (addition 1 2 3)

  it would also be:

  (function parameter parameter parameter)

  and so is:

  (http-request "http://www.google.com")

  (function parameter)
If you use infix notation, you're writing half your code in a competely different semantic to the other half. I can't imagine it helping people really get a proper grasp of how Common Lisp works.
jrapdx3
> Don't know if there is a similar package for Scheme.

I have to agree with others in the thread that infix in Lisp/Scheme is not the convention, and IMO an awkward fit. Don't recall encountering infix in any published/shared code I've seen, it may exist, but to learn Scheme becoming comfortable with s-expr notation is definitely necessary.

However, there is SRFI 105[0] which describes "curly infix expressions". It's implemented in Guile 2.x, possibly available in a few others but evidently not had a lot of uptake among Schemes.

[0] http://srfi.schemers.org/srfi-105/srfi-105.html

Edit: added URL

21
Math does also have `sum` and `product` in the form of Sigma and Pi. Of course, not exactly the same thing (since they operate over a set, not discrete elements).

I would venture to say that the reason infix notation is naturally preferred is related to our psychology, the same way most human languages are SVO (Subject Verb Object) or SOV. VSO languages (Lisp like) are less prevalent.

In general my opinion is that when a majority vastly prefers one alternative, there is usually a strong reason for it (even if it may be irrational) and it's foolish to go against the grain.

Jtsummers
Infix is mostly used, in programming, within mathematical and logical expressions. But the majority of my code spends its time in some kind of chain of function calls, which has the verb first. Maybe if I did more with OO-languages I'd see it differently?
AnimalMuppet
Interesting. OO syntax often is object.function(arguments), which is subject-verb-object order. I never thought of it that way before. You can throw some adverbs in among the arguments, too.
knughit
That's correspondent with how Java and especially Obj-C and super especially AppleScript programmers try to write code that reads like COBOL, er, English.
knughit
Lisp is VOO, not SVO.

Java is SVO.

C is VOO too.

stan_rogers
I seem to recall that SOV (reverse Polish notation) is marginally more prevalent than SVO among the world's languages... though it is true that most creoles are SVO, which does at least seem to indicate that it's a default of sorts.
mbrock
Nobody claimed Lisp syntax was optimal for math papers. Neither is C syntax. The Lisp syntax does have advantages for program source code. Sure, it has disadvantages too. Everything is a compromise.

The Lisp syntax is so incredibly controversial, and that fact itself is incredibly strange to me. I see it as a pragmatic engineering decision: let's represent source code as syntax trees, and then sophisticated editing modes become straightforward, macros become straightforward, and the syntax becomes very uniform.

This big thread indicates another reason Lisp isn't popular: because people keep arguing back and forth about the textual syntax, rather than discussing actual experiences with using it.

lispm
There are actual features which make Lisp a bit more difficult to understand and a few are related to syntax: especially the code as data feature. Some elements of the language have different purposes: both as code and as data. Symbols can be data and they can be identifiers. Lists can be data and they can group elements of the programming language. Others have only one purpose. For example an array is always data.

Symbols and lists behave differently depending on the context:

Examples for Lisp snippets:

   (foo bar baz)  ; it could be a macro, function or special operator form

   (quote (foo bar baz))   ; here it is data

   (defun do-something (foo bar baz) (a b c))  ; here it is an arglist

   (defun do-something (a b c) (foo bar baz))  ; one element later it is a form
These context need to be learned and actual visual clues are a) the symbol in front and b) the structure of the expression.

This is puzzling for a lot of people. A few never really take that hurdle.

kruhft
Yes, they learn the second syntax from birth. There have been arguments to teach the lisp syntax in mathematics due to it being easier to understand with multiple arguments:

    (+ x y z a) instead of (x + y + z + a)
Also, there are no order of operations problems with the lisp syntax like there are with traditional mathematical notation (unless you use parens, which makes it look even more lispy).
Shorel
I found math major students to grasp Lisp much faster than C.

Therefore I would say the answer is simply familiarity and concern for the audience.

greydius
So why don't we write all binary operations that way? eg. x f y instead of f(x,y). I've always felt more comfortable with prefix notation, especially because it easily generalizes to more than two arguments. I think infix notation is an accident of mathematical history.
knughit
Welcome to Haskell, where anything can be infix :-)
greydius
That can be nice in a lot of situations. e.g.

    (+) 4 2
 vs. 
    (+) <$> Just 4 <*> Just 2
I usually prefer the applicative style above to

    liftA2 (+) (Just 4) (Just 2)
because it preserves the "form" of the original expression and generalizes to more arguments. ie. it doesn't require liftAn for whatever n number of arguments my function takes.
ACow_Adonis
With all due respect, math papers don't, I think, pretend that their syntax makes any claims to optimality of any kind.

Indeed, most math syntax (in my experience) has a very explicit reason why it's used: historical circumstance, convention and common tradition.

weavie
Arithmetic is one place where infix notation is generally easier to read. If I were writing a program that basically just did a load of mathematics I may even consider using a different language.. However looking over the software I generally develop, I probably need to use arithmetic in about .01% of the code.
wolfgke
> Hint: if the first notation is so superior, why don't math papers use it.

As a mathematician I'd love to use it in my papers, but no reviewer would accept such a paper.

stray
I have no idea why the people who write math papers make the choices they make.

But I'd like to point out that in your second example the parentheses are needed because infix notation is inherently more complicated.

In the first example however, the notation is far simpler: a simple list of function plus zero or more arguments.

lispm
Math papers use a very complex 2d notation last I've looked.
dragonwriter
> Hint: if the first notation is so superior, why don't math papers use it.

Math papers usually use neither the first nor the second.

they use:

  (a + b)(c + d)
in the example you propose, and, reversing the operators so that the first style would have:

  (+ (* a b) (* b c))
and the second:

  (a * b) + (c * d)
math papers would usually have:

  ab + cd
So, I'm not sure "math papers do it differently" is the argument you want to use to advance your second syntax over the first.

Of course, since in lisp + and * are variadic rather than binary operators, they are a lot more like the pi and sigma operators applied to sets in mathematics than binary operators. Which are prefix, not infix. So, there's that.

whitegrape
Additionally there's more than one macro system out there to allow for infix math in Lisp... And for non-mathy things, in Clojure at least you're often using the threading macro -> or some variation of do/doto.
stray
It's probably because in algol derived languages -- when you encounter parentheses, something weird is happening -- something you've got to put extra thought into.

Maybe the ordering of something is being forced. Maybe something else is going on, but whatever it is requires more thought than things that are parentheses free.

So you look at Lisp and your brain locks up the brakes, with "WTF is going on here??? I'm out".

lawpoop
I guess that's ironic, but with people coming up used to all the ornate syntax, one of the common balks is "all those parenthesis, it all looks the same" and "there is no syntax, how do you read this."

It's like going from Arabic numerals to counting by groups of five; initially, it feels like you're losing expressive power. And, of course, at a glance, you can't read "|||||||||||||||||||||||||||||" as quickly as you can "28".

kruhft
Here's a good wiki on the topic:

http://c2.com/cgi/wiki?LispLacksVisualCues

After a brief period of usage 'the parens disappear' and you just read the code by indentation.

marssaxman
So, uhh... why not use a notation where nesting is expressed via indentation, then? I don't understand how the syntax can be considered superior if the way people actually cope with it is to hide another syntax inside it.

I was dumping ASTs as part of a little language project recently and my first impulse was to render them as S-expressions. Alas, it just wasn't readable; I couldn't make any sense of it. Indented YAML style lists, though? The structure pops right out and the information I wanted was immediately obvious. There were no constraints here, I was free to render text in any way that suited me; the Lisp style syntax just wasn't helpful.

scentoni
A Lisp with significant indenting (like Python) would bear a strong resemblance to Haskell.
tilt_error
I prefer having a parser produce an abstract syntax tree. From an expressiveness viewpoint, you get a good deal of raw power from being able to manipulate this directly instead of having to instruct a lexer/parser to do it for you. I don't necessarily think this is a good thing though.
reitanqild
I know almost nothing about lisp, but what comes to mind is car, cdr which aren't exactly the most descriptive keywords of programming languages I have seen.

(I think they are replaced in modern versions but my point still stands as I remember the old ones, not the new)

defgeneric
Yes but can you do caaaaaar or caaddaar or cdaar, etc. with head and tail?

In 5 characters with cadar you can express walking along a tree structure to get exactly the node you want.

AnimalMuppet
Sure. caaaaaar -> heaaaaaad. cadar -> heaiad. It's one more character, but if you really want to express yourself that way, there's no reason you couldn't...
davexunit
car, cdr, cadr, and friends are discouraged in some Lisp communities where pattern matchers are available.
kruhft
Yes, sometimes 'car' and 'cdr' are replaced with 'first' and 'rest' and are some of the first things you cover when learning the language, so I don't think the names would really be hindering adoption for those that try to learn the language. The benefits of car and cdr are that they can be composed: (caadr l) instead of (car (car (cdr l))) for example.
AnimalMuppet
Well, if you use "first" and "rest", then (caadr l) could become (firrest l) or something like that...
bhrgunatha
I like Racket's second, third, fourth,... etc. [1]

I don't think there's an equivalent to cddadr for example, but at that level of deconstruction you're better off abstracting the data structure (maybe a struct [2]) or using some other mechanism like match [3]

[1] http://docs.racket-lang.org/reference/pairs.html?q=second#%2...

[2] http://docs.racket-lang.org/reference/define-struct.html?q=s...

[3] http://docs.racket-lang.org/reference/match.html?q=match#%28...

adrianm
If you mean Lisp as a straightforward expression of "Lambda calculus" then I would agree.

However, Lisp as in Common Lisp most certainly has a good amount of syntax. And let's not forget macros which amount to user defined syntactic extensions.

Here are some examples of syntax built into the standard:

Lambda lists have varying syntax depending on context. http://www.lispworks.com/documentation/lw70/CLHS/Body/03_d.h...

Declarations have both standardized and implementation defined syntax for introducing information into the compile-time environment: http://www.lispworks.com/documentation/lw70/CLHS/Body/03_c.h...

Type specifiers introduce new syntax for both standardized and user-defined types: http://www.lispworks.com/documentation/lw70/CLHS/Body/04_bc....

Logical pathnames: http://www.lispworks.com/documentation/lw70/CLHS/Body/19_ca....

Feature expressions: http://www.lispworks.com/documentation/lw70/CLHS/Body/24_aba...

And of course, programmable reader macros which is how syntax for every single language primitive in the language is introduced: http://www.lispworks.com/documentation/lw70/CLHS/Body/02_d.h...

Here's an example of a complex standardized macro with its own domain specific syntax (loop): http://www.lispworks.com/documentation/lw70/CLHS/Body/06_a.h...

Let's not forget that most of what one might think of as built-in features in Common Lisp are actually standardized extensions to the language built with macros.

All of the power, expressivity, and extensibility of Common Lisp is what makes it my favorite programming language. It's what makes everything like above possible and gives power back to the user. But ignoring the syntactic complexity will not win us any followers!

TLDR: Common Lisp isn't simple, but it exposes one of the most powerful and empowering programming environments we have.

kruhft
> If you mean Lisp as a straightforward expression of "Lambda calculus, then I would agree.

That's what I was talking about. The language, being programmable, especially with read macros, can be used to create a very syntactically full language, but at it's basic core level, there is really just '(', ')', '.' and symbols.

Avshalom
There aren't a lot of symbols to Lisp but there's plenty of syntax

Using Racket:

  (if bool then else) instead of (if bool then) or (if (bool then) (bool else))
  (if (> x y)
    (x)
    (y)) ;fails for numbers because (x) is considered a function call (even though 3 is an invalid identifier and thus can be assumed to be always be a number).
 (define (fun x y) (...)) instead of (define fun (x y) (...)) or (define ((fun (x y)) (...)))
That's syntax.

Just because I'm not using {}'s here and infix there doesn't make it any less syntax. That's just the two most basic forms too; bring in loop? forget about it. This also ignores things like '(@,) or (x . y) but I'm not a lisper so I don't know how often that actually comes up

stray
I think you're conflating syntax with semantics.
Avshalom
I am not. Syntax is the structure, semantics the meaning (I mean more or less).

(def (fun x y) (...)) is syntactically different than (def fun (x y) (...)) even if they are semantically equivalent.

greydius
The syntax is the same. Both are s-expressions. The difference is how a particular implementation interprets them. In this example, it would depend on the semantics of def.
lispm
That's only the syntax of s-expressions - a data format.

The Lisp syntax is defined on top of s-expressions.

For example Common Lisp has a CASE operator. That's the EBNF syntax:

    case keyform {normal-clause}* [otherwise-clause] => result*
    normal-clause::= (keys form*) 
    otherwise-clause::= ({otherwise | t} form*) 
An example:

    (case id
      (10 (foo))
      (20 (foo) (bar))
      (otherwise (baz)))
The expressions are written using s-expressions as data. But still there is structure in those s-expressions, described by the EBNF syntax of CASE.

Every special operator and every macro provides syntax. Since users can write macros themselves, everybody can extend the syntax. On top of s-expressions.

greydius
That is interesting. I've always considered lisp in terms of denotational semantics. In fact, I wrote a toy lisp in which the complete grammar was basically

    list -> ({symbol | number | string | list}*)
and then it was up to the interpreter to decide the meaning of special forms. (I say "basically" because there was also desugaring of '(...) to (quote ...)).
Avshalom
(3) vs 3 is a both really. In say smalltalk you can call 3 and it would return 3 because semantically it's an object where as in lisp it's not callable (even if in CL it may be represented as a CLOS object I don't know)

syntactical ( ) isn't actually a procedure call we can see this in (define (id x y) (..)) or (let ((x 3)) ...) in the theoretically pure Lisp semantically it's just a leaf in the tree but as part of an if-block in a real language it gets treated as procedure call even if it makes no sense.

mroll
Lisp as the idea has no syntax. Racket is a dialect of that idea, and the authors have decided to add syntax.
Avshalom
Lisp "as the idea" is not a programming language. Racket is a language, Common Lisp* is a language. No one writes code in the IDEA of lisp, indeed no one can because no computer yet can pull instructions out of what ever aether contains platonic ideals.

* using SBCL: (defun foo (x y) (...)) instead of Racket (define (foo x y) (...)) is again an example of syntax.

brianclements
Technically, this might be syntax, but as someone who is learning Racket (and programming) in the beginning stages, it's so much less syntax to remember then even python (underscore, double underscore, with, decorators, list comprehensions etc all have their own syntax nuances), the only syntax I see in Racket is the s-expression, the quote, and the dots. Everything else is just the flow of programming logic. It really does free my mind to work on the problem domain itself! Been enjoying SICP so much.
Avshalom
Racket doesn't get quite as bad (well it does but it tries to keep things looking like S-exps) but consider CL's Loop macro http://www.unixuser.org/~euske/doc/cl/loop.html loop is (from what I understand) idiomatic too. Yes it's a macro (so is (defun ...) though) but it's syntax a CLer needs to know in order to deal with CL in the wild. Format is famously even worse.
baldfat
Even Racket says loops are unRacket like and so does R. I avoid loops at all cost and use list whenever possible.
aidenn0
Loop is idiomatic, but whether or not it is syntax is arguable, as it is implemented entirely as a macro.
adwf
A lot of people abandon loop for precisely that reason (it's un-lispy) and use Iterate.

https://common-lisp.net/project/iterate/

Even the ITA/Google style guide says to avoid loop if possible:

https://google.github.io/styleguide/lispguide.xml#Iteration

lispm
But the ITERATE macro is syntax, too.

Almost every macro in Lisp provides syntax.

aidenn0
An equivalent to iterate/loop where each compound form need be replaced by an anonymous function and each binding is replaced by a dictionary entry could be implemented completely as a function. Is this also new syntax?

If not, how is the macro different other than implicitly changing the evaluation?

for a more simple example, why is the idiom CALL-WITH-FOO (implemented as a function) not syntax while WITH-FOO (implemented as a macro) is? What precisely is syntax is somewhat nebulous (if I use a regex library in C, have I added syntax to the language? Regexes certainly are syntax, despite being wrapped in a C string).

adwf
Yes, but I thought his point was more that whilst Lisp has a very easy, simple and regular syntax, ie. (func arg1 arg2 (func arg3)) and so on, it's less simple and regular when you get to the loop macro (loop arg keyword arg keyword...). Hence why I mentioned the Iterate library as something a lot of people use to get back to the regular syntactical appearance.

It's one of the strengths of Lisp imo; that you don't need to think much about how the parser is going to interpret your code (ie. missing semi-colons, whitespace, use curly brace here, square bracket there, etc.), just stick to (func arg1 arg2) and all you're left with is your own logic errors.

breuleux
It's debatable whether "simple and regular syntax" is a strength or a weakness. Lisp/Scheme might be too regular for their own good. Consider the following statements in Scheme, for instance:

    (lambda x (+ x x))
    (cond (> x 2) (+ x x))
    (if (> x 2)
        (do-this when-true)
        (also-do-this when-true))
They are syntactically correct (technically), but they are probably not what you meant. So you still have to pause and ask yourself how cond works... except the parser will not help you.

That is to say, a problem with s-expressions is that they are so regular that everything looks the same, and when everything looks the same, it can become an obstacle to learning. Mainstream languages are not very regular, but they are more mnemonic. I think Lisp works best for a very particular kind of mind, but that for most programmers its strengths are basically weaknesses.

aidenn0
SBCL will warn or error at compile time on the first two, and there are similar issues to the third one in many languages; it's a semantics issue more than a syntactic issue.
mkramlich
best constructive takedown of Lisp I've read, thank you. I've had a love/hate relationship with Lisp for years. Yes, its strength is also its weakness. Its so much harder on the programmer at read/review time. Even though at write time its power is unmatched, almost intoxicating.
lispm

    (if (> x 2)
        (do-this when-true)
      (also-do-this when-true))
In some other language:

    x > 2 ? doThis(whenTrue) : alsoDoThisWhenTrue();
Same problem. Maybe even slightly worse. For example it could be:

    x > 2 ? doThis(whenTrue) ; alsoDoThisWhenTrue();
To spot the difference between a colon and the semicolon: tough.
lispm

    (func arg1 arg2 (func arg3))
That's the syntax of function calls.

But Lisp has a few special forms and zillions of macros. Most of them are syntax.

Lisp has IF. What is the syntax of IF?

    IF form then-form else-form+
Lisp has COND. What is the syntax of COND?

    cond {clause}*
    clause::= (test-form form*) 
 
List has DEFUN. What is the syntax of DEFUN?

    defun function-name lambda-list [[declaration* | documentation]] form*
Now what is the syntax for LAMBDA-LIST?

    lambda-list::= (var* 
                    [&optional {var | (var [init-form [supplied-p-parameter]])}*] 
                    [&rest var] 
                    [&key {var | ({var | (keyword-name var)} [init-form [supplied-p-parameter]])}* [&allow-other-keys]] 
                    [&aux {var | (var [init-form])}*]) 
and so on...

> It's one of the strengths of Lisp imo; that you don't need to think much about how the parser is going to interpret your code (ie. missing semi-colons, whitespace, use curly brace here, square bracket there, etc.), just stick to (func arg1 arg2) and all you're left with is your own logic errors.

What you describe is just the data syntax for s-expressions. Not the syntax of the programming language Lisp.

adwf
> What you describe is just the data syntax for s-expressions. Not the syntax of the programming language Lisp.

Exactly. The data syntax if what most people worry about. The names of the verbs (funcs/methods/etc.) may change from language to language, but the data syntax is what trips people up. I think Lisp has one of the simplest and clearest. There are very few cases of "oh you can't write that there, only nouns are allowed in that position".

I agree with your point, but I think we're arguing slightly different points here ;)

aidenn0
with regards to Naugty Dog, The Jak & Daxter games were written entirely in GOAL, an in-house scheme implementation that compiled down to assembly.
chadzawistowski
GOAL and GOOL were both used by that studio: "Game Oriented Action Lisp" and "Game Oriented Object Lisp".

They switched to C++ because it was too hard to find good lisp devs.

lispm
They switched to C++ because they were bought by Sony and integrated into their landscape. They thought that sharing C++ code would be useful. As it turned out, they put Scheme back into their production pipeline.
chadzawistowski
Oh, good to know!
samth
That's not quite right. These days Naughty Dog uses a DSL called DC built in Racket to write all the "data" in the game (everything from cut scenes to character attributes). Running DC produces data files shipped on the DVD of the game, and used by the big C++ engine that's running on the PlayStation.

Dan Leibgold gave a talk about their system at RacketCon a few years ago: https://www.youtube.com/watch?v=oSmqbnhHp1c

viperscape
might like this: http://practical-scheme.net/docs/gdc2002.html it's about using scheme in production house for final fantasy movie
drmeister
Christian Schafmeister here - thank you for those kind words. I'm using Common Lisp as the basis for a programming environment for developing programmable matter (big, smart molecules and materials). I'll be announcing it soon - stay tuned. Designing molecules is one of the hardest problems in the world and it needs the most expressive, powerful language - Common Lisp. Oh - and C++, there's plenty of C++ in there as well :-).
noselfrighteous
Beautiful ideas! Do you have a way to control the final stereo-isomer that comes out of the synthesis? I'm thinking of the "256 stereo-isomer" molecule that you mentioned. Or is it a case of brute force and select afterwards?
drmeister
We have absolute control over the final stereo-isomer that comes out of the synthesis. The large molecules are assembled from building blocks that each contain two stereo centers. We synthesize all four stereo-isomers of the building blocks in separate bottles and then put them together in different sequences to create the large molecules. Where the programming (Clasp Common Lisp in the molecular design language that I'll announce soon) comes in is we can build computer models of all stere-isomers and, in software, figure out which ones can do the job that we want. Then we just synthesize that and test it in the lab.
noselfrighteous
Awesome! Thanks for that.
girvo
This is why I love HN! Amazing video, and that project sounds fascinating. Where can I go to keep an eye on it?
JabavuAdams
Very, very interesting stuff, thanks.

Every couple of years I spend a couple of months with Lisp and then decide that I actually want to use Lisp to generate code in other languages. Recently I've been on a modern C++ kick, and have been really amazed at how Clang and LLVM are being used to do code indexing.

So, C++ + CL + LLVM + scientific computing ... wow!

agumonkey
I too enjoyed the spiroligomer talk, not all of it, but the deep down approach felt good. If I had more biochem knowledge I'd assemble a team.
cperkins
Amazing work.
surprisetalk
Your "molecular metaprogramming" presentation is, without exaggeration, one of the most beautiful lectures I've ever encountered.

You've instantly inspired me to change career paths. This weekend I'm going to set up a home chemistry lab so that I may one day contribute to the amazing body of work you've started.

Does anybody on HN have some recommendations for learning intermediate chemistry? or setting up home labs? Just for context, I have math/CS degrees and have already taken introduction courses to physics, chemistry, and biology.

drmeister
Chris Schafmeister here - wow. Well, just make sure you always wear your safety goggles.
surprisetalk
Will do, chief! Thanks again for the inspiration.
chm
Synthetic chemistry is not really something you want to learn on your own in your basement. You can do it, but you're much much much better off just following real laboratory courses in college. They'll teach you proper lab safety in a safe environment, and the range of reactions you'll be able to perform will be much wider than what you could do in your basement. Most undergrads will perform a Grignard reaction, but I would not advise you do that in your basement.

If you're interested in theory, then it's a whole other thing.

(I'm a chemist.)

surprisetalk
I obviously have no idea what can/can't be done at home yet :)

But UCLA is right down the street; I'll see what they have to offer.

Thanks for the tip!

chm
Anything could be done at home, but at what cost (safety + economic)? If you get some lab experience by following courses, you might even land an internship in a synthesis lab if you're lucky :)
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