Software and real carpentry

planeI like Software Carpentry, a non-profit organization teaching basic computing skills to researchers. But if I had one little criticism it would be that there wasn’t enough carpentry, with tenon saws, and mortising chisels, and rabbet planes. I like actual carpentry, I can’t tell you why, its a bit like asking why somebody likes cheese, the answer is ‘yes’.

At work I mess around with software tools to do genomics, bioinformatics, and population genetics. At home I mess around with tools. At work this year I was talking to two postdocs about an approach to a genomics problem and made some quip about the importance of sharpening your axe before starting to fell a tree. Nobody laughed and I decided to pretend that it was insightful wisdom. Then I started to wonder if I could pass off a whole range of rough woodworking folklore as insightful bioinformatics wisdom? So here goes, I’ll prepare my whetstone, sharpen my irons, and let the sawdust fly…

“If you only have 3 hours to chop down a tree, spend the first 2 sharpening your axe”

This one comes in many forms, often erroneously attributed to Abraham Lincoln, sometimes there is a lumberjack about to die, don’t worry, he’s fine. For bioinformatics though I think the rationale is that preparation and optimization are the essence of getting things done quickly, not hastily launching into the task with a dull axe.

“Measure twice cut once”

This is an old English proverb. I like to think of it as a rationale for unit testing code.

Carpenters and chips

“The best carpenters make the fewest chips” -English proverb, c.1500s

“The carpenter is not the best who makes more chips than all the rest” – Arthur Guiterman (1871-1943)

The best bioinformaticians write the least code

“When you need it to hold you’d better glue and screw it”

Yep, always glue AND screw. I’m not going to give you the bioinformatics translation for everything, where’s the fun in that?


“Without craftsmanship, inspiration is a mere reed shaken in the wind” Johannes Brahms

“Where you find quality, you will find a craftsman, not a quality-control expert” -Robert Brault

“He who works with his hands is a laborer. He who works with his hands and his head is a craftsman. He who works with his hands and his head and his heart is an artist” – St. Francis of Assissi

“When you’re a carpenter making a beautiful chest of drawers, you’re not going to use a piece of plywood on the back, even though it faces the wall and nobody will ever see it. You’ll know it’s there, so you’re going to use a beautiful piece of wood on the back. For you to sleep well at night, the aesthetic, the quality, has to be carried all the way through.” ― Steve Jobs

I really have trouble justifying the Steve Jobs approach sometimes, but its important to consider this, a lot


“One only needs two tools in life: WD-40 to make things go, and duct tape to make them stop.” unknown; attributed to G. Weilacher

What would the bioinformatics equivalents of WD40 and duct tape be?

“A simple [work]bench is like Tuscan pasta soup. You think it will be better if you add more stuff. But getting the basics right is way more important, and the extras won’t make up for a poorly prepared stock.” Adam Cherubini

For me the Tuscan pasta soup stock is unix

“Only those who have the patience to do simple things perfectly ever acquire the skill to do difficult things easily.” Friedrich von Schiller (1759-1805)

This was I think the 1st version of the Larry Wall perl rationale ‘to make the easy things easy, and the hard things possible’

“Any intelligent fool can make things bigger, more complex, and more violent. It takes a touch of genius – and a lot of courage – to move in the opposite direction.” E.F. Schumacher

A violent analysis, I like that idea

Bad advice, usually

The only really good place to buy lumber is at a store where the lumber has already been cut and attached together in the form of furniture, finished, and put inside boxes. -Dave Barry

No no no, always do it yourself, I’m not even joking, don’t use somebody’s GUI

Woodworking minus patience equals firewood

Law of the Workshop: Any tool, when dropped, will roll to the least accessible corner. -Author Unknown

Law of bioinformatics: Any code, when dropped, will roll your data to the least accessible corner

“Blunt tools are sometimes found of use where sharper instruments would fail” -Charles Dickens, Barnaby Rudge

I think Dickens was talking about perl again

“He says no varnish can hide the grain of the wood; and the more varnish you put on the more the grain will express itself” -Charles Dickens, Great Expectations

Pie charts, clearly

Good workmen never quarrel with their tools. Byron

I’ve quarreled with a LOT of tools. I only included him here because he was Ada Lovelace’s dad

“When the only tool you have is a hammer, you tend to see every problem as a nail” Abraham Maslow

BLAST, always hit it with BLAST, and don’t worry if it bends, you can just whack it down into the wood with a BioPython script, nobody will notice

“The things I make may be for others, but how I make them is for me” – Tony Konovaloff

I like this one

“Have thy tools ready. God will find thee work” -Charles Kingsley

I hope god understands full economic costing

“Remember, a chip on the shoulder is a sure sign of wood higher up” -Brigham Young

“I have little patience with scientists who take a board of wood, look for its thinnest part, and drill a great number of holes where drilling is easy.” ― Albert Einstein

Reviewer 3 accuses me of drilling in thin wood, but they don’t understand the pressure I’m under to publish


For safety is not a gadget but a state of mind. -Eleanor Everet

Check stuff, always check, and back it up, twice, also version control


Some of these, quite a few, I just knew and was able to sagely trot out. The rest I harvested from the web including here and here and here and here

One Comment Add yours

  1. Dave Lunt says:

    Yes that is my actual plane. I apologise to all woodworkers, you’re right its dirty and set up badly (look at the shavings). But in my defence this was when I’d just found it at a car boot sale, and was in the process of restoring it. Its much cleaner and happier now.


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