The Phosphoproteomic pocket watch – evolution and medicine

Derek Lowe

… as in all of molecular biology, closer inspection not only reveals a wealth of impressive detail, but huge numbers of things which do not so much appear to have been carefully crafted by a divine hand, as much as assembled by a blind lunatic with infinite time, infinite willingness to tinker (and a correspondingly infinite willingness to accept whatever works as soon as it does), and infinite supplies of duct tape, super glue, and baling wire. What’s more, the whole mechanism keeps falling apart over time in subtle (and not so subtle) ways, which just leads to casual repurposing of the altered pieces.

I learned how this happens by analyzing 19th century freight train breaking systems when I was 17.

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When will AI explore equivalent representations in math-space?

Wiles proof of Fermat’s Last Theorem borrowed from from algebraic geometry and number theory (Wikipedia). Presumably these are equivalent representations for some problems. I imagine this as the grown-up equivalent of switching from Cartesian to polar coordinates to solve a freshman physics problem.

I wonder when AI will start exploring math-space, searching for more of these unexpected alignments and concordances.

It feels like that might happen soon, but I have no idea how it would work.

Update: from the Wikipedia article on Wiles proof, a much better example of what I’m trying to describe:

Japanese mathematician Goro Shimura, drawing on ideas posed by Yutaka Taniyama, conjectured that a connection might exist between two different mathematical objects then being studied, known as elliptic curves and modular forms.

Taniyama and Shimura posed the question whether, unknown to mathematicians, the two kinds of object were actually identical mathematical objects, just seen in different ways.

What I’m describing is an automated search for “identical mathematical objects … seen in different ways”.

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I like post titles

DeLong’s feed is largely subject free now:This annoys. If a post is more than a few sentences it needs a title. I scan hundreds of posts a day, only read tens of them.

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June 5 2018: Google has no hits comparing Apple Swift Playgrounds to Google Grasshopper

Apple’s iPad-only Swift Playgrounds (learn Swift) has been out for months.

Google’s smartphone-only Grasshopper (learn JavaScript) has been out since April.

Today my Google search found zero comparisons of the two approaches. (Ok, it found one webspam algorithmically generated page. That actually counts as -1.

Even five years ago Google would have found many by now.

The web is dead.

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Using the found phone alert to find special needs person

We rely on Find Friends to support independent life for our special needs kids. Sometimes location tracking doesn’t work though — particularly on buses.

Find has a great feature for phones in a family group. If the phone can’t be found it offers to notify when found.

Works great.

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Alas, no Flickr support for Aperture

With Flickr’s acquisition by Smugmug I thought It’d try Aperture’s Flickr export again.

Alas, it no longer works. I guess the API changed.

You can still sort of export to iCloud photostreams as long as you don’t try simultaneously using I don’t recommend this though, I think it’s crashy under Sierra. I’ve seen photostreams obliterated and thousands of thumbnails scattered across an Aperture database.

Probably the only ‘safe/sane’ photo sharing from Aperture now is export images/video to the file system then use an uploader This is semi-automatic with a Google Drive folder that supports Google Photos. (Though I quite dislike Google Photos because you can’t specify an album destination during upload.)

I do miss the glory days of photo sharing.

I’m mildly curious to see if Apple will introduce shared Libraries and Library Management for What a disappointment that product has been.

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Treat your arthritic knees with …

Weight lifting.

On a cellular level, what stimulates your chondrocytes, the stem cells that grow new cartilage, is cyclical loading. It’s a pattern of force that’s associated with things like running, jumping or weight lifting. These cells aren’t stimulated in the same way by lower-impact activities like using an elliptical machine or cycling.

For cartilage to remain healthy and regenerate in the way that it does for someone who is in their teens or 20s, the preponderance of evidence suggests that cyclical loading in the form of running or weight lifting is a really effective way to do that.

To a physician of my age this is like treating asthma with smoking.

It does match my experience though. When my familial arthritis kicked in I thought my CrossFit days were done. Instead my knees feel better when I’m doing my wall balls and back squats…

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I don’t think I should expect a refund.

I liked it for offline use, especially when traveling in areas with poor cell reception or where I had no data plan.

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This is how bad my Facebook ads are now …

This is how bad my Facebook ads are now … If I see an ad that’s close to my interests I click on it. Excluding those that I know, from past experience, go to unreadable sites.

That’s unusual. Mostly I get featured articles from sites a friend supposedly likes. If I click on them I get a flurry of ads. Basically, garbage.

We buy a lot of stuff. I have the credit card statements. My interests are easy to find, Facebook knows my Groups and Page Likes. AI need not apply, this is stone simple stuff.

And yet … crap ads.

Is anyone shorting Facebook yet?

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Facebook’s other ad problem: they aren’t any good

For some time I’ve been hiding or blocking irrelevant, uninteresting, misplaced or repulsive Facebook ads. All done with Facebook’s tools. I’ve even directly modified my ad interests.

The result?

My ads are getting less relevant and less interesting.

This is nuts. My family does a lot of stuff. Our Amazon spend is scary. There should be useful ads. Something is broken.

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Pigouvian taxation of the ad-click – it’s just me

As of April 2018 Google has no hits on the concept of Pigouvian taxation of ad-clicks as a core mitigation of the Facebook-Google problem.

My posts don’t show either of course; once Google would have found them. So there may be others like me, but nobody with an audience.

I’m disappointed Krugman or DeLong haven’t brought this up.

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Apple and me

I’ve lived through several OS transitions. Microsoft did them best. Their transitions had the lowest expenses and the least data loss. Apple did the biggest transition. OS/2 and GEOS died.

We all expect another transition from Apple; some mixture of macOS and CPU transition. This follows on years of Apple macOS disappointments — for me, above all, the way Apple ended Aperture.

I expect this transition to go badly for me. So my Apple relationship is officially cold. Not divorce yet, but the lawyer is in Contacts.

I’m not buying anything from Apple unless there is very clear immediate value and a clear exit strategy. I’ve ended our family Apple Music subscription. I’ll look for an alternative to iTunes movies. No earPods, no Apple Watch.

I’m staying on Sierra and Aperture through 2019.

Divorce will be painful, but Apple is likely past redemption. Its path lies elsewhere.

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The world is hard for the ungifted – bugs.

Google Maps wouldn’t let me switch from bike to drive directions. App state was confused, the left most icon inaccessible.

So I switched from bike to walk. That reset the app state and made drive accessible.

A routine bug workaround. In the iOS 11 era we run into this sort of thing a few times a day. Barely notice them any more.

There are so many bugs. Apple has the most now, but they are everywhere. The bike share I used this morning has a 15 sec delay in releasing a bike, if you don’t know that then you think the transaction failed. A bug equivalent.

If you are a global genius you may not notice these. If you merely have a knack, and are not yet too old, they are a minor annoyance. If you are an Old, as I am, they are ticks of the reapers clock, they take a bit longer to solve from year to year.

Ahh, but if you don’t have a knack … you didn’t get the academic gene, didn’t go to college, didn’t get the orthogonal geek gene … then this might be Hell. A regular reminder that you are not Elite. That the world has moved on and left you behind. That what you have, what you can do, what you have done … it doesn’t count any more.

Imagine what that feels like. Who do you vote for?

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Siri did something weird and disturbing

I said “Hey Siri, remind me to fix Kateva”. (Shorthand for fix

Siri created a reminder “Fix Kateva thunder desensitization”.

That isn’t a random error. I believe I had that as a task name in – years ago. Spotlight can’t find it on my iPhone now though. ToDo can’t find it either.

So where did Siri get that from?

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Ad-click business models are a civilizational threat. Tax the click.

Olds like me wonder “what happened?”

The current theory goes like this

1. In the 90s the Internet, especially Google, became ad-click funded. (The click is important. Not funded by dollars sold, funded by click.)

2. Slowly Google and others discovered that emotionally extreme material generated more clicks. Again, clicks, not necessarily sales. (We don’t know if this is because the material selects for ad-clickers or encourages ad-clicks. I’ve probably clicked 4 ads in my life.)

3. Ads on kitten videos and white-nationalism and “viral content” got more clicks.

4. The algorithms encoded this knowledge and began tailoring content based on interest “hints”.

Lately researchers have been quantifying this. They found emotionally engaging content drives more clicks, and it is easier to invent that content than it is to find it. So the mass web became a tool for disseminating false content.

The effect is so powerful non-researchers see it in simple YouTube tests, aided in this case by a disaffected Google engineer:

Basically the dark side of humanity is amplified by Pay-per-click advertising business models.

The good news is there are obvious fixes. The same fixes used for other addictive social harms like tobacco. Regulation and taxes. For example, tax click-based ad revenue heavily.

To know the enemy is to understand the fix.

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Did CSS kill tables on the web?

Once upon a time there were fabulous tools for creating HTML tables.

Twenty years later the dominant web authoring tool, WordPress, has no native table support.

I have never gotten a good explanation for the death of tables.

So I’ll venture a guess.

I think it was CSS. I wonder if it’s just too hard to put HTML’s table model together with CSS.

If this is true then my CSS dislike will double …

Update 2/19/2018: @clarkgoble creates his tables in Numbers then posts into MarsEdit (choose paste and preserve formatting!). I tried it and it works! I also installed the popular tables plugin for WordPress but it’s a poor substitute for native support. I wish MarsEdit did tables, but they didn’t make the recent big update.

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Old iPhone weirdness: Favorites include Message and FaceTime references

This is an old weirdness. shows a “Favorites” list. The list includes phone number references of course, but it can also hold FaceTime audio (UI for adding FaceTime audio is obscure), FaceTime video, and Message references. Favorites only show in, not in or

Favorites should logically be its own app or a part of, not a part of

(There’s probably a name for people who find this noteworthy.)

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My periodic test of Google Translate

Inspired by The Shallowness of Google Translate – The Atlantic I repeated an old test using Hostadter’s concluding paragraph. I did a round-trip translation from English to Chinese and back.


When, one day, a translation engine crafts an artistic novel in verse in English, using precise rhyming iambic tetrameter rich in wit, pathos, and sonic verve, then I’ll know it’s time for me to tip my hat and bow out.


One day, a translation engine used English poetry to create an artistic novel, with exquisite rhythms, rich wit, sadness, and sound, so I knew it was time to give me a little hat.

This is a real improvement over the last time I tried this. The “little hat” is goofy, but the result evokes a similar meaning.

It is a better result than I expected.

If I were writing for a Chinese audience, I could try this round-trip technique and tweak the English until it worked. Then have a native read the Chinese.

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Why do healthy young people sometimes die of influenza?

Our best guess is “bad luck”. Maybe they had another infection that interacted with influenza. Maybe their immune system was transiently disordered. Maybe they had an obscure genetic trait that set things down a bad path.

I’ve seen some long tortured explanations, but in this epidemic it seems bad luck. Sometimes lightning hits us.

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How much did the cost of software maintenance increase between 2000 and 2017?

I’m guessing severalfold cost increase due to security issues. Much higher patch frequency driven by security findings and OS changes.

IT budgets, especially in government, have not kept pace. Internally developed software is no longer cost effective.

Lots of implications we don’t understand yet. Some workflows will need to be simplified or change to fit generic tools … or even revert to pre-software modes.

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Returning from a Nordic ski resort in genteel decline …

This resort was in Northern Minnesota, along the Gunflint Trail. Could be anywhere though; every one we’ve visited in the past 15 years has had better days.

Lovely times when there is snow, but always with some melancholy. The world has moved on. There’s not enough consistent snow cover to sustain Nordic skiing in North America.

It was a beautiful sport – especially on narrower classic trails through woods. Our snowless winters feel longer for its passing.

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Off the grid: More iOS bugs

Off the grid I discover new iOS bugs. Choosing an alarm I’m given a list of tunes, but turns out many are not on device. Had to choose from playlist.

Apple assumes unlimited high speed data in its designs now.

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Refurb goods and shortened warranties

When my son’s XBOX ONE died age 18m I was happy to have my AMEX extended warranty at hand.

Except, they correctly pointed out, it was a refurb and had a limited 90 day warranty.

Oddly enough I’d never run into this before; I assumed a normal warranty. Why buy something the seller predicts will fail prematurely? That would require a hell of a discount.

If I ever buy refurb again the product will have to have a full warranty period.

Penance paid, lesson learned, shared, etc.

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Unsurprising news from physician payment experiments.

This week we learned:

  • If you pay physicians based on how patients do they avoid caring for high risk patients. Who then do worse.
  • Conversely physicians who care for wealthy healthy patients get more rewards, so health card dollars are flowing to wealthy patient care.

This surprised nobody with a brain.

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Pinboard increasingly unreliable.

I pin a lot as part of my microblog posting. More and more authentication challenges. Maybe result of some bot attack/password reset?

I think I’m going to have to switch my flow around. Make it WordPress centric.

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How many calories does menstruation use?

I couldn’t find a scholarly article on this. Which is weird. Maybe research is old.

Women’s magazines estimate around 200-300 calories, they typically source a physician known to the journalist.

At the high end that is 3,600 calories a year, roughly a 1lb yearly weight gain if not menstruating and nothing else changes.

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Neural networks 2018

The speed of neural network development feels faster than anything in my lifetime. Maybe early web was similar.

This is bigger potential impact though.

2018 is going to be too interesting.

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Consequences of bundling with macOS.

The only sensible way to use macOS is to wait 8 months for bugs to be fixed and OS ecosystem to be updated.

That means waiting 8 months for bug fixes.

On the other hand, one gets a mature update yearly with 3 months of tweaks.

Not all bad, but 8 months is a long time to wait for big bug to be fixed.

I’m still on Aperture, so still but abstract. Aperture looks better all the time.

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