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Ray Lee
Works at Tapestry Systems, Inc.
Attended Cal Poly San Luis Obispo
Lives in San Luis Obispo, CA
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Ray Lee

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Making DNA for humans from scratch, to order. Our new tools for editing our genome have opened up a lot of possibilities. Now's the time to think through the implications.

"Scary and fascinating. I don't know which is going to happen first: widespread embryo selection, embryo editing with CRISPR, iterated embryo selection, or whole-genome synthesis, or some combination of all of them..."
 
Exciting and scary. Consider CRISPR: you need 100+ edits for a serious intelligence boost, and you'll want to do edits for other traits like schizophrenia. It's not at all obvious that it's safe to do that many edits to one embryo, or that that many edits won't have unintended consequences you can't catch as simply as doing a whole-genome sequence afterwards to look for mutations. So if you want to do a lot of edits... why not synthesize the entire genome as desired? Now the marginal cost of an edit is $0. You can make every edit you want, even the SNPs with posterior probabilities of increases barely >50%. Hsu's 'flip all the switches' scenario for IQ1000+ suddenly becomes doable, potentially within a decade or two, without depending on CRISPR scaling to hundreds of edits, multi-generational accumulating effects from embryo selection, or iterated embryo selection. Oh, and you can 'flip all the switches' on as many SNPs or rare mutations as you want, and if you don't know what you want, simply delete the entire 80k+ mutational load and produce the modal human on everything else.

"But George Church, a professor of genetics at Harvard Medical School and one of the organizers of the new project, said that if the changes desired are extensive, at some point it becomes easier to synthesize the needed DNA from scratch. “Editing doesn’t scale very well,” he said. “When you have to make changes to every gene in the genome it may be more efficient to do it in large chunks.”"

No kidding.

Yes, it'll cost $1b for the first genome, but it's easy to replicate genomes. Once you have the optimized genomes with the equivalent of thousands of edits, you can easily replicate it into eggs or sperms, and offer it for near-free to anyone who wants them for fertility procedures; half of 1000 is still an incredible game-changer. At 10k+ parents a year in the USA alone, the $1b will be amortized almost immediately ($1000 an IQ point NPV, IQ500+, 1000 * 500 * 10000 = paid off the first year based on IQ alone). Heck, there may be plenty of people willing to adopt/be surrogate parents to a pure-bred offspring. And if DNA synthesizing follows a cost curve remotely like DNA sequencing has...

Scary and fascinating. I don't know which is going to happen first: widespread embryo selection, embryo editing with CRISPR, iterated embryo selection, or whole-genome synthesis, or some combination of all of them (iterated embryo selection to pick up the tagged causal variants, creating an optimal-selected genome which is then sequenced and edited in arbitrary ways for a final genome synthesis and CRISPR spotchecks?).

Fulltext: http://science.sciencemag.org/content/early/2016/06/01/science.aaf6850.full
The formal announcement of the plans, which leaked last month, seeks to raise $100 million this year. The total price tag could exceed $1 billion.
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H Abreu
 
Hacker exploits in human DNA. shudder

Ray Lee

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Our beautiful world, microscopic edition.
Viscous fingers form between air and titanium dioxide sol-gel in this photograph. The two fluids are trapped in a thin gap between glass plates – a set-up known as a Hele-Shaw cell. The dendritic...
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Ray Lee

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The Babylonians discovered an early form of Calculus back around 1600 BCE (integration by trapezoids). They then applied it to the motions of Jupiter to predict where the 'White Star' would be over time, back in ~50 BCE, roughly 1400 years before Europeans would rediscover it. And they did it all in base 60.
Clay tablets document precocious astronomical calculations by 50 B.C.E.
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Ray Lee

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Beautiful data! This is an elevation map of the Willamette River in Oregon, covering a 50' range.

"The shades of white show changes in elevation, between 0 to 50 feet. This brings out the changes made by the river channel in the last 12,000 to 15,000 years, in the time since the landscape was basically swept clean by the Missoula floods."

http://www.thisiscolossal.com/2015/11/willamette-river-history-dan-coe/


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Ray Lee

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A little bit of physics zen for your Thursday.
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H Abreu
 
Wow. And slo-mo makes it even more magic.
Have him in circles
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Ray Lee

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Our beautiful universe, stellar-go-boom edition. This is "V838 Monocerotis" over a 4 year time-lapse.

We're not sure what triggered the outburst. Regardless, what we're seeing below is the 'light echo' from the event. Waves of light were emitted from the star. What looks like debris from an explosion is that light bouncing off the gas in the nebula surrounding that star.

Wikipedia has more detail if you're interested: https://en.wikipedia.org/wiki/V838_Monocerotis

(h/t +Andrew Rader's twitter stream)
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Ray Lee

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This is pretty. The idea is to take an existing artistic style (such as The Scream, or Picasso, or somesuch) and use that style to repaint a video. It's used to nice effect in the final example, a transfer of an ink-wash style to an existing rendering.

https://www.youtube.com/watch?v=vQk_Sfl7kSc
 
Big improvement in video style transfer: https://www.youtube.com/watch?v=vQk_Sfl7kSc

"Artistic style transfer for videos", Ruder et al 2016:

"In the past, manually re-drawing an image in a certain artistic style required a professional artist and a long time. Doing this for a video sequence single-handed was beyond imagination. Nowadays computers provide new possibilities. We present an approach that transfers the style from one image (for example, a painting) to a whole video sequence. We make use of recent advances in style transfer in still images and propose new initializations and loss functions applicable to videos. This allows us to generate consistent and stable stylized video sequences, even in cases with large motion and strong occlusion. We show that the proposed method clearly outperforms simpler baselines both qualitatively and quantitatively."

I like the ink wash transfer example at the end of the YT video.
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We'll see that in movies. . .

Ray Lee

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Skepticism is good, as long as we're also skeptical of our own conclusions. Especially when repeated data says we may be wrong.

“There is a 97% expert consensus on a cohesive theory that's overwhelmingly supported by the scientific evidence, but the 2–3% of papers that reject that consensus are all over the map, even contradicting each other. The one thing they seem to have in common is methodological flaws like cherry picking, curve fitting, ignoring inconvenient data, and disregarding known physics.” For example, one skeptical paper attributed climate change to lunar or solar cycles, but to make these models work for the 4,000-year period that the authors considered, they had to throw out 6,000 years' worth of earlier data."_

http://www.scientificamerican.com/article/why-climate-skeptics-are-wrong/
Or why climate skeptics are wrong
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Ray Lee

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Remember when "Dolphin Safe Tuna" labels came around? Seen any lately? It turns out that despite citizens in the USA passing a law requiring such labeling, Mexico fought against it, and won, in the WTO.

If this seems okay to you, then you'll love the TPP.

http://boingboing.net/2015/11/24/wto-rules-against-us-dolphin-s.html
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Ray Lee

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This is great! (Easy to read, and accurate too.) "The Space Doctor's Big Idea"

Randall Munroe of XKCD fame explains Einstein's Relativity using only the ten hundred words people use most often. ('Thousand' isn't one of the top one thousand words we use most often.)

http://www.newyorker.com/tech/elements/the-space-doctors-big-idea-einstein-general-relativity?intcid=mod-most-popular#_ftnref1


Einstein’s theory of general relativity, explained using only the thousand most common words in English.
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That is a great use of the 1k most common words. 

Ray Lee

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tl;dr:

"The history of the U.S. refugee program demonstrates that the lengthy and extensive vetting that all refugees must undergo is an effective deterrent for terrorists. Since 1980, the U.S. has invited in millions of refugees, including hundreds of thousands from the Middle East. Not one has committed an act of terrorism in the U.S. Traditional law enforcement and security screening processes have a proven record of handling the threat from refugees."

The bullet points without the supporting arguments:

"1. The Paris attackers were not refugees
2. U.S. refugees don’t become terrorists
3. Other migration channels are easier to exploit than the U.S. refugee process
4. ISIS sees Syrian refugees as traitors
5. Turning away allies will make us less safe
6. America should demonstrate moral courage"

https://niskanencenter.org/blog/six-reasons-to-welcome-syrian-refugees-after-paris/
Rejecting refugees now would be a senseless approach that will make America less safe.
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Ray Lee

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This is cool. A new welding technique that's 50% stronger and uses 80% less energy. The first photo below is showing copper welded to titanium, from the OSU link below. Related, photos of Kelvin-Helmholtz instabilities in clouds.

Making cars of the future stronger, using less energy
New welding technique can weld “un-weldable” metals
https://news.osu.edu/news/2015/10/29/vfaweld/
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Education
  • Cal Poly San Luis Obispo
Basic Information
Gender
Male
Story
Tagline
Itinerant software architect, part time physics hobbiest, full time curmudgeon. Post-bitter. Writing my life-poem one day at a time, just like the rest of us.
Introduction
Our lives are the greatest art project we'll ever take on.

I live a charmed life. I write custom software for odd-ball businesses. I have wonderful friends that take me to exotic locales. I putter around with a little research in my spare time.
Work
Occupation
Software Architect
Employment
  • Tapestry Systems, Inc.
    Owner, Software Architect, 1996 - present
  • Bronco Communications, LLC
    CTO, 2004 - 2010
  • ITT Federal Services Corporation, SMTO
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Currently
San Luis Obispo, CA
Previously
Santa Maria, CA
Great food! I had the BBQ lamb burrito, which was tender and delicious. The service was fast and friendly, the prices reasonable. Worth the stop if you're passing through!
Public - a year ago
reviewed a year ago
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