Science

Dr. Greene, working with a student, has also found that “squirrels understand ‘bird-ese,’ and birds understand ‘squirrel-ese.’ ” When red squirrels hear a call announcing a dangerous raptor in the air, or they see such a raptor, they will give calls that are acoustically “almost identical” to the birds, Dr. Greene said. (Researchers have found that eastern chipmunks are attuned to mobbing calls by the eastern tufted titmouse, a cousin of the chickadee.)

The titmice are in on it too.  The article has numerous further points of interest.

Don’t Fear the CRISPR

by on May 18, 2015 at 7:00 am in Medicine, Science | Permalink

I’m honored to be here guest-blogging for the week. Thanks, Alex, for the warm welcome.

I want to start with a topic recently in the news, and that I’ve written about in both fiction and non-fiction.

In April, Chinese scientists announced that they’d used the CRISPR gene editing technique to modify non-viable human embryos. The experiment focused on modifying the gene that causes the quite serious hereditary blood disease Beta-thalassemia.

You can read the paper here. Carl Zimmer has an excellent write-up here. Tyler has blogged about it here. And Alex here.

Marginal Revolution aside, the response to this experiment has been largely negative. Science and Nature, the two most prestigious scientific journals in the world, reportedly rejected the paper on ethical grounds. Francis Collins, director of the NIH, announced that NIH will not fund any CRISPR experiments that involve human embryos.

NIH will not fund any use of gene-editing technologies in human embryos. The concept of altering the human germline in embryos for clinical purposes has been debated over many years from many different perspectives, and has been viewed almost universally as a line that should not be crossed.

This is a mistake, for several reasons.

  1. The technology isn’t as mature as reported. Most responses to it are over-reactions.
  2. Parents are likely to use genetic technologies in the best interests of their children.
  3. Using gene editing to create ‘superhumans’ will be tremendously harder, riskier, and less likely to be embraced by parents than using it to prevent disease.
  4. A ban on research funding or clinical application will only worsen safety, inequality, and other concerns expressed about the research.

Today I’ll talk about the maturity of the technology. Tomorrow I’ll be back to discuss the other points. (You can read that now in Part 2: Don’t Fear Genetically Engineered Babies.)

CRISPR Babies Aren’t Near

Despite the public reaction (and the very real progress with CRISPR in other domains) we are not near a world of CRISPR gene-edited children.

First, the technique was focused on very early stage embryos made up of just a few cells. Genetically engineering an embryo at that very early stage is the only realistic way to ensure that the genetic changes reach all or most cells in the body. That limits the possible parents to those willing to go through in-vitro fertilization (IVF). It takes an average of roughly 3 IVF cycles, with numerous hormone injections and a painful egg extraction at each cycle, to produce a live birth. In some cases, it takes as many as 6 cycles. Even after 6 cycles, perhaps a third of women going through IVF will not have become pregnant (see table 3, here). IVF itself is a non-trivial deterrent to genetically engineering children.

Second, the Chinese experiment resulted in more dead embryos than successfully gene edited embryos. Of 86 original embryos, only 71 survived the process. 54 of those were tested to see if the gene had successfully inserted. Press reports have mentioned that 28 of those 54 tested embryos showed signs of CRISPR/Cas9 activity.

Yet only 4 embryos showed the intended genetic change. And even those 4 showed the new gene in only some of their cells, becoming ‘mosaics’ of multiple different genomes.

From the paper:

~80% of the embryos remained viable 48 h after injection (Fig. 2A), in agreement with low toxicity of Cas9 injection in mouse embryos  […]

ssDNA-mediated editing occurred only in 4 embryos… and the edited embryos were mosaic, similar to findings in other model systems.

So the risk of destroying an embryo (~20%) was substantially higher than the likelihood of successfully inserting a gene into the embryo (~5%) and much higher than the chance of inserting the gene into all of the embryo’s cells (0%).

There were also off-target mutations. Doug Mortlock believes the off-target mutation rate was actually much lower than the scientists believed, but in general CRISPR has a significantly non-zero chance of inducing an unintended genetic change.

CRISPR is a remarkable breakthrough in gene editing, with applications to agriculture, gene therapy, pharmaceutical production, basic science, and more. But in many of those scenarios, error can be tolerated. Cells with off-target mutations can be weeded out to find the few perfectly edited ones. Getting one complete success out of tens, hundreds, or even thousands of modified cells can suffice, when that one cell can then be replicated to create a new cell line or seed line.

In human fertility, where embryos are created in single digit quantities rather than hundreds or thousands – and where we hope at least one of those embryos comes to term as a child – our tolerance for error is dramatically lower. The efficiency, survivability, and precision of CRISPR all need to rise substantially before many parents are likely to consider using it for an unborn embryo, even to prevent disease.

That is, indeed, the conclusion of the Chinese researchers, who wrote, “Our study underscores the challenges facing clinical applications of CRISPR/Cas9.”

More in part two of this post on the ethics of allowing genetic editing of the unborn, and why a ban in this area is counterproductive.

Tyler and I are delighted to have the great Ramez Naam guest blogging for us this week. Ramez spent many years at Microsoft leading teams working on search and artificial intelligence. His first book, More Than Human: Embracing the Promise of Biological Enhancement was a thought provoking look at the science and ethics of enhancing the human mind, body, and lifespan. More recently, I enjoyed Ramez’s The Infinite Resource: The Power of Ideas on a Finite Planet, an excellent Simonesque guide to climate change, energy and innovation.

Frankly, I didn’t expect much when I bought Ramez’s science fiction novel, Nexus. Good non-fiction authors don’t necessarily make good fiction authors. I was, however, blown away. Nexus is about a near-future in which a new technology allows humans to take control of their biological operating system and communicate mind to mind. Nexus combines the rush of a great thriller, the fascination of hard science fiction and the intrigue of a realistic world of spy-craft and geo-politics. I loved Nexus and immediately bought the second in the trilogy, Crux. I finished that quickly and I am now about half-way through the just released, Apex. Thus it’s great to have Ramez guest blogging as I race towards the end of his exciting trilogy! The trilogy is highly recommended.

Please welcome Ramez to MR.

Nexus Cover


NYTimes: While everyone welcomes Crispr-Cas9 as a strategy to treat disease, many scientists are worried that it could also be used to alter genes in human embryos, sperm or eggs in ways that can be passed from generation to generation. The prospect raises fears of a dystopian future in which scientists create an elite population of designer babies with enhanced intelligence, beauty or other traits.

Does the author really think that smart, beautiful people are a bad thing? Should we shoot the ones we have now? (It seems unlikely that we are at a local maximum).

Sometimes my fellow humans depress me. But I hope for better ones in the future.

NBC: A poker showdown between professional players and an artificial intelligence program has ended with a slim victory for the humans — so slim, in fact, that the scientists running the show said it’s effectively a tie .The event began two weeks ago, as the four pros — Bjorn Li, Doug Polk, Dong Kim and Jason Les — settled down at Rivers Casino in Pittsburgh to play a total of 80,000 hands of Heads-Up, No-Limit Texas Hold ’em with Claudico, a poker-playing bot made by Carnegie Mellon University computer science researchers.

…No actual money was being bet — the dollar amount was more of a running scoreboard, and at the end the humans were up a total of $732,713 (they will share a $100,000 purse based on their virtual winnings). That sounds like a lot, but over 80,000 hands and $170 million of virtual money being bet, three-quarters of a million bucks is pretty much a rounding error, the experimenters said, and can’t be considered a statistically significant victory.

The computer bluffed and bet against the best poker players the world has ever known and over 80,000 hands the humans were not able to discover an exploitable flaw in the computer’s strategy. Thus, a significant win for the computer. Moreover, the computers will get better at a faster pace than the humans.

In my post on opaque intelligence I said that algorithms were becoming so sophisticated that we humans can’t really understand what they are doing, quipping that “any sufficiently advanced logic is indistinguishable from stupidity.” We see hints of that here:

“There are spots where it plays well and others where I just don’t understand it,” Polk said in a Carnegie Mellon news release….”Betting $19,000 to win a $700 pot just isn’t something that a person would do,” Polk continued.

Polk’s careful wording–he doesn’t say the computer’s strategy was wrong but that it was inhuman and beyond his understanding–is a telling indicator of respect.

The University of Toronto’s commercialization office states that it is “in a class with the likes of MIT and Stanford.” But Stanford has generated $1.3-billion (U.S.) in royalties for itself and the Massachusetts Institute of Technology issued 288 U.S. patents last year alone; U of T generates annual licensed IP income of less than $3-million (Canadian) and averages eight U.S. patents a year. Statistics Canada reports that in 2009, just $10-million was netted by all Canadian universities for their licences and IP. Even when accounting for universities that have open IP policies, this is a trivial amount by global standards.

That is from Jim Balsillie, and is interesting more generally, most of all on Canada and innovation.  For the pointer I thank Scott Barlow.  My previous post on this topic is here.

Whale fact of the day

by on May 7, 2015 at 1:47 pm in Food and Drink, Science | Permalink

Scientists at UBC have discovered — by accident — a rorqual whale can take a gulp of water that’s bigger than its massive body, then bounce back to its normal shape.

The whale has nerves to its mouth and tongue that can stretch to double their normal length, then snap back without damage, said Wayne Vogl, a professor in the department of cellular and physiological sciences at UBC.

“The nerves that supply these remarkably expandable tissues in the floor of the mouth of rorqual whales … are very stretchy, they’re like bungee cords,”

It was a surprising discovery, as most vertebrate nerves are more of a fixed length, said Vogl.

whale-graphic

There is more here.

The end of doggie privacy?

by on May 6, 2015 at 1:05 pm in Data Source, Law, Science | Permalink

Dogs can run, but they can’t hide from PooPrints.

BioPet Vet Lab, which specializes in canine genetic testing, is partnering with the appropriately named London borough of Barking and Dagenham to track down dog owners who fail to remove their pets’ public deposits.

Starting in September 2016, people who don’t pick up after their dogs could be fined 80 pounds, or about $125. The registration of dogs’ DNA could become mandatory five months earlier if a pilot program proves successful.

There is more here, via Ray Lopez.  And here is a related story from Vancouver.

*Digital Gold*

by on May 6, 2015 at 9:37 am in Books, Economics, History, Science | Permalink

The author is Nathaniel Popper and the subtitle is Bitcoin and the Inside Story of the Misfits and Millionaires Trying to Reinvent Money.

This excellent work is the book on Bitcoin you’ve been waiting for, most importantly it doesn’t require that you are the kind of person who wants to read a book on Bitcoin.  I devoured my copy right away, it is full of information, explanation, and good humor, definitely recommended and entertaining throughout.

Here is Popper’s piece on Bitcoin and Argentina, here is Popper on Twitter.

Ramez Naam has an opinion, backed up by some reasonable estimates:

For most of the US, this battery isn’t quite cheap enough. But it’s in the right ballpark. And that means a lot. Net Metering plans in the US are filling up. California’s may be full by the end of 2016 or 2017, modulo additional legal changes. That would severely impact the economics of solar. But another factor of 2 price reduction in storage would make it cheap enough that, as Net Metering plans fill up or are reduced around the country, the battery would allow solar owners to save power for the evening or night-time hours in a cost effective way.

That is also a policy tool in debates with utilities. If they see Net Metering reductions as a tool to slow rooftop solar, they’ll be forced to confront the fact that solar owners with cheap batteries are less dependent on Net Metering.

That same factor of 2 price reduction would also make batteries effective for day-night electricity cost arbitrage, wherein customers fill up the battery with cheap grid power at night, and use stored battery power instead of the grid during the day. In California, where there’s a 19 cent gap between middle of the night power and peak-of-day power, those economics look very attractive.

And the cost of batteries is plunging fast. Tesla will get that 2x price reduction within 3-5 years, if not faster.

Read the whole thing, and note the discussion of India too.

No Font of Wisdom

by on May 3, 2015 at 7:49 am in Science | Permalink

You will not understand this post better just because it is hard to read. Small n study magnified by Gladwell, Kahneman et al. doesn’t replicate. ∑Àgain.

More here.

Hat tip: Nathaniel Bechhofer

From Robert Trivers. Here is Trivers on William Hamilton:

Certainly one of the most creative minds I have ever met in biology. I still remember the day a graduate student came running down the hall saying “Have you heard Hamilton thinks that bacteria use clouds for dispersal? As quick as you can say “Bill Hamilton”, I asked “Has he shown how the bacteria get the rain to fall where they want it to?” And indeed his idea humbled me because ever since I had been coming to Jamaica I had heard rural people tell me “trees draw rain” as in, don’t cut them down, and I had thought to myself you poor benighted souls, you have the correlation right but causality wrong—naturally, where it rains more, trees are more apt to grow. Now Bill suggested they Jamaicans may well have had it right all along—lower temperatures over wooded areas could itself be a useful signal.

Robot sentences to ponder

by on April 26, 2015 at 4:00 pm in Economics, Science | Permalink

Harnessing high-powered computing, color sensors and small metal baskets attached to the robotic arms, the machine gently plucked ripe strawberries from below deep-green leaves, while mostly ignoring unripe fruit nearby.

Such tasks have long required the trained discernment and backbreaking effort of tens of thousands of relatively low-paid workers. But technological advances are making it possible for robots to handle the job, just as a shrinking supply of available fruit pickers has made the technology more financially attractive.

…Machines are doing more than picking produce. Altman Specialty Plants Inc., one of the country’s largest nurseries, has been using eight, squat robots for the past two years to ferry more than 1.2 million potted roses and other plants to new rows as they grow larger. The $25,000, self-driving machines have occasionally gotten stuck in mud, but they freed eight workers for other jobs and ultimately paid for themselves in 18 months, said Becky Drumright, Altman’s marketing director.

And we used to say that gardening was one of the hardest jobs to automate.  By Ilan Brat, there is more here.

Claims about embryos

by on April 24, 2015 at 12:29 am in Current Affairs, Philosophy, Science | Permalink

A pressing question, said Rudolf Jaenisch, an M.I.T. biology professor, is why anyone would want to edit the genes of human embryos in order to prevent disease. Even in the most severe cases, involving diseases like Huntington’s in which a single copy of a mutated gene inherited from either parent is enough to cause the disease with 100 percent certainty, editing poses ethical problems. Because of the way genes are distributed in embryos, when one parent has the gene, only half of the parent’s embryos will inherit it. With gene editing, the cutting and pasting has to start immediately, in a fertilized egg, before it is possible to know if an embryo has the Huntington’s gene. That means half the embryos that were edited would have been normal — their DNA would have been forever altered for no reason. “It is unacceptable to mutate normal embryos,” Dr. Jaenisch said. “For me, that means there is no application.”

If I were grading an undergraduate philosophy class, I am not sure Dr. Jaenisch would exceed a C minus with that answer (the source article is here).  Besides I have never known a normal embryo.  Then there is the all too obvious question as to why it should be acceptable to abort embryos, but not to modify or mutate them.  Oops.

The better arguments are surely the slippery slope worries that embryo tinkering will change the nature and future of humanity in dangerous ways, perhaps producing too much conformity, too much zero-sum competition (“buy the Harvard splice”), too much discrimination against various “types,” too much induced family loyalty, legal discouragement of rebellious genes, excess advantages for elites, too many decisions which too explicitly lower the social status of some groups of people, and perhaps ultimately too much drift from the world we know (and love?).

Those are my worries.  Whether or not they are valid, they would seem to merit at least a C+.  But many commentators wish to ensure these issues are not actually argued.  Will this prove the new face of anti-scientific, anti-philosophical thinking?  Check out the closing quotation from Professor Daley at Harvard, and his use of the word “deranged.”

A lot of parents will strongly desire some future version of this product, and I believe a number of countries are going to be willing to proceed with such innovations, if and when they become possible.  They’ll also be willing to live with the costs of the failures in the meantime.  So I don’t think the strategy of shutting down debate is going to fare so well in this case.

…the warden of the Lee Correctional Institute, Cecilia Reynolds, said that in recent weeks her officers found 17 phones in one inmate’s cell. She said she suspected that the phones continue to come in on drones.

There is more here, interesting throughout.  How about this bit?:

Prison officials, echoing Ms. Reynolds, say that convicts and their families and friends are willing to pay more than $1,000 to get a device – like an iPhone — into a prison. Smartphones are so desirable because unlike pay phones at prisons, they are not recorded or monitored, enabling gang leaders to freely run their criminal activities from behind bars. The phones also allow them to watch pornography and communicate surreptitiously with fellow prisoners.

The phones are essential for coordinating with smugglers using drones, because the prisoners need to know where to find the deliveries in the yard. Most important for the smugglers, the prisoners can then use the phones to quickly pay them.

How about blocking cell phone signals inside the jail?  Elsewhere, a possibly radioactive drone was found on the roof of the office of Prime Minister Abe.  As I’ve said already on Twitter, the drone wars have begun…