Daniel Lemire's blog

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Science and Technology links (March 24, 2017)

There are many claims that innovation is slowing down. In the XXth century, we went from horses to planes. What have we done lately? We have not cured cancer or old age. We did get the iPhone. There is that. But so what? There are many claims that Moore’s law, the observation that processors gets twice as good every two years or so, is faltering if not failing entirely. Then there is Eroom’s law, the observation that new medical drugs are getting exponentially expensive. I don’t think that anyone questions the fact that we are still on an exponential curve… but it matters whether we make progress at a rate of 1% a year or 5% a year. So what might be happening? Why would we slow down? Some believe that all of the low-hanging fruits have been picked. So we invented the airplane, the car, and the iPhone, that was easy, but whatever remains is too hard. There is also the theory that as we do more research, we start duplicating our efforts in vain. Knott looked at the data and found something else:

One thought is that if R&D has truly gotten harder, it should have gotten harder for everyone. (…) That’s not what I found when I examined 40 years of financial data for all publicly traded U.S. firms. I found instead that maximum RQ [R&D productivity] was actually increasing over time! (…) I restricted attention to a particular sector, e.g., manufacturing or services. I found that maximum RQ was increasing within sectors as well. I then looked at coarse definitions of industry, such as Measuring Equipment (Standard Industrial Classification 38), then successively more narrow definitions, such as Surgical, Medical, And Dental Instruments (SIC 384), then Dental Equipment (SIC 3843). What I found was that as I looked more narrowly, maximum RQ did decrease over time (…) What the pattern suggests is that while opportunities within industries decline over time, as they do, companies respond by creating new industries with greater technological opportunity.

The way I understand this finding is that once an industry reaches maturity, further optimizations will provide diminishing returns… until someone finds a different take on the problem and invents a new industry.

With time, animals accumulate senescent cells. These are cells that should die (by apoptosis) but somehow stick around. This happens very rarely, so no matter how old you are, you have very few senescent cells, to the point where a biologist would have a hard time finding them. But they cause trouble, a lot of trouble it seems. They might be responsible for a sizeable fraction of age-related health conditions. Senolytics are agents that help remove senescent cells from your tissues. There is a natural product (quercetin), found in apples and health stores that is a mild senolytic. (I do not recommend you take quercetin though eating apples is fine.) A few of years ago, I had not heard about senolytics. Judging by the Wikipedia page, the idea has emerged around 2013. A quick search in Google Scholar seems to reveal that 2013 is roughly accurate. (Update: Josh Mitteldorf credits work by Jan van Deursen of Mayo Clinic dating back to 2011) You may want to remember this term. Anyhow, the BBC reported on a recent trial in mice:

They have rejuvenated old mice to restore their stamina, coat of fur and even some organ function. The findings, published in the journal Cell, showed liver function was easily restored and the animals doubled the distance they would run in a wheel. Dr de Keizer said: “We weren’t planning to look at their hair, but it was too obvious to miss.” “In terms of mouse work we are pretty much done, we could look at specific age-related diseases eg osteoporosis, but we should now prepare for clinical translation.”

At this point, the evidence is very strong that removing senescent cells is both practical and beneficial. It seems very likely that, in the near future, older people will be healthier through senolytics. However, details matter. For example, senescent help your skin to heal, so removing all of your senescent cells all the time would not be a good thing. Moreover, senolytics are likely slightly toxic, after all they get some of your cells to die, so you would not want to overdose. You probably just want to maintain the level of senescent cells at a low level, by periodic “cleansing”. How to best achieve this result is a matter of research. On a related note, Amazon’s CEO Jeff Bezos invested several of his own millions in a company that aims to clear up senescent cells.

Are professors going to move to YouTube and make a living there? Some are doing it now. Professor Steve Keen has gone to YouTube to ask people to fund his research. Professor Jordan Peterson claims that he makes something like 10k$ a month through donations to support his YouTube channel. I am not exactly sure who supports these people and what it all means.

We are inserting synthetic cartilage in people with arthritis.

It seems that the sugar industry paid scientists to dismiss the health concerns regarding sugar:

The article draws on internal documents to show that an industry group called the Sugar Research Foundation wanted to “refute” concerns about sugar’s possible role in heart disease. The SRF then sponsored research by Harvard scientists that did just that. The result was published in the New England Journal of Medicine in 1967, with no disclosure of the sugar industry funding.

I think we should all be aware that sugar in large quantities makes you at risk for obesity, heart disease, and diabetes. True dark chocolate is probably fine, however.

It seems that when it comes to fitness, high-intensity exercises (interval training) works really well, no matter your age: it improves muscle mitochondrial function and hypertrophy in all ages. [Translation: you have more energy (mitochondrial function) and larger muscles (hypertrophy).] So the treadmill and the long walks? They may help a bit, but if you want to get in shape, you better crank up the intensity.

John P. A. Ioannidis has made a name for himself by criticizing modern-day science. His latest paper is Meta-assessment of bias in science, and the gist of it is:

we consistently observed that small, early, highly-cited studies published in peer-reviewed journals were likely to overestimate effects.

What does it mean in concrete terms? Whenever you hear a breakthrough for the first, take it with a grain of salt. Wait for the results to be confirmed independently. Also, we may consider established researchers as more reliable, as per the paper’s results.

Viagra not only helps with erectile dysfunction, it seems that it keeps heart disease at bay too. But Viagra is out of patent at this point, so pharmaceutical companies are unlikely to shell out millions to market it for other uses. Maybe the government or academics should do this kind of research? When thinking about computer performance, we often think of the microprocessor. However, storage and memory are often just as important as processors for performance. The latest boost we got were solid-state disks (SSD) and what difference does it make! Intel is now commercializing what might be the start of a new breakthrough (3D XPoint). Like a disk, the 3D XPoint memory is persistent, but it has latency closer to that of internal memory. Also, unlike our solid-state drives, this memory is byte addressable: you can modify individual bytes without having to rewrite entire pages of memory. In effect, Intel is blurring the distinction between storage and memory. For less than 2k$, you can now get a fancy disk having hundreds of gigabytes that works a bit like internal memory. The long-term picture is that we may get more and more computers with persistent memory that has nearly the performance of our current volatile memory, but without the need to be powered all the time. This would allow our computers to have a lot more memory. Of course, for this to happen, we need more than just 3D XPoint, but chances are good that competitors are hard at work building new types of persistent memory.

Leonardo da Vinci once invented a “self-supporting bridge”. Basically, given a few straight planks, you can quickly build a strong bridge without nail or rope. You just assemble the planks and you are done. It is quite impressive: I would really like to know how da Vinci’s mind worked. Whether it is was ever practical, I do not know. But I came across a cute video of a dad and his son building it up.

We have been told repeatedly that the sun was bad for us. Lindqvist et al. in Avoidance of sun exposure as a risk factor for major causes of death find contrary evidence. If you are to believe their results, it is true that if you spend more time in the sun, you are more likely to die of cancer. However, this is because you are less likely to die of other causes:

Women with active sun exposure habits were mainly at a lower risk of cardiovascular disease (CVD) and noncancer/non-CVD death as compared to those who avoided sun exposure. As a result of their increased survival, the relative contribution of cancer death increased in these women. Nonsmokers who avoided sun exposure had a life expectancy similar to smokers in the highest sun exposure group, indicating that avoidance of sun exposure is a risk factor for death of a similar magnitude as smoking. Compared to the highest sun exposure group, life expectancy of avoiders of sun exposure was reduced by 0.6–2.1 years.

Sun exposure is good for your health and makes you live longer. No, we do not know why.

Our DNA carries the genetic code that makes us what we are. Our cells use DNA as a set of recipes to make useful proteins. We know that as we age, our DNA does not change a lot. We know because if we take elderly identical twins, their genetic code is very similar. So the body is quite careful not to let our genes get corrupted. Random mutations do occur, but a single cell being defective is hardly cause for concern. Maybe you are not impressed to learn that your cells preserve their genetic code very accurately, but you should be. Each day, over 50 billion of your cells die through apoptosis and must be replaced. You need 2 million new red blood cells per second alone. Anyhow, DNA is not the only potential source of trouble. DNA is not used directly to make the proteins, our cells use RNA instead. So there is a whole complicated process to get from DNA to protein and even if your DNA is sane, the produced protein could still be bad. A Korean team recently showed that something called “nonsense-mediated mRNA decay” (NMR), a quality-control process for RNA, could improve or degrade the lifespan of worms if it is tweaked. Thus, even if you have good genes, it is possible that your cells could start making junk instead of useful proteins as you grow older.

Our bodies are built and repaired by our stem cells. Though we have much to learn, we know that injecting stem cells into a damaged tissue may help make it healthier. In the future, it is conceivable that we may regenerate entire organs in vivo (in your body) by stem cells injections. But we need to produce the stem cells first. The latest trend in medicine is “autologous stem cell transplantation”. What this means is that we take your own cells, modify them as needed, and then reinject them as appropriate stem cells where they may help. This is simpler for obvious reasons than using donated stem cells. For one thing, these are your own cells, so they are not likely to be rejected as foreign. But a lot of sick people are quite old. Are the stem cells from old people still good enough? In Regenerative capacity of autologous stem cell transplantation in elderly, Gonzalez-Garza and Cruz-Vega tell us that it is indeed the case: stem cells from elderly donors are capable of self-renewal and differentiation in vitro. That’s true even though the gene expression of the stem cells taken from elderly donors differs from that of younger donors.

In a Nature article, researchers report being able to cause a tooth to regrow using stem cells. The subject (a dog) saw a whole new tooth grow and become fully functional. If this works, then we might soon be able to do the same in human being. Can you imagine regrowing a whole new tooth as an adult? It seems that we can do it.

Back in 2010, researchers set up the ImageNet challenge. The idea was to take a large collection of images and to ask a computer what was in the image. For the first few years, the computers were far worse than human beings. Then they got better and better. And better. Today, machines have long surpassed human beings to the point of making the challenge less irrelevant in the same way Deep Blue defeating Kasparov made computer Chess programs less exciting. It seems like the competition is closing down a last workshop: “The workshop will mark the last of the ImageNet Challenge competitions, and focus on unanswered questions and directions for the future.” I don’t think that the researchers imagined, back in 2010, that the competition would be so quickly defeated. Predicting the future is hard.

A new company, Egenesis wants to build genetically modified pig that can be used as organ donors for human beings. George Church from Harvard is behind the company.

Intel, the companies that make the microprocessors in your PCs, is creating an Artificial Intelligence group. Artificial Intelligence is quickly reaching peak hype. Greg Linden reacting to “TensorFlow [an AI library] is the new foundation for Computer Science”: “No. No, it’s not.” Currently, if you want to stop an incoming rocket or a drone, you have to use a missile of your own. That’s expensive. It looks like Lockheed Martin has a laser powerful enough to stop a rocket or a drone. In time, this should be much more cost effective. Want to protect an airport from rockets and drones? Deploy lasers around it. Next question: can you build drones that are impervious to lasers?

Andy Pavlo is a computer science professor who tries to have real-world impact. How do you do such a thing? From his blog:

(…) the best way to have the most impact (…) is to build a system that solves real-world problems for people.

Andy is right, of course, but what is amazing is that this should even be a question in the first place. Simply put: it is really hard to have an impact on the world by writing academic papers. Very hard.

There is a new planet in our solar system: “it is almost 10 times heavier than the Earth”. Maybe.

Western Digital sells 14TB disks, with helium. This is huge.

Netflix is moving from a rating system based on 5 stars to a thumbs-up, thumbs-down model.

In a New Scientist article, we learn about new research regarding the “rejuvenation of old blood”. It is believed that older people have too much of some factors in their blood, and it is believed that simply regularizing these levels would have rejuvenation effect. But, of course, it may also be the case that old blood is missing some “youthful factors” and that other tissues than the blood, such as the bone marrow, need them. This new research supports this view:

When Geiger’s team examined the bone marrow of mice, they found that older animals have much lower levels of a protein called osteopontin. To see if this protein has an effect on blood stem cells, the team injected stem cells into mice that lacked osteopontin and found that the cells rapidly aged.

But when older stem cells were mixed in a dish with osteopontin and a protein that activates it, they began to produce white blood cells just as young stem cells do. This suggests osteopontin makes stem cells behave more youthfully (EMBO Journal, doi.org/b4jp). “If we can translate this into a treatment, we can make old blood young again,” Geiger says.

Tech people often aggregate in specific locations, such as the Silicon Valley, where there are jobs, good universities, great experts and a lot of capital. This lead to rising cost of living and high real estate prices. Meanwhile, you can buy houses for next to nothing if you go elsewhere. It seems that the price differential keeps on rising. Will it go on forever? Tyler Cowen says that it won’t. He blames the high real estate prices on the fact that technology disproportionally benefits specific individuals. However, he says, technology invariably starts to benefit a wider share of the population, and when it does, real estate prices tend toward a fairer equilibrium.