Archive for the 'General Science' Category

Jul 23 2021

AI Advances Mapping of Human Proteome

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In 2003 the largest ever international cooperative scientific project was completed, at a cost of about $1 billion – the mapping of the human genome. This came with much fanfare, with the media hyping all the medical benefits that would soon flow. Of course, basic science progress often precedes clinical applications by decades, so the hype was not necessarily wrong, just premature. But it was an immediate boon to research, and those benefits are being felt today.

Perhaps the next big mapping project in biology is the human proteome, the characterization of every human protein. (I’ll also give a nod to the connectome project, the mapping of every connection in the human brain, but that will likely take much longer.) A new study published in Nature announces a significant leap forward in mapping the human proteome, using artificial intelligence (AI), specifically AlphaFold2 ┬ádeveloped by DeepMind. To understand what they accomplished, however, we need to go over some basic concepts and terminology.

A gene is essentially a code for a sequence of amino acids, which make up proteins. So if we have mapped the entire sequence of bases (of which there are four – GATC) in a gene, we know the sequence of amino acids in the protein it codes for. So then, you might ask, if we have already mapped all the human genes, why is that not the same thing as a map of all the human proteins? This is because a protein is more than just a sequence of amino acids. A short chain of 2 or more amino acids is called a peptide, and a long chain is therefore a polypeptide. But we still don’t have a protein. A protein is a polypeptide that folds itself into a specific three-dimensional structure. It is that three-dimensional structure which determined the function and properties of the protein.

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Jul 09 2021

The North American Heatwave

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It has become a mantra of climate scientists that global warming is just what it says – global. It is a statistical average over time. It cannot be tied to any specific weather event, even if it predicts that statistically such events are more likely. However, the current heat wave in the North American Northwest is so statistically extreme, that climate scientists are discussing it in very different terms. For example, the BBC reports:

Its initial calculations suggest the odds of the sort of temperatures experienced in Canada occurring without climate change are very low indeed, says Professor Stott.

“It is telling us that changes in average climate are leading to rapid escalation not just of extreme temperatures, but of extraordinarily extreme temperatures,” he adds.

It’s like that UFO meme – “We’re not saying it’s global warming, but it’s global warming.” They can still only make statistical statement, but the probability of such an extreme heat wave is vanishingly small without AGW. This was the hottest June on record in North America. It was the fourth hottest June on record for the world. According to NOAA, 2020 was the second hottest year globally on record, just behind 2016.

Remember, 10-20 years ago, when the global warming deniers were saying that we haven’t had any global warming since 1998? They did a little cherry picking and chose 1998 as a baseline because it was a peak in the short term fluctuations caused by El Nino. It created the illusion that the warming trend had stopped, but it was always nonsense. But they used that to predict that global warming had stopped, that it was always just part of the natural cycle, and was regressing to the mean. Nothing to see here.

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Jul 08 2021

Are Hydroponics Coming?

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I have been hearing about hydroponics – the growing of plants in water without the use of soil – for my whole life. Epcot showcased them decades ago as the farming of the future. Hydroponic farming exists. I can buy hydroponic lettuce at the supermarket. But despite the hype, it remains a small percentage of global agriculture. Hydroponics appears to be experiencing some rapid growth, however. In 2020 the global market was estimated to be $9.3 billion, and projected to almost double by 2026.

Modern hydroponics can be traced to botanist Julius von Sachs who in 1860 published the nutrient mixture necessary to add to water, demonstrating for the first time exactly which nutrients plants needed to grow. Since then several hydroponic systems have been developed and today modern hydroponics is very sophisticated, with precise nutritional and environmental control to optimize growing.

The potential advantages of hydroponics sound very impressive, with the only real downside is that startup costs can be high and overall price of produce is higher than conventional farming. The reason hydroponics remains niche is that it may not be as economically viable, but as systems improve this is changing. The other clear downside is that hydroponics uses much more energy. Conventional farming is mostly powered by the sun, where hydroponic farming relies heavily on grow lights. A 2015 estimate found that hydroponics used 11 times the energy of conventional farming. Here are the advantages:

Hydroponic farming allows for vertical farming, because it is not dependent on the soil. This allows for greater plant yield per unit of land, which is becoming farming’s most precious resource. Estimates of the land advantage depend on the crop and the height of the vertical farm, so there is no one figure, but it varies from several times to hundreds of times the yield of soil-based farming. Vertical hydroponic farms can be designed for optimal land use if desired, easily resulting in hundreds of times the yield of soil-based farming.

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Jun 25 2021

CRISPR-Act3.0

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Bonus points for anyone who has managed to commit to memory what the CRISPR acronym stands for – Clustered Regularly Interspaced Short Palindromic Repeats. I still have to look it up each time to make sure I get it right, but I’m getting there. I first wrote about CRISPR in 2015. It is a method of editing genes derived from bacteria. CRISPR itself is a means of targeting a specific sequence of DNA; you load it with the desired gene sequence and it will find the corresponding sequence in the DNA. Of course, it has to do something once it gets there, so CRISPR is also combined with a payload, such as Cas9, which are molecular scissors that will cut the DNA a the targeted location.

Since the potential for the CRISPR-Cas9 system in genetic engineering was realized, the technology has been on a steep climb of advancement. This was a new platform, one that had the advantage of being relatively quick, easy, and cheap. This means that genetics researchers round the world were all able to play with their new toy, and not only find uses for it but find ways to improve it. The basic technology slices DNA at a desired location. One limitation of this technology, as accurate as it is, there are still off-target effects. But researcher have already started to unpack how to make CRISPR slower but more accurate (vs faster but less accurate). They know how to dial in the accuracy, and it’s likely this aspect of the technology will improve further.

Also, once you make a slice in the DNA this can have a couple of effects. If all you want to do is kill the cell (like a cancer cell) you just make a bunch of slices and be done with it. If you want to inactivate a single gene your job may also be done. However, if you want to edit the gene then there is another step. You need to coax the cell into using its own repair mechanism to fix the break in the DNA while simultaneously inserting a new bit of DNA into the break. This is full gene editing, and while it’s still a bit tricky, it is much faster and cheaper than other methods.

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Apr 23 2021

A “Decisive Decade” for Climate Action

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After four years of backsliding on tackling climate change, it is good to see the US once again taking it seriously and trying to lead the world on climate action. Good intensions are necessary, but insufficient, however. The Biden Administration pledges a 50-52% decrease in CO2 emissions from 2005 levels by 2030. That sounds ambitious, and it is, but it is also not enough. It helps clarify how big the task is we have before us, but also how high the stakes are. Some recent studies also help clarify the picture.

First, a recent study yet again dispenses with the false dichotomy that dealing with climate change is about the environment vs the economy. Wrong. Climate change hurts the environment and the economy – so both of these concerns are in alignment. This study was done by a large insurance company (who are used to estimating risk and cost) and they concluded that climate change will cost the world economy $23 trillion in lost productivity by 2050 (compared to where we would be without climate change). Failing to tackle climate change is the costly option. Further, these costs will disproportionately affect poorer countries, increasing the wealth gap between rich and poor nations and likely causing political instability (not to mention a climate refugee crisis).

This does not even account for health care costs and lost productivity due to poor health from pollution. These costs are estimated to be hundreds of millions of dollars per year for the US and several billion worldwide.

Even if we just look at climate change through an economic lens, investing in clean energy is a no-brainer. Green technologies are the technologies of the future, and so it also makes sense for any country to invest in this industry to be competitive. Investing in these technologies would be a massive boost to our economy, with each dollar spent being returned many times over. Failure to do so is economic malpractice. Clinging to dirty 17th century technology is a loser’s strategy.

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Apr 13 2021

A CRISPR Genetic On-Off Switch

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Our knowledge of genetics and the tools to engineer or modify genetics continues to rapidly progress. The most celebrated recent advance was CRISPR (clustered regularly interspaced short palindromic repeats), a bacteria-derived system that can easily target any sequence of DNA using a guide RNA. CRISPR is like the targeting system and it can be paired with various payloads, most commonly Cas9, which is an enzyme that will cut both strands of DNA at the desired location. CRISPR was actually discovered in 1993, but the CRISPR-Cas9 system was first used for gene editing in 2013, an advance that won the Nobel prize in chemistry in 2020.

We are still, however, on the steep part of the learning curve with this powerful technology, and now researchers have published perhaps the greatest advance since 2013 – a way to use CRISPR as an on-off switch for genes. At the very least this will revolutionize genetic research. But it also has incredibly therapeutic potential, although other hurdles remain for applications in living organisms.

Using CRISPR-Cas9 for gene editing basically comes in two forms, knocking in genes or knocking out genes. Knocking out genes is by far the easier of the two. CRISPR targets the gene you want to silence, or knock out, and Cas9 will make a double strand cut in the DNA. The cells natural repair mechanism, called non-homologous end joining (NHEJ), the joins to the two cut ends together. This repair mechanism, however, is very imprecise and frequently introduces errors. Many of those errors will cause a shift in the genetic sequence that essentially ruins to code, effectively turning off the gene. This change is permanent, and will be carried to all later generations.

Knocking in a gene is more difficult. You not only have to make the cut at the desired location, you have to provide the genes sequence you want inserted and you need a different DNA repair mechanism called homology-directed repair (HDR), which is more precise and preserves the genetic sequence so that the gene remains active. But NHEJ is much more common than HDR, and so the trick is finding ways to enhance HDR repair so that a new gene can be successfully inserted at the repair site.

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Apr 08 2021

Possible New Force

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Physicists are all verklempt. Prof Ben Allanach, from Cambridge University said:

“This is the moment that I have been waiting for and I’m not getting a lot of sleep because I’m too excited.”

What could have scientists so excited? A muon that wobbled a little faster than it’s supposed to. In an experiment at the Fermi National Accelerator Laboratory (Fermilab) in Batavia, Illinois (the Muon g-2 experiment), physicists accelerated the subatomic particle muons and exposed them to a magnetic field. Muons are like electrons but 200 times heavier. They have a charge so should respond to a magnetic field by wobbling as they swing around the accelerator, and they did, but they did it a little faster than the standard model predicts they should. It was as if a force not contained within the standard model was acting on them. This experiment adds to another in Japan and yet another at the LHC also hinting at new physics. The statistical power of the Fermi results is at 4.1 sigma, or a 1 in 40,000 probability of being by chance alone. Five sigma (one chance in 3.5 million) is the threshold when the physics community accepts a claim as proven.

This is a big deal, perhaps even bigger than when the LHC confirmed the existence of the Higgs boson. That confirmed a prediction of the standard model, which is nice, but does not point the way to new physics. What physicists desperately want to do is break the standard model, to find some provable phenomenon that violates the standard model, which should lead to the discovery of a new particle or perhaps even a new force outside the current model. This is what would create the next great discovery in physics and perhaps solve some enduring mysteries, like what the hell is responsible for the acceleration of the expansion of the universe?

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Feb 19 2021

CRISPR-Edited Bananas

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In the British Drama, Years and Years, they imagine the very near future. I do wonder what someone from 2010 would have thought about a tv show accurately depicting 2020. In any case, one of the throw-away lines of the show was that there are no more bananas. The writers did their research – that the Cavendish banana will disappear sometime in the 2020’s is extremely likely. It is being threatened by a fungus called Tropical Race 4 (TR4), which a century ago wiped out the previous commercial dessert banana, the Gros Michel (it’s not extinct, but cannot be grown commercially anymore).

TR4 is now on every continent that grows bananas. It is literally just a matter of time before the entire commercial Cavendish market is wiped out. TR4 and similar funguses also threaten other banana varieties (more like plantains) that provide a staple source of nutrition for large segments of the world (about 400 million people). So this is not just about no longer having access to a favorite dessert fruit – this can create a serious threat to food security in parts of the world.

Part of the problem is that all Cavendish banana plants are clones. The plants are triploid hybrids, which is why they don’t produce seeds. This also makes them sterile. They are reproduced by taking new shoots that grow off the underground bulb (or corm). For this reason the entire Cavendish industry is basically comprised of clones. This is the ultimate monoculture – which leaves them particularly susceptible to disease, such as TR4.

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Dec 21 2020

2020 One of Hottest Years

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The year 2020 will be either the hottest year on record, or just behind the hottest year, 2016. The top 10 hottest years have all been from 1998 and later, with every year starting at 2013 being in the top 10. 2020 will now knock 1998 off the list, making the 10 warmest years all since 2005. The reason 1998 stuck on the list so long is because it was an outlier El Nino year, a weather pattern that tends to produce warmer weather. Next year, 2021, is likely to be a bit cooler because it is a La Nina weather pattern, which tend to be cooler. What does all this mean for the global warming debate?

First, it’s not much of a debate, at least not scientifically. There is a solid scientific consensus that average global temperatures are increasing, and that anthropogenic factors are mostly responsible for this forcing. Don’t believe the nonsense about there not being a consensus or that it is all based on one flawed paper – in fact, there is a consensus about the consensus. The debate is entirely cultural and political, not scientific. The evidence and the consensus are strong enough that any lay person who refuses to accept this scientific consensus is reasonably called a global warming denier.

The denier position is based on a number of logical fallacies and misleading arguments. They attack the very concept of a scientific consensus, and turn the technically true into a misleading point by saying that “science is never settled”. Well…yes, science is always open to revision by new data and new interpretations and theories. But that is not the point, making their argument a straw man. No one is talking about metaphysical certitude, or not being open to revising our climate models or projections with new data. Science, however, does not just exist in the abstract, sometimes we make important decisions based upon the current state of the science. The point is whether or not climate science is confident enough in its projections of global warming to use as a basis for policy. Saying that “science is never settled” is therefore a non sequitur. It is, in fact, a bit of deliberate misdirection.

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Dec 10 2020

The Decade of Climate Change

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Of course there are many important issues facing the world, but arguably drastically reducing carbon emissions is near the top of the list. The 2020s is likely to be a pivotal decade for this effort, and will have a dramatic and long lasting effect. The reason for this is that we are nearing the end of our “carbon budget” – the cumulative amount of carbon we can release into the environment without causing warming >1.5C above pre-industrial levels. We are very close to exhausting this budget, and in fact most experts have set their sights on 2C as the goal, believing it is already too late to keep global warming below 1.5C. Without a major effort in this decade, we will miss the more liberal 2C target, we will have exhausted our carbon budget, and it will no longer be possible to avoid serious consequences of global warming. In fact, it’s possible it would then be too lake to stop a cascade of events that will eventually lead to 5-6C of warming through triggering threshold positive feedback events. This may take hundreds of years to play out, but it still may be unavoidable at that point.

This is really the last decade we have to ensure a high probability of avoiding significant global warming by drastically reducing our carbon emissions. This means transforming our energy and transportation sectors into mostly carbon free technology. Industrial emissions will be harder, and require various technological advances, but any such advances there will help as well. This means, at the very least, we have to stop burning fossil fuel. This in turn means electric vehicles (with perhaps some role for hydrogen and biofuel), and an energy infrastructure built on renewable sources (wind, solar, geothermal, hydroelectric) and nuclear with some grid storage. All of this is achievable with current technology, and will reap benefits beyond climate change, such as reduced health care costs and deaths from pollution.

Often, those who push back against the suggestion that we need to make this change to our civilization a priority frame the choice before us as a false dichotomy – the climate vs the economy. More people will be harmed by the economic costs of decarbonization than will benefit from reducing carbon emissions, they claim. Often this strategy is coupled with denial of climate change itself, or unsupported assertions that climate change will not be so bad. They will often point to the most extreme predictions of climate change and argue that the entire field is “alarmist”.

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