Archive for the 'General Science' Category

Oct 19 2021

Net Zero by 2050

Published by under General Science

Next month the UN will host the 26th conference on climate change, the COP26. At this point the discussion is not so much what the goal should be, it’s how to achieve that goal. The Paris Accords set that goal at limiting global warming to 1.5 C above pre-industrial levels. In order to achieve this outcome goal the consensus is that we need to achieve the primary goal of net zero green house gas (GHG) emissions by 2050. There is considerable disagreement about whether or not net zero by 2050 will achieve the outcome goal of limiting warming to 1.5 C. Some experts think it’s already too late for 1.5 C, and we should be planning on at least 2.0 C and what the world will be like with that much warming.

Either way, there is agreement that we should focus instead on what we can actually do, achieve net zero by 2050, rather than the outcome which we cannot predict with that level of precision. If we agree on this goal, the conversation then shifts to the question of how we can achieve this goal. From one perspective the answer is easy – we need to stop burning fossil fuels, convert those industries with the greatest carbon footprint to produce less CO2, and add some carbon capture to compensate for whatever CO2 emissions we cannot fully get rid of. But that’s like saying – in order to win football games you need to score more points than the other team, mostly through touchdowns and field goals. That’s correct, but doesn’t really give you the information you need. How, exactly, will we achieve these ends?

This is the conversation we should have been focusing on for the last 20 years, rather than dealing with denialists who refuse to accept the scientific reality, or the delay tactics by industry and their paid representatives (i.e. politicians). It’s pretty clear at this point we are never going to convince the deniers (not in this political climate – and I’m sure the comments to this post will adequately demonstrate my point), and industry is going to run out the clock any way they can. The bottom line is that achieving net zero by 2050 will require leaving fossil fuels in the ground, unburned. For the fossil fuel industry this means leaving a lot of money on the table, which is not going to happen simply out of a desire to be good corporate citizens.

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Oct 12 2021

Making Proteins with Plant Molecular Farming

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As the world is contemplating ways to make its food production systems more efficient, productive, sustainable, and environmentally friendly, biotechnology is probably our best tool. I won’t argue it’s our only tool – there are many aspects of agriculture and they should all be leveraged to achieve our goals. I simply don’t think that we should take any tools off the table because of misguided philosophy, or worse, marketing narratives. The most pernicious such philosophy is the appeal to nature fallacy, where some arbitrary and vague sense of what is “natural” is used to argue (without or even against the evidence) that some options are better than others. We don’t really have this luxury anymore. We need to follow the science.

Essentially we should not fear genetic technology. Genetically modified and gene edited crops have proven to be entirely safe and can offer significant advantages in our quest for better agriculture. The technology has also proven useful in medicine and industry through the use of genetically modified microorganisms, like bacteria and yeast, for industrial scale production of certain proteins. Insulin is a great example, and is essential to modern treatment of diabetes. The cheese industry is mostly dependent on enzymes created with GMO organisms.

This, by the way, is often the “dirty little secret” of many legislative GMO initiatives. They usually include carve out exceptions for critical GMO applications. In Hawaii, perhaps the most anti-GMO state, their regulations exclude GMO papayas, because they saved the papaya industry from blight, and Hawaii apparently is not so dedicated to their anti-GMO bias that they would be willing to kill off a vital industry. Vermont passed the most aggressive GMO labeling law in the States, but made an exception for the cheese industry. These exceptions are good, but they show the hypocrisy in the anti-GMO crowd – “GMO’s are bad (except when we can’t live without them)”.

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Oct 05 2021

2021 Nobel Prize in Physics

Syukuro Manabe, Klaus Hasselmann, and Giorgio Parisi share this year’s Nobel Prize in Physics for their work increasing our understanding of how complex systems work. This is a powerful tool for understanding the world, which reminds me of previous advances in our understanding of how gases behave.

Gases are a phase of matter in which high energy particles are bouncing around at random. It would be impossible to predict the pathway of any individual gas molecule. However, collectively all of this random complexity follows very predictable laws. Similarly, weather is a very complex system. We can predict weather that is about to happen, but beyond a few days it becomes increasingly difficult. The system is simply too chaotic. However, climate (long term weather trends) follows theoretically predictable patterns. The trick is to see the hidden patterns in the chaos, and that is the work that these three physicists did.

Manabe and Hasselmann share half the prize for their work on climate models:

Syukuro Manabe demonstrated how increased levels of carbon dioxide in the atmosphere lead to increased temperatures at the surface of the Earth. In the 1960s, he led the development of physical models of the Earth’s climate and was the first person to explore the interaction between radiation balance and the vertical transport of air masses. His work laid the foundation for the development of current climate models.

About ten years later, Klaus Hasselmann created a model that links together weather and climate, thus answering the question of why climate models can be reliable despite weather being changeable and chaotic. He also developed methods for identifying specific signals, fingerprints, that both natural phenomena and human activities imprint in the climate. His methods have been used to prove that the increased temperature in the atmosphere is due to human emissions of carbon dioxide.

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Sep 27 2021

Footprints Are Oldest Evidence of Humans in North America

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The story of exactly how and when people from other continents populated the Americas is still unfolding. Scientists have uncovered stunning new evidence – score of human footprints in New Mexico dating to 21-23 thousand years ago, 5-7- thousand years older than the previous oldest evidence.

The evidence is pretty clear now that humans evolved in Africa and later spread throughout the world. We were not the first hominid species to leave Africa, that was Homo erectus, who spread to Europe and Asia about 1.8 million years ago. Meanwhile those that remained in Africa continued to evolve into other species, including Homo heidelbergensis, which is the current best candidate for the most recent common ancestor between modern humans and Neanderthals. Heidelbergensis also migrated out of Africa, and in Europe and Asia evolved into Neanderthals (who were well established by 400,000 years ago). Meanwhile their cousins back in the homeland evolved into modern humans.

Modern humans migrated out of Africa about 80,000 years ago, and spread throughout the world. Getting to Europe and Asia is easy, because they are all connected by land. Getting to the pacific islands was probably through a combination of land bridges during times of low ocean levels and traveling across water by some means, probably with short distance island hopping. The same is true of Australia, some combination of land bridges and island hopping.

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Aug 10 2021

IPCC 2021 Report on Climate Change

Published by under General Science

The Intergovernmental Panel on Climate Change (IPCC) has just produced their sixth report. This report builds on their previous work, and the current version (AR6) is the product of 234 scientists from around the world. This is essentially an update from their previous reports, taking into account all new evidence that has come to light. You can read the full report, or the executive summary for policymakers, or if you want more detail, the technical summary. Many news outlets, like the BBC, have also put out a highlight summary of their own.

I am not going to produce my own summary, just read the executive summary if you want the details. It’s only 39 pages. Instead, I am going to make some general observations.

First, for those who say there is no such thing as consensus in science, you are straight-up wrong. That is a strawman and denialist talking point. The strawman is the ubiquitous talking point that science is not determined by consensus. Of course it isn’t – consensus is determined by the science. The IPCC report is a great example of what consensus in science means – 234 experts pour over all the available evidence and then hash out a joint statement about what that evidence says. Next to each and every point there is a confidence notation, which they quantify – unlikely, likely, very likely, etc., with percentage confidence indicated for each notation. They are acknowledging the uncertainty, which torpedoes another strawman, equating consensus with certainty, or that the science is “settled” or that further research or debate is being shut down. This is all nonsense. The IPCC is simply a list of specific scientific statements, with a summary of the current evidence and degree of confidence.

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Aug 02 2021

Farming Microbes

Published by under General Science

In 1968 Paul Ehrlich wrote the controversial book, The Population Bomb, in which he argued that we had lost to battle to feed the world and would soon face massive starvation. He also argued that overpopulation was the number one threat to the environment. In a 2018 review, Smithsonian Magazine argues that Ehrlich’s book, in addition to being clearly wrong in its predictions, had a large effect on the environmental movement itself, moving it toward believing that overpopulation was their most urgent issue. This in turn also lead to a host of repressive and abusive policies around the world, especially toward women.

Even today, whenever I blog about related issues such as organic farming, it is common for someone in the comments to essentially argue that we need to allow millions or billions of people to starve to death in order to control population, which is the single most important thing. The “overpopulation purists” are following in Ehrlich’s legacy.

Ehrlich, however, was completely wrong in his predictions because he missed the green revolution, the remarkable ability for technology to be leveraged to increase the productivity of an acre of farmland several fold. We are now facing a similar situation, with scientists warning that the world population will likely increase to about 10 billion people by sometime around 2050. Yet, we are already exploiting most of the available arable land, so simply expanding farmland is not a great option. Any further expansion will extend into progressively less productive land, or into forests or occupied land. Further, land use is the greatest impact that farming, and in fact humans, have on the environment. If anything we should be looking for ways to return land to a natural ecosystem, in order to minimize extinctions due to loss of habitat.

Just because I disagree strongly with the overall position of the overpopulation purists, that doesn’t mean they don’t have somewhat of a point. It is probably a good idea to stabilize the human population on the Earth at some point. Fortunately, we know from experience how to do this – when we lift people out of crushing poverty and grant basic rights to women, then populations stabilize (without having to starve anyone). These are things we should be doing anyway, and we have an extra incentive to do so.

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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  developed 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

Published by under General Science

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

Published by under General Science

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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