The future did not seem to work!

When I started my career in chemistry as an undergraduate, chemists were an optimistic bunch, and everyone supported this view. Eventually, so it was felt, chemists would provide a substance to do just about anything people wanted, provided the laws of physics and chemistry permitted it. Thus something that was repelled by gravity was out, but a surprising lot was in. There was a shortage of chemists, and good paying jobs were guaranteed.

By the time I had finished my PhD, governments and businesses everywhere decided they had enough chemists for the time being thank you. The exciting future could be put on hold. For the time being, let us all stick to what we have. Of course there were still jobs; they were just an awfully lot harder to find. The golden days for jobs were over; as it happened, that was not the only thing that was over. In some people’s eyes, chemicals were about to become national villains.

There was an element of unthinking optimism from some. I recall in one of my undergraduate lectures where the structure of penicillin was discussed. Penicillin is a member of a class of chemicals called beta lactams, and the question of bacterial tolerance was discussed. The structure of penicillin is (https://en.wikipedia.org/wiki/Penicillin) where R defines the carboxylic acid to that amide. The answer to bacterial tolerance was simple: there is almost an infinite number of possible carboxylic acids (the variation is changing R) so chemists could always be a step ahead of the bugs. You might notice a flaw in that argument. Suppose the enzymes of the bug attacked the lactam end of the molecule and ignored the carboxylic acid amide? Yes, when bacteria learned to do that, the effectiveness of all penicillins disappears. Fortunately for us, this seems to be a more difficult achievement, and penicillins still have their uses.

The next question is, why did this happen? The answer is simple: stupidity. People stopped restricting the use to countering important infections. They started to be available “over the counter” in some places, and they were used intermittently by some, or as prophylactics by others. Not using the full course meant that some bacteria were not eliminated, and since they were the most resistant ones, thanks to evolution when they entered the environment, they conveyed some of the resistance. This was made worse by agricultural use where low levels were used to promote growth. If that was not a recipe to breed resistance, what was?

The next “disaster” to happen was the recognition of ozone depletion, caused by the presence of chlorofluorocarbons, which on photolysis in the upper atmosphere created free radicals that destroyed ozone. The chlorofluorocarbons arose from spray cans, essential for hair spray and graffiti. This problem appears to have been successfully solved, not by banning spray cans, not by requesting restraint from users, but rather by replacing the chlorofluorocarbons with hydrocarbon propellant.

One problem we have not addressed, despite the fact that everyone knows it is there, is rubbish in the environment. What inspired this post was the announcement that rubbish has been found in the bottom of the Marianna trench. Hardly surprising; heavy things sink. But some also floats. The amounts of waste plastic in the oceans is simply horrendous, and only too much of it is killing fish and sea mammals. What starts off as a useful idea can end up generating a nightmare if people do not treat it properly. One example that might happen comes from a news report this week: a new type of plastic bottle has been developed that is extremely slippery, and hence you can more easily get out the last bit of ketchup. Now, how will this be recycled? I once developed a reasonably sophisticated process for recycling plastics, and the major nightmare is the multi-layered plastics with hopelessly incompatible properties. This material has at least three different components, and at least one of them appears to be just about totally incompatible with everything else, which is where the special slipperiness comes from. So, what will happen to all these bottles?

Then last problem to be listed here is climate change. The problem is that some of the more important people, such as some politicians, do not believe in it sufficiently to do anything about it. The last thing a politician wants to do is irritate those who fund his election campaign. Accordingly, that problem may be insoluble in practice.

The common problem here is that things tend to get used without thinking of the consequences of what is likely to happen. Where things have gone wrong is people. The potential failure of antibiotics is simply due to greed from the agricultural sector; there was no need for its use as a growth promoter when the downside is the return of bacterial dominance. The filling of the oceans with plastic bags is just sloth. Yes, the bag is useful, but the bag does not have to end in the sea. Climate change is a bit more difficult, but again people are the problem, this time in voting for politicians that announce they don’t believe in it. If everybody agreed not to vote for anyone who refused to take action, I bet there would be action. But people don’t want to do that, because action will involve increased taxes and a requirement to be better citizens.

Which raises the question, do we need more science? In the most recent edition of Nature there was an interesting comment: people pay taxes for one of two reasons, namely they feel extremely generous and want to good in the world, or alternatively, they pay them because they will go to jail if they don’t. This was followed by the comment to scientists: do you feel your work is so important someone should be thrown into jail if they don’t fund it? That puts things into perspective, doesn’t it? What about adding if they question who the discovery will benefit.

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Cancer: the problem.

I read an interesting blog recently entitled “The War on Cancer” (http://sten.astronomycafe.net/the-war-on-cancer/). Apparently, in the US a little under 600,000 people die of it each year. The author, Dr Sten Odenwald, then set out to illustrate that funding for cancer research is far too low. I think it was President Nixon who coined the phrase, “war on cancer”, and set it as an objective, in the same way Kennedy had set the Moon landing as an objective, but this was doomed to fail, at least in the spectacular way. The reason is the nature of cancer, which, as an aside, is not one disease. We have been trying to cure this for a very long time, but with mixed results. Gaius Plinius Secundus recommended a poultice of broccoli for breast cancer, and asserted it works. There are indeed agents in broccoli that will deal with some breast cancers, but by no means all, and even then, the cancer would need to be near the surface. There are at least twenty different types of breast cancer. Drugs like tamoxifen stop the growth of at least one type, monoclonal antibodies help in some others. So we have made some progress, but there are still severe problems, especially if the tumour metastasizes (dislodges cells to other parts of the body).

It is the nature of cancer that is the problem. Cells grow around nucleic acid, and nucleic acids reproduce by base pairing, then splitting, each strand now being the frame for the production of more nucleic acid. Thus after splitting, when a new double helix is finished being assembled, the amount of nucleic acid has doubled, so a new pair of cells is possible, the old cell having been destroyed. So what can go wrong? You will usually read that copying is not correct, or something is added to the double helix, but I don’t believe that. It is the peculiar nature of the hydrogen bonding that either the correct nucleic acid goes onto the growing strand or nothing does. That is why reproduction is so accurate. In the double helix, the reactive sites are protected, as they are in the interior of the helix, and the outside is the phosphate. A further substitution on the phosphate to make a tri-ester would be a nuisance, but it would not be very stable, and it would repair itself. Further, it would require a highly reactive reagent to do this, as it is exceedingly difficult to make phosphate esters in cold water other than through enzymatic catalysis. No, I think the problem probably arises during the splitting stage when the reactive sites become exposed. If something happens to the nitrogen functions, then that will block the formation of the next double helix at that point.

At that stage, the body will attack the nucleic acid at that point, and the next usual outcome will be that the various parts of the strand will be degraded, and the bits reused or excreted. But if the problem occurred in certain places, it may be that what is left can start reproducing. If that happens you have something growing that has no function for you, BUT it looks like it is part of your body, because up to a point it is. The growth just keeps growing, and reproducing itself. The reason there are so many different cancers is there are so many places where a nucleic acid could go wrong, and each different place that can reproduce will lead to a growth that is slightly different from any others. Because it looks like part of your body, your natural defences ignore it.

So far, we have largely relied on surgery, radiation or drugs. So, how is progress? In some cases, such as leukemia, progress is good, and it is often curable. In other cases, life can be extended, but according to Wikipedia, since Nixon declared war on cancer, the US alone has spent $200 billion on research. Between 1950 and 2005, the death rate, adjusted for population size and age has declined by five per cent. On the other hand, while in remission many patients have had life extended.

However, we should ask, are we doing anything wrong? I think we are, and one problem relates to intellectual property rights. Here is an example of what I mean. In the 1980s I was involved in a project to extract an active material from a marine sponge. My company developed some scale-up technology and made a few grams of this material, which, from reports I received, if the odd microgram was introduced to a solid tumour, the tumour blistered and died, leaving a well-repaired skin outside wherever the organ was. This property was limited to studies on rats, probably with external carcinoma. Anyway, the company that hired us ran into difficulty with its source of funds and went bankrupt, however, somehow ownership of the intellectual property lived on. At the time, there was no known technique of introducing a material as reactive as this to internal tumours, nor did we know whether that would even be beneficial. Essentially, the project was in an early stage, and maybe the material would not be beneficial. Who knows? The problem is, now we don’t know and nobody is likely to work further because the patents have expired. Any company working on that will have all the expense, and then somebody else can come in and take the benefits. In my opinion, this is not a desirable outcome. We should not have a situation where promising knowledge simply gets lost because of formal procedure.

Equally, we should not have the situation where drugs become ridiculously expensive. Why should the unfortunates who get a rather rare cancer have to pay the huge prices of drug companies? I am not saying drug companies should not get a fair return, but I think society should pay for this. Think of it as compulsory insurance. The alternative is a family might have to decide whether to bankrupt themselves, kill the grandchildren’s education prospects to buy a year or so for grandmother, or whether to just let her die. What sort of society is it that allows this?

Cancer is one of those diseases that everybody comes into contact with one way or another. In my case, my father died of pancreatic cancer, and I am a widower because of cancer. Yes, these things happen, but isn’t it in everybody’s interest to try and do what we can to at least minimize the harsh effects?

Evidence that the Standard Theory of Planetary Formation is Wrong.

Every now and again, something happens that makes you feel both good and depressed at the same time. For me it was last week, when I looked up the then latest edition of Nature. There were two papers (Nature, vol 541 (Dauphas, pp 521 – 524; Fischer-Gödde and Kleine, pp 525 – 527) that falsified two of the most important propositions in the standard theory of planetary formation. What we actually know is that stars accrete from a disk of gas and dust, the disk lingers on for between a million years and 30 million years, depending on the star, then the star’s solar winds clear out the dust and gas. Somewhere in there, planets form. We can see evidence of gas giants growing, where the gas is falling into the giant planet, but the process by which smaller planets or the cores of giants form is unobservable because the bodies are too small, and the dust too opaque. Accordingly, we can only form theories to fill in the intermediate process. The standard theory, also called oligarchic growth, explains planetary formation in terms of dust accreting to planetesimals by some unknown mechanism, then these collide to form embryos, which in turn formed oligarchs or protoplanets (Mars sized objects) and these collided to form planets. If this happened, they would do a lot of bouncing around and everything would get well-mixed. Standard computer simulations argue that Earth would have formed from a distribution of matter from further out than Mars to inside Mercury’s orbit. Earth the gets its water from a “late veneer” from carbonaceous chondrites from the far side of the asteroid belt.

It is also well known that certain elements in bodies in the solar system have isotopes that vary their ratio depending on the distance from the star. Thus meteorites from Mars have different isotope ratios from meteorites from the asteroid belt, and again both are different from rocks from Earth and Moon. The cause of this isotope difference is unclear, but it is an established fact. This is where those two papers come in.

Dauphas showed that Earth accreted from a reasonably narrow zone throughout its entire accretion time. Furthermore, that zone was the same as that which formed enstatite chondrites, which appear to have originated from a region that was much hotter than the material that, say, formed Mars. Thus enstatite chondrites are reduced. What that means is that their chemistry was such that there was less oxygen. Mars has only a small iron core, and most of its iron is as iron oxide. Enstatite chondrites have free iron as iron, and, of course, Earth has a very large iron core. Enstatite chondrites also contain silicates with less magnesium, which will occur when the temperatures were too hot to crystallize out forsterite. (Forsterite melts at 1890 degrees C, but it will also dissolve to some extent in silica melts at lower temperatures.) Enstatite chondrites also are amongst the driest, so they did not provide Earth’s water.

Fischer-Gödde and Kleine showed that most of Earth’s water did not come from carbonaceous chondrites, the reason being, if it did, the non-water part would have added about 5% to the mass of Earth, and the last 5% is supposed to be from where the bulk of elements that dissolve in hot iron would have come from. The amounts arriving earlier would have dissolved in the iron and gone to the core. One of those elements is ruthenium, and the isotope ratios of Earth’s ruthenium rule out an origin from the asteroid belt.

Accordingly, this evidence rules out oligarchic growth. There used to be an alternative theory of planetary accretion called monarchic growth, but this was soon abandoned because it cannot explain first why we have the number of planets we have where they are, and second where our water came from. Calculations show it is possible to have three to five planets in stable orbit between Earth and Mars, assuming none are larger than Earth, and more out to the asteroid belt. But they are not there, so the question is, if planets only grow from a narrow zone, why are these zones empty?

This is where I felt good. A few years ago I published an ebook called “Planetary Formation and Biogenesis” and it required monarchic growth. It also required the planets in our solar system to be roughly where they are, at least until they get big enough to play gravitational billiards. The mechanism is that the planets accreted in zones where the chemistry of the matter permitted accretion, and that in turn was temperature dependent, so specific sorts of planets form in zones at specific distances from the star. Earth formed by accretion of rocks formed during the hot stage, and being in a zone near that which formed enstatite chondrites, the iron was present as a metal, which is why Earth has an iron core. The reason Earth has so much water is that accretion occurred from rocks that had been heat treated to about 1550 degrees Centigrade, in which case certain aluminosilicates phase separated out. These, when they take up water, form cement that binds other rocks to form a concrete. As far as I am aware, my theory is the only current one that requires these results.

So, why do I feel depressed? My ebook contained a review of over 600 references from journals until a few months before the ebook was published. The problem is, these references, if properly analysed, provided papers with plenty of evidence that these two standard theories were wrong, but each of the papers’ conclusions were ignored. In particular, there was a more convincing paper back in 2002 (Drake and Righter, Nature 416: 39-44) that came to exactly the same conclusions. As an example, to eliminate carbonaceous chondrites as the source of water, instead of ruthenium isotopes, it used osmium isotopes and other compositional data, but you see the point. So why was this earlier work ignored? I firmly believe that scientists prefer to ignore evidence that falsifies their cherished beliefs rather than change their minds. What I find worse is that neither of these papers cited the Drake and Righter paper. Either they did not want to admit they were confirming a previous conclusion, or they were not interested in looking thoroughly at past work other than that which supported their procedures.

So, I doubt these two papers will change much either. I might be wrong, but I am not holding my breath waiting for someone with enough prestige to come out and say enough to change the paradigm.

Trump and Climate Change

In his first week in office, President Trump has overturned President Obama’s stopping of two pipelines and has indicated a strong preference for further oil drilling. He has also denied that climate change is real. For me, this raises two issues. The first is, will President Trump’s denial of climate change, and his refusal to take action, make much difference to climate change? In my opinion, not in the usual sense, where everybody is calling for restraint on carbon dioxide emissions. The problem is sufficiently big that this will make only a minor difference. The action is a bit like the Captain of the Titanic finding two passengers had brought life jackets so he confiscates them and throws them overboard. The required action was to steer away from a field of icebergs, and the belief the ship was unsinkable was just plain ignorant, and in my opinion, the denial that we have to do something reasonably dramatic about climate change falls into the same category. The second issue is how does science work, and why is it so difficult to get the problem across? I am afraid the answer to this goes back to the education system, which does not explain science at all well. The problem with science for most people is that nature cares not a jot for what you feel. The net result is that opinions and feelings are ultimately irrelevant. You can deny all you like, but that will not change the consequences.

Science tries to put numbers to things, and it tries to locate critical findings, which are when the numbers show that alternative propsitions are wrong. It may be that only one observation is critical. Thus Newtonian mechanics was effectively replaced by Einstein’s relativity because it alone allowed the calculation of the orbital characteristics of Mercury. (Some might say Eddington’s observation of light bending around the sun during an eclipse, but Newton predicted that too. Einstein correctly predicted the bending would be twice that of Newton, but I think Newton’s prediction could be patched given Maxwell’s electrodynamics. For Newton’s theory, Mercury’s orbit was impossible to patch.)

So what about climate change? The key here is to find something with the fewest complicating factors, and that was done when Lyman et al. (Nature 465: 334-337, 2010) measured the power flows across ocean surfaces, and found there was a net input of approximately 0.6 W/m². That is every square meter gets a net input of 0.6 Joules per second, averaged over the 24 hr period. Now this will obviously be approximate because they did not measure every square meter of ocean, but the significance is clear. The total input from the star is about 1300 W/m² at noon, so when you allow for night, the fact that it falls away significantly as we get reasonably away from noon, and there are cloudy days, you will see that the heat retained is a non-trivial fraction of the input.

Let us see what that means for the net input. Over a year it becomes a little under 19 MJ for our square meter, and over the oceans, I make it about 6.8 x 10²¹ J. There is plenty of room for error there (hopefully not my arithmetic) but that is not the point. The planet is a big place, and that is really a lot of energy: about a million million times 1.6 tonnes of TNT.

That has been going on every year this century, and here is the problem: that net heat input will continue, even if we totally stopped burning carbon tomorrow, and the effects would gradually decay as the carbon we have burnt gradually weathers away. It would take over 300 years to return to where we were at the end of the 19th century. That indicates the size of the physical problem. The fact that so many people can deny a problem exists, with no better evidence than, “I don’t believe it,” is our current curse. The next problem is that just slowing down the production of CO₂, and other greenhouse gases, is not going to solve it. This is a problem that has crept up on us because a planet is a rather large object. It has taken a long time for humanity’s efforts to make a significant increase to the world’s temperatures, but equally it will take a long time to stop the increase from continuing. Worse, one of the reasons the temperature increases have been modest is that a lot of this excess heat has gone into melting ice. Eight units of water at ten degrees centigrade will melt one unit of ice, and we end up with nine units of water at nought degrees Centigrade. The ice on the planet is a great restraint on temperature increases, but once the ice in contact with water has melted, temperatures may surge. If we want to retain our current environment and sea levels, we have some serious work to do, and denying the problem exists is a bad start.