Science

Covid and Smoking

A paper was published in April 2020 on the open science platform, Qeios. The topic was the potential benefit of tobacco smoking to protect against Covid-19.

The conclusions in the article were based on data from observational studies and not randomised clinical trials. We have already discovered issues which arise from observational studies, collider bias being one of them.

Collider bias happens when two variables, e.g., risk factor and outcome, influence a third, namely, the likelihood of being sampled. In our case, the sampling occurred on or before April 2020, in the earlier part of the pandemic. As you may recall, testing was in the developing stages, and the focus was on front-line health workers and patients with severe symptoms. In technical terms, the sample was not random or representative.

Therefore, the data space has narrowed down to health workers, and within those, there are smokers and non-smokers. As a consequence of the testing strategy, the survey censored out the smokers who had no symptoms. And this exaggerated proportion of non-smokers who had symptoms in the sample.

References

Low incidence of daily active tobacco smoking in patients with symptomatic COVID-19: Qeios, CC-BY 4.0 · Article, April 21, 2020

Collider bias undermines our understanding of COVID-19 disease risk and severity: Nature Communications, 2020, 11:5749

Randomised Controlled Trials: BMJ

Covid and Smoking Read More »

LCA of carrier Bags

I’m sure this has bothered most of us at some point. It is about the use of plastic bags. Plastic consumption and its environmental effect due to poor biodegradability frequently come under the public discourse. And here is an interesting research report based on the Life Cycle Analysis (LCA) of a few commonly used carrier bags in the UK, published by the Environment Agency (2011).

LCA is a standard methodology to estimate the material, energy usage, and environmental impact throughout a product’s lifecycle (‘cradle to grave’). The study covered only the carriers available from the UK. The material in focus was conventional HDPE, HDPE with pro-degradant additive, starch-polyester (biopolymer), paper, heavy-duty LDPE, non-woven PP and cotton bag.

The end-of-life processes for the different materials included landfill and incineration (for all) and mechanical recycling and composting, where applicable.

The following table contains the energy use and waste generation from 1000 bags of each material.

Bag TypeElectricity
(kWh)		Heat
(from
NG)
(kWh)		Heat
(from
Fuel oil)
(kWh)		Waste
(g)
Conventional HDPE6.151418.4
HDPE + additive6.392426.1
biopolymer17.2494.8
LDPE32.5813.953171.2
Non-woven PP87.755,850
Cotton111,800

The study assumed the reuse of about 40% of all lightweight carrier bags as bin liners.

The next one up was the global warming potential. GWP (excluding primary reuse) for the cotton bag (250 kg CO2 eq.) was more than ten times that of any other bag! It was followed by PP (22), LDPE (7), paper (6), biopolymer (5), HDPE (2.1) with additive and HDPE (2), in descending order. In other words, a cotton bag requires to be used 173 times to match HDPE and PP 14 times.

Here is a summary:

Bag typeSensitivityGWP
(kg CO2 eq)
HDPEBaseline1.578
HDPERecycling1.400
HDPERecycling
(no reuse)		1.785
HDPE
prodegradant		Baseline1.750
biopolymer Baseline4.184
biopolymer Composting2.895
biopolymer Composting
(no reuse)		3.329
Paper bag
(4 uses)		Baseline1.381
Paper bag
(4 uses)		Recycling1.090
Paper bag
(4 uses)		Composting1.256
LDPE
(5 uses)		Baseline1.385
LDPE
(5 uses)		100%
Recycling		1.196
PP
(14 uses)		Baseline1.536
PP
(14 uses)		100%
Recycling		1.292
Cotton bag
(172 uses)		Baseline1.579

To conclude

HDPE bags have the lowest environmental impact among lightweight bags on 8 out of 9 counts.
The starch-polyester (biopolymer) bag has the highest impact in 7 out of 9.
The paper bag needs to be used four times to match HDPE’s global warming potential.
The cotton bag has a greater impact than the HDPE bag in 7 out of 9 categories, even when used 173 times.
The key to reducing the impact is to reuse as much as possible.

Reference

Life cycle assessment of supermarket carrier bags: a review of the bags available in 2006

LCA of carrier Bags Read More »

The Trouble with Evolution

With millions of pieces of evidence, the theory of evolution is as factual as, say, Newton’s laws of motion! Yet, how it’s taught in schools requires a reexamination before it can achieve its intended goals of education. Some items need attention before introducing the subject to the interested parties.

Lamarck’s theory

The theory that says evolution is the adaptation of organisms to their environment has only historical relevance. It is not how evolution works. People are stuck to Lamarck’s theory, partly because it was taught before Darwin’s and also because it fits our fantasy of conversion and purpose. We will address these two terms soon. To repeat: individual organisms don’t evolve or pass their aspirations to offspring through genes.

Metaphors taken literally

We already know that nature doesn’t select anybody. Also, physical strength and superiority have nothing to do with the survival probability of a species. Yet, we carry the burden of natural selection and survival of the fittest in their literal meaning. These terms are strictly metaphors to communicate, perhaps wrong choices from people who lived a hundred years ago!

Another common feature in science communication is to say genes want to copy and spread. It creates a false notion of purpose in listeners’ minds. Again, a gene has no brain to decide anything, unlike humans, who are involved in designing artefacts for their use. You know, this purpose is not that purpose!

It goes in branches

This one came from a cartoonist – the money to the man. It is not a conversion process that works linearly. Once a species passes the baton, it doesn’t exit the scene. Evolution steps are random branching processes. So monkeys may survive, and so do apes or the great apes. Some may perish as well.

In summary

The features we see in today’s organisms are not part of any plans for perfection but simply a collection of clues about our past.

The Trouble with Evolution Read More »

Darwin’s moth for Darwin’s Orchid

Remember the story of Tiktaalik, the missing piece in the evolution that connected fishes and four-legged animals? Here is another equally exciting example. And how Darwin predicted the existence of a species after seeing a flower!

In 1862, Charles Darwin received a box of orchids from a well-known grower of his time. Among them was Angraecum Sesquipedale. Check the link to see how it appears. Look at the long spur or nectary, the nectar-secreting organ in the flower. Seeing the extraordinarily long nectary, Darwin wondered about the existence of moths with long tongues. As nectar-liking moths are crucial agents for pollination, such an orchid would not have evolved without the help of a moth with fitting organs.

In 1907, years after Darwin’s death in 1892, the culprit was found – Xanthopan Morganii Praedicta, from Madagascar!

To conclude this story, in the 1990s, biologists made direct observations of the meeting of the two. See the cover page of the Botanica Acta of 1997.

Reference

Arditti et al., ‘Good Heavens what insect can suck it’– Charles Darwin, Angraecum sesquipedale and Xanthopan morganii praedicta, Botanical Journal of the Linnean Society, 2012, 169, 403–432.

Darwin’s moth for Darwin’s Orchid Read More »

Drake Equation – The Probability of ET

If you recall, we had used the concept of joint probability to explain the swiss cheese models of viral infection. That the probability of someone getting infected by a virus is a joint probability of several independent events.

In 1961, Frank Drake made the following equation to invoke some thoughts on estimating the probability of life outside earth.

N = R* x fp x ne x fl x fi x fc x L

  • N: number of civilisations in the galaxy with which communication might be possible
  • R*: average rate of star formation in the galaxy
  • fraction of those stars having planets
  • fraction of those planets that could support life per star
  • fraction of those that could go on to make intelligent life
  • fraction of that civilisation that could develop technologies
  • the length of time they could release detectable signals into space

Choice of parameters

The choice of the parameters is the difficult part and what invited criticisms of the equation.

Drake Equation – The Probability of ET Read More »

Evolution vs Conversion

Misconceptions about evolution exist due to humans’ inability to comprehend the enormousness of time. That leads to common misconceptions such as, “I haven’t seen a monkey giving birth to a human”, “if humans evolved from monkeys, why do monkeys still exist?” etc.

Firstly, monkeys did not evolve into humans. In the evolution tree (remember: it’s a tree and not a line), monkeys are not our ancestors; they are cousins. In other words, the common ancestors of monkeys and humans (apes) existed about 30 million years ago. The monkeys we see today had a trajectory from that time to the present, just like their distant cousin, humans, in that period.

The same goes for chimpanzees and humans. Chimpanzees are our closest cousins, and that branch goes back 5-7 million years ago. A rough sketch of the branching business is shown below.

Understanding Evolutionary Trees: Evo Edu Outreach (2008) 1:121–137

Evolution vs Conversion Read More »

Salamander Reporposed!

Salamanders are fascinating creatures that have drawn plenty of spotlight from biologists due to their significant position in our evolutionary path. These are amphibians, and it was no coincidence that they drew attention, as a missing piece between creatures of water and that of land, from scientists in the 19th century, inspired by the recent theory of evolution.

In one such pursuit, what the famous zoologist and the Professor at the Museum of Natural History in Paris, Auguste Dumeril, found provides a live example of the wonders of repurposing animal functions.

In 1864, Dumeril received six salamanders from a lake in Mexico. They were large adults with feathery gills and aquatic body shapes characteristic of life in water. He kept them together and even had them produce fertilised eggs. The children that came out of the cage shocked the researcher; they showed little resemblance to their parents. No gills and aquatic tail; they appeared like the terrestrial variety.

It was found out much later that there are two pathways of development for the salamander larvae, according to the surrounding environment. The salamander in the aquatic habitat goes through the default pathway, but the one on land undergoes this metamorphosis. We now know the change gets triggered by the amount of thyroid hormone in the bloodstream that activates or kills some cells. Same gene, same creature but a change of environment yielding dramatic change in the appearance of the end product!

Reference

Some assembly required: Neil Shubin

Salamander Reporposed! Read More »

Common Sense Continued

The not-so-hidden secret is that biological innovations never come about during the great transition they are associated with.

Neil Shubin, Some Assembly Required

Another case of common sense is the theory of evolution.

Theorem of evolution

While it is no more topic of debate, thanks to millions of data collected in the last one hundred odd years, the concept of evolution has confused the generations since the day it was proposed.

Evolution of common sense

The first one was the remnants of Lamarckian thinking that essentially assumes that evolution is what an organism aspires and achieves, in its lifetime, to adapt to its environment. For example, a giraffe, in pursuit of high-lying leaves, stretches its neck so much that its child gets her neck a little longer than her mother, and it continues.

The other group is less dramatic with their approach, though commonsensical. Feather occurred to birds because it enabled the birds to fly, which helped them to survive in that environment. Similarly, lungs and limbs happened just about when the water-living creatures prepared to come out to the land.

More and more pieces of evidence proved that this understanding is wrong. The features such as the lungs or the wings were part of predecessor creatures ages before they transformed into their next level. For example, fishes of all species had swim bladders that enabled them to navigate different depths in the water. As genetic studies have later found, the genes responsible for these air sacs are the same that propelled the development of lungs. In other words, when the fish’s successor came to land, it just repurposed the swim bladder for breathing.

Inventions to products

A closer analogy is the example of green hydrogen as a vector of decarbonised energy. Hydrogen production through water electrolysis using renewable electricity such as solar PV is considered a commercial-ready option for a carbon-free energy future. To anybody who followed the history of science, electrolysis is by no means a new technology.

Alkaline water electrolysis technology is more than 120 years old. It has been serving the niche market of caustic and chlorine until now.

Similar story for solar PV. Bell Labs announced a solar battery in 1954 that could produce electricity whenever a thin slice of silicon was contacted by sunlight, being celebrated as a miracle device by the leading newspapers of that time. At the time of its invention, it was so expensive that Bell Labs calculated a cost of $1.5m to power one home using their technology!

But nothing happened for another 65 years!

Repurposing under societal pressure

This chemistry of evolution, where the ingredients were made in the distant past, but mixing happens only today, has confused people and led to creating two bands of commentators. The first group, the Vaclav Smil-type, develops some allergy to “high-tech worshippers” and claims whatever happens today was a result of the 1880s. The second group are mesmerised by the speed at which discoveries are happening right in front of their eyes. Both got carried away by the chemistry of evolution.

Common Sense Continued Read More »

Climate Change and Common Sense

To all the people in the northern hemisphere who are currently reeling under extreme heat waves: your assessment of global warming is correct, but not for the reasons you think you are seeing.

Common sense is a general intelligence that enables a person to manage concrete everyday situations. It is common sense to switch the power off before removing a bulb from its holder. Wearing a protective glove before touching the metal pot on the kitchen hob is another.

In a survey conducted in Australia between 2010-14, 22% of the respondents thought climate change was not happening. When specifically asked about what their opinions are based on, about 37% of them attributed to common sense. It might sound absurd that about 20% of the people who believed in human-induced climate change also attributed their belief to common sense. And the views of both parties are not surprising. Phenomena such as global warming are understood only through the laborious examination of scientific data from hundreds of sources through the lens of mathematical models. And there is nothing commonsensical about it!

The offspring of hindsight

It is a fact that some of the lessons learned from science can later become part of the common sense knowledge in everyday life. But trusting that the opposite is also true is dangerous. We have seen multiple examples of logical fallacies previously. Availability bias is one of them. For a climate sceptic, the last year’s winter might be the guiding principle, whereas, for a climate believer, it’s the heat wave of this summer. One can prove either of these as instances of random events, even when the number of hard facts on climate change is irrefutable.

Overdependence on experience

Common sense is primarily a manifestation of personal experience; science, on the other hand, is a rational, evidence-based approach that operates through the collaborative actions of hundreds of trained minds. While individual scientists are fallible mortals with cognitive biases and beliefs, the rigour of methodology – validation and falsification – known as the scientific method, by its community elevates science from those shortcomings.

Climate Change and Common Sense Read More »

Randomness and Doctrine of Signature

Take a carrot, cut a slice, and look closely. Does it resemble your eyes? See what I meant; it provides the nutrient that is good for the eyes. Have you ever wondered why the tomatoes cut through the middle appear like your heart? Do you know that the polyunsaturated fats of walnut boost your brain? Don’t you know kidney beans are the best thing for your kidney?

The seed for the brain

Start with Mr Walnut. Here is what it looks like:

walnut, nut, shell-3072652.jpg

So naturally, it should be related to the brain. Isn’t it? Well, let me search: yes, it has polyunsaturated fats that are good for the brain! Well, that can also be good for the heart. But that is not the point. And it does not resemble my heart. What about sunflower seeds, flax seeds or flax oil, and fish, such as salmon, mackerel, herring, albacore tuna, trout, corn oil, soybean oil, and safflower oil. They all can give you similar nutrients. But they don’t look like a brain. So, let walnut be the brand ambassador of my brain. Why not? By the way, Cahoon et al. searched the literature but could not find any strong association between walnut and cognitive power. Maybe, they did not search deep enough!

Carrot for your eyes

Cut a carrot and see if it appears like your eyes.

carrot, leek, healthy-1256008.jpg

No? If not, cut it until you see some part that resembles your eyes. Come on; you can do it. But what about these: tomatoes, red bell pepper, cantaloupe, mango, beef liver, and fish oils. They, too, contain vitamin A. So what?

Vitamin A is not going to give you night vision. But it should be part of your diet as it helps manage your health, including eye health. Also, carrot doesn’t come packed with vitamin A. But it contains its precursor beta carotene.

Kidney beans

beans, legumes, food-1001032.jpg

What is the difference between kidney beans and other lentils? Or between blueberries, seabass, egg white, garlic, olive oil, bell peppers, and onions? Well, the key difference is that except for kidney beans, none of the others resembles my kidneys. So, even if they are better food for kidneys than these beans, I am not interested in them.

What about eating jelly beans? Something to research on.

Where do these come from?

Human beings are masters of finding patterns around them and making up stories to support their imagination. The doctrine of signature, too, belongs to that category. It is also a favourite for the creationist folks. Why else is that food created with the shape of your organ? There must be a purpose.

Walnut intake, cognitive outcomes and risk factors: a systematic review and meta-analysis: Pubmed

Cooking Legumes: A Way for Their Inclusion in the Renal Patient Diet: Pubmed

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