Some Qs people asked me on science and my replies to them - part 26

                                                                  Interactive science series

Q: I'm a perfectly healthy 17-year old who's never had a vaccination. As a vaxxer, how do you explain that? I’ve also not been to a doctor for more than 5 years, and the last one I visited was probably a chiropractor anyways. I only get sick about once a year (flu season probably) usually mildly.

Krishna: Maybe because of ‘herd immunity’! When most people around you get vaccinated, that would prevent the spread of diseases. Read my article to know more about it here: vaccine-woes

Q: What is metastasis cancer?

Krishna: When Cancer cells that originate at a particular part of the body dislodge themselves , travel and go to some other part of the body and cause cancer in another organ of the body i.e., when the cancer has spread to other parts of the body, it is called metastatic cancer. The liver, lungs, lymph nodes, and bones are common areas of spread or metastasis. Even when cancer spreads to a new location, it is still named after the area of the body where it started.

Q: What is the difference between a scientific thinking and ordinary thinking? How can the latter take help from the former? 

Krishna: Scientists are trained to think differently from ordinary people.

 I will give an example here...

Two months back I went to one of my cousin's house. She was distressed. All the leaves of plants in her home garden were disappearing overnight and the plants were left bare with just stalks. She was performing 'pujas' worshiping all the Gods she knew. But there was no change. " Some devil is doing this to my plants during nights", she said. I was about to laugh but controlled myself because that would have angered my cousin.

The moment I saw those plants, I realized what happened. I went near them and searched for insects and  larvae. I couldn't find any! So I bent down and saw in the soil the evidence! Yes, larval poop! The round, black bead like things that larvae drop after consuming food - leaves in this instance. The larvae might have moved to some other place after consuming all the food available or they might have metamorphosed into adults and flown away! But their excreta gave them away.

I had proof of little brownish-black balls that look like peppercorn - which are actually a caterpillar's excreta. 

I told my cousin what to do to control the pests and she followed it. Now her garden is back to normal again!

Hmm. That is the difference! We search for real causes of phenomenon and try to find creative solutions to the problems with our knowledge and change the situations. Others will panic and perform pujas, pray or cry but can't change any thing.

If you are a scientist, you base your reality on knowledge you have - on data, math, science, and reason. You also have the mind to accept your failure. When something contradictory has passed through a rigorous review by your peers, you realize that you were incorrect in your findings, you alter your findings to adjust to the new reality. No ego issues here. Nothing else impacts your reality - media doesn't impact you, the politicians don't affect you, others' ideas and opinions hardly matter to you - just the cold hard data. Your emotions are irrelevant because you have the scientific facts staring you in the face. You can't get angry  on any one. There are no villains and heroes, just evidence. It's a much easier environment to make a rational decision in. Science is the best guide.

Scientists, by and large, are often motivated by non-materialistic concerns such as curiosity, helping the world by finding solutions. So selfless pursuits make the scientific community unbiased. Filtering out inconvenient data is unscientific, as is presenting opinion as fact. Science inherently pushes new boundaries. Science is all about rationality, weighing up the evidence and coming to a conclusion. 

Scientists are acutely conscious of how existing beliefs can skew one's analysis of the data.  This makes them move away from them. They become progressive.

The public however, has the opposite system for analysis, which they receive daily from a media that fails to hold anyone accountable, a stupid movement with impeccable messaging skills, activists with loud and biased voices, and political  parties that are completely inconsistent and off the reservation with their messaging, people and peers around them who don't have any idea of nonsense they are telling them.  People have no time to research and evaluate facts and data.  They have no correct knowledge. They have jobs and families. Nuance is not their core focus. They have commercials, vapid talking heads, and a bunch of falsely equivalent messaging in their face, with no consistent simple resource to tell them the truth in any way that they trust. And if they did have that resource, the opposite-view-holders would find a way to discredit it and general public have large quantities of uncontrolled emotions to deal  with that screw up their thinking process. Facts don't matter for them because most of them can't differentiate between facts and fiction! In fact facts entrench normal people deeper in their beliefs.  If you challenge their underlying principals by showing them facts, you essentially are making them question their entire belief system. Then they would fight with all their might to resist you! Most people when backed into that corner, rely on their cognitive dissonance to protect themselves. It's far easier to ignore one thing, even if is based on neutral reasoning, and keep your entire belief system stable. 

Then they create false villains, enemies for their supporters to hate. When you insinuate that someone's ideas are not only incorrect, but the people creating those ideas are stupid and evil, it allows your supporters to further shun rational scientific debate, and instead focus on the evil people perpetuating ideas that will bring about the apocalypse. You then don't have to discredit any other of their ideas, as your supporters know that everything from that source is clearly evil and full of lies. You can then focus on vilifying the next person.

A worst situation to be in!

Once, their world is enlightened with knowledge, Scientists can't even imagine placing themselves in the dark world of general public. They want to get immunized themselves from such a scenario. That is why they try to keep away from people by living in fort-like labs. 

But to bring a change in the ordinary world is important too, even though it is extremely difficult. A scientist's time is precious - s/he can't spare much time on this aspect. Co-operation from general public is utmost important for the scientists to come out of their forts.

So what is the solution? General Public: Don't fall prey to silly talk. Find out who the experts are. Then consult specialists who can deal with things in the right way. Let me also warn you not all scientists and experts can do unbiased reasoning. You should develop the ability to find out who the genuine ones are. 

Listen to what scientists  say. They might say things that are completely contrast to your belief system. Don't get emotional and angry. Try think about what they say. Do neutral reasoning. Then you will understand why they say what they say. 

Then decide for yourself who to follow or what to do.

Q: Why do scientists wear white coats in their labs?

Krishna: 1. Not to spoil my clothes. While working in chemistry labs, several times hazardous chemicals not only spoiled my clothes, but put little holes in them! My mother used to scold me for being careless. But when you are in a lab, you forget everything, you get excited with the wonderful environment you are in, get carried away and do things without giving much importance to your dress or personal safety! I caused two fire accidents in my lab!

2. To reduce the amount of microbes you carry out of the lab. While going out after conducting experiments, we remove our coats, gloves etc. and wash our hands  so that contamination can be reduced.

3. Men of science began wearing white coats so they can assure the world that  they are clean and pure. White denotes purity of thought and deeds.

4. The reason lab coats are white is that they can be bleached repeatedly for sterilization without causing too much damage to the fabric or making colors run.

5. To protect sensitive equipment by covering your dust-gathered clothes.

6. You can easily detect them when they are covered with dirt or contamination and can be discarded.

7. They look 'scientific' to the world outside! Don't they? :)

Q: Why do our ears form wax?

Krishna: According to latest reports, wax is secreted in the ear canal to clean it! Earwax, secreted in the ear canal, protects ears from building up dunes of debris from particles wafting through the air. The wax creates a sticky particle-trapper inside the canal. The goo coats hairs and haphazardly pastes them into a loose net. Then, by a process not yet fully understood, bits of particle-dirtied wax leave the ear, taking their burden of debris with them.

Earwax may accomplish such a feat because trapping more and more dust turns it from gooey to crumbly. Our jaw motions might help shake loose these crumbs. A video inside the ear of someone eating a doughnut showed earwax bucking and shifting. This dust-to-crumb scenario needs more testing, but researchers point out that earwax might someday inspire new ways of reducing dust buildup in machinery such as home air-filtration systems.

Q: How do inanimate molecules know how to proceed with reactions and make important decisions in living systems? They don't have their own will and are not conscious to do that!

Krishna: This again is science, according to scientists!

There is a huge thermodynamic driving force for the biological machines in the cell to carry out the process like, for example, DNA replication. A suitable analogy would be a water wheel combined with a Rube Goldberg machine.
Life, in essence, is a byproduct of the gradients created by the separation of metabolites and biological processes are a consequence of that dispersion of energy. DNA replication itself is a product of chemical transformations from the abundance of proteins, nucleic acids, and small molecules going from a high energy state to a lower energy state just like water going down a waterfall.

Consider this: NTPs (nucleoside triphosphates) are high energy molecules and want to go to lower energy NMPs or dinucleotides. The only way for them to get to this state would be through catalysts via various enzymes. In that process, the energy is used to carry out other processes and motions.

During the polymerization event, you generate multiple tangles. Entropically both of these polymers would like to be waving freely in solution rather than being twisted around each other. As a result, the two DNA helices will separate from each other. In the process of leaving each other, the concentration of the products also decreases allowing for the forward reaction to continue.
There is no will required. It's just molecules contributing to the universe's gradual decline of free energy.

According to scientists, "Life, in essence, is a byproduct of the gradients created by the separation of metabolites and biological processes are a consequence of that dispersion of energy."

Isn't that wonderful?!

Q: How do cells make proteins in living systems?

Krishna: Whenever the body needs a protein, a cell or a group of cells goes into action to implement a series of complex processes. This may be a type of protein that the cell may need to use in its own structure or that it will export for outside use. The cell itself decides which proteins it will use within its own structure, but when it comes to making proteins for outside use, special messenger proteins are sent to the cell.

 All information about the particular protein's structure is encoded in the nucleus within the DNA. All instructions relevant to the protein to be made are copied from the DNA with the aid of many enzymes and a strand of RNA molecule produced from this DNA. The protein will be produced according to the information in this RNA, which has been copied from the DNA. And so, this RNA is referred to as messenger RNA (mRNA). The synthesis of RNA from DNA is called transcription .
From this strand the protein will be synthesized, this is called translation. 
 The mRNA, having received its instructions, heads towards the ribosomes-the cell's main production units. The ribosomes read the instructions, starting from the beginning of the RNA strand. Each code in the DNA is made up of three bases called a codon, and represents one amino acid in the protein chain.

 Using the order it has obtained from the RNA, the ribosome joins together the amino acids to form a chain.  One by one, the amino acids are brought to a molecule called the transfer RNA, or tRNA. Every tRNA carries its own special amino acid. The tRNA carries the amino acid on one end and on the other, the code with the address where the tRNA will deposit its load (the anticodon).

 The tRNA that arrives at the ribosome aligns along the mRNA transcript at the described address. There it deposits the amino acid it is carrying and moves away from the ribosome. The ribosome moves one codon (three bases) along the mRNA transcript. Another tRNA molecule arrives at the new address and aligns along the mRNA, depositing its amino acid. Once all of the codons have been "read," the amino acids join together to form a protein molecule.

As you can imagine, the event crudely outlined in a few sentences above, in reality occurs as a result of processes that are highly complex. 
The first has to do with the beginnings of protein synthesis. How does a cell-which cannot be seen with the naked eye, formed from mindless molecules-make the decision to start producing something? The ability to decide, think, and evaluate is a feature of conscious living things. Obviously, unconscious molecules of carbon, hydrogen, oxygen and nitrogen atoms don't possess the ability to make decisions. There must be another power inspiring the cell to make these decisions and then directing it accordingly. This is scientific code written in cells's DNA and RNA.

Once a decision is made, the next step is for the messenger RNA to read the instructions encoded within the DNA. The enzyme responsible for producing RNA finds in the DNA only the instructions needed for the desired protein-but in reality, the process is extremely difficult. Finding the relevant information in the DNA means locating and extracting an instruction consisting of 900 base pairs from a store of 5 billion. This is like trying to find one particular sentence in a 20-volume encyclopedia, without any help. However this problem has been made easy in an awe-inspiring way: The relevant portion of the DNA has been marked by "start" and "stop" labels that the enzyme can find.

But how does this work in an actual cell? And why make RNA first and then protein? Why not make protein from the DNA directly? Well the DNA is located in the nucleus of the cell, here RNA is transcribed but protein is not translated. After transcription the RNA is relocated to the cytoplasm of the cell, here it is translated into protein. So the separation of nucleus and cytoplasm prevents protein from being made directly from DNA. But there are other reasons why RNA is made. I will name a few, but not all (there are so many).
First, the DNA is well protected in the nucleus against everything that floats around in the cytoplasm, which prevents the DNA from getting damaged. The transcription of DNA to RNA prevents that the DNA has to be translated itself in the cytoplasm and thereby prevents DNA damage. Another reason is that we only have 1 copy of DNA in each cell, but sometimes we need a lot of the same protein. Therefore it would be convenient if we could make more than one copy of the same protein at the same time. When the DNA is transcribed into RNA 10x, the are 10 RNA templates to make protein from. So protein can be made 10x as fast. So making RNA prevents DNA damage and provides flexibility in the amount and speed of protein synthesis.

Watch this video to understand the process more easily:

Q: What are some of the greatest innovative products from plastic?

Krishna: 1. Plastic Roads!

2. Producing crude oil from plastic waste:

Q: How do you know what source of scientific studies to trust?

Krishna: This article will help you in finding out what to trust in science and how to trust science stories:

How to trust science stories: A guide for common man

Q:How do you fabricate your research data?
I’m doing a research paper and have completed a survey. So the correlation doesn’t seem like working well. I want to publish the paper anyhow. How do I fabricate the data perfectly?
Krishna: You shouldn’t do that! No!
That is if you want to be honest. You can’t escape with that … you will get caught at one of these stages …
the peer review level
post publication level
replication level
Need I tell you what happens after that?

Q: What are alternative medical practices you mentioned in your articles?

Krishna: 1. Natural Product therapy 2. Mind - body therapies 3. Homeopathy, Naturopathy , Ayurveda,

Traditional Chinese Medicine (TCM) -   including acupuncture, acupressure, and herbal medicine.

4.  Manipulative and Body-Based Methods - These methods include reflexology, osteopathy, and rolfing,   chiropractic and massage therapy, 5. Energy Therapies like reiki. 

Q: How do I get rid of a bad omen?

Krishna: Develop rational thinking! Try to analyze the fear you are facing neutrally and critically. Soon you will get rid of fears of bad omens and the thoughts that are bothering you.

Q: Are all natural products good for health?

Krishna: When something is called "Natural" people think that means it's good. When something is called "Artificial" people think that means it's bad. Of course this is a commercial marketing ploy employed by people to deceive others.  You can't know if something is good or bad without doing a study and at least getting "inconclusive" results. Many natural things are extremely unhealthy. Many artificial things are healthy. So don't get deceived by labels.

Q: Why can't science explain everything in this world ... like "the soul", "God", "chakras" etc. Don't you think it is inadequate?

Krishna: Science, by definition, is the systematic pursuit of knowledge, using demonstrable, quantitative methods. If something exists in this universe, scientists will find it and tell you about it. If the answers given by science don't go well with your world view, don't blame science for it.

Q: What is the secret of innovation?
Krishna: Knowledge plus creativity plus the urge to help the world around.

Q: How memorable is the feeling of getting the first journal publication for students?

Krishna: Felt happy and relieved for a moment but no time to even think about it more than that! Moved on to publish another one - we had a dead line - publish at least two papers in two years for the junior research fellowship to get promoted to the senior one. Otherwise it would be withheld!

But definitely gained more confidence to move quickly. 

Q; Can scientists create DNA?

Krishna: 

Yes! Of course! Artificial genetic material can be reliably created that not only interacts like its natural counterpart, but can even be ‘read’ by cells. Chemicals are chemicals whether they are used by Nature or human beings to create synthetic organic molecules of life’s matter.

At the very root of DNA’s structure are four letters, referring to nucleobases (or usually just called ‘bases’): A, C, G, and T. These are shorthand for adenine, cytosine, guanine, and thymine. These four molecules are the ‘nitrogenous bases’ of nucleotides. These bases form pairs and lead to configurations that cause the classic DNA helical structure to develop.

Decades after the discovery of DNA and its implication in human genetics, in 2006, scientists developed artificial DNA bases, which have a novel bonding pattern. The artificial bases (called Z and P) bond similarly to how GC and AT (natural DNA bases) bond. In fact, using a method known as X-ray crystallography, researchers have observed that these artificial bases can be incorporated into natural strands of DNA and even show similar function to fully natural DNA bases when interacting with proteins inside of cells.

In 2014, researchers researchers announced the creation of a living cell that had two ‘foreign’ DNA building blocks in its genome. The team inserted the two into a bacterial cell, a strain of E. coli. When the cell reproduced, unwinding its double helix and reconstituting it in new cells, X and Y replicated as well, their chemical bond just as stable as the A-T and C-G pairings in DNA’s normal sequence. The leader of the Scripps research team, Floyd Romesberg, calls the organism “semi-synthetic.”