SCI-ART LAB

Science, Art, Litt, Science based Art & Science Communication

Q: Why is personalised genes based treatments difficult?

Krishna: The biochemical pathway that shapes evolution is dense with inherited redundancies, according to scientists. Genetic information from our ancestors trails along forever in an incremental physical record that interacts significantly with our own most recently evolved and internally complex genetic network, which in turn interacts with the environment, creating almost infinite combinations and potential health outcomes.

Individual genes do not determine sickness or health on their own, the geneticists say, but act in concert with groups of other genes, all in various stages of mutation—in ways that they are just beginning to be understood. Genes do not work alone, and so no single gene can be considered to be good, bad or neutral in all contexts.

A new research paper (1) explains that "unnecessary" complexity in the evolutionary pathway needs to be fully unpacked—down to the genomic variations between individual cells in the same person—before personalized medicine can be used effectively for improving human health.

Our bodies have an immense ability to change and to cope with issues that arise. Context matters in our genome. Even a simple single mutation can have a profound effect on the body, when acting in combination with others. This complexity is till being studied.

However, the scientists conclude that precison medicine is still crtical to the future of medicine, but that the same technology that idenitied the "necessary" complexity of the genome also needs to be applied to the entire blueprint—including the "unnecessary" elements—creating a longer, more compicated road to the same destination.

Any disease we see is a result of the interactions between necessary and unnecessary complexity the experts say. Nature does not go back in time. It goes forward, and as it encounters challenges, it comes up with solutions. Our genes carry the history of all the changes that have occurred over many generations. It may not be necessary to our function today, but it is embedded in our genes.

Complexity is not a curse. It's a reflection of our evolutionary history, and it needs to be recognized as an important part of the body that medicine is trying to treat. Beyond personalized medicine complexity bears on the evolution of life itself.

You cannot have a single and everlasting solution. It is as compound as any living system is.

Q: Is the  convalescent plasma therapy  right choice?

Q: Can we rely on 'immunity passports'?

Krishna: It is still in the experimental stage. Until facts get established, we cannot say it is the right choice. COVID 19 itself is highly complex disease. Moreover, it is new. Scientists are still trying to understand what exactly is happening during the infection. 

A study published on May 3rd in the journal Immunity (2), says the immunity responses of different patients are not all the same. While the 14 patients examined in the study showed wide-ranging immune responses, results from the 6 of them that were assessed at two weeks after discharge suggest that antibodies were maintained for at least that long. Additional results from the study indicate which parts of the virus are most effective at triggering these immune responses and should therefore be targeted by potential vaccines.

It is not clear why immune responses varied widely across the patients. The authors say this variability may be related to the initial quantities of virus that the patients encountered, their physical states, or their microbiota. Other open questions include whether these immune responses protect against COVID-19 upon re-exposure to SARS-CoV-2, as well as which types of T cells are activated by infection with the virus. It is also important to note that the laboratory tests that are used to detect antibodies to SARS-CoV-2 in humans still need further validation to determine their accuracy and reliability.

High concentration of  neutralizing antibodies that bind to the virus  can have some effect. Neutralizing antibodies prevent infectious particles from interacting with host cells.

Do those who recover from the disease have immunity and can get immunity passport to work?

There is no clear answer to this question, experts say, even if many have assumed that contracting the potentially deadly disease confers immunity, at least for a while. Being immunised means that you have developed an immune response against a virus such that you can repulse it. Our immune systems remember, which normally prevents you from being infected by the same virus later on.

For some viral diseases such a measles, overcoming the sickness confers immunity for life.

But for RNA-based viruses such as SARS-CoV-2 - the scientific name for the virus that causes the COVID-19 disease - it takes about three weeks to build up a sufficient quantity of antibodies, and even then they may provide protection for only a few months. At least that is the theory. In reality, the new coronavirus has thrown up one surprise after another, to the point where virologists and epidemiologists are sure of very little.

Accuracy of the tests is a big issue where atleast some percentage are false positives or false negatives.. This has been discussed in this article: Coronavirus: surprisingly big problems caused by small errors in testing (4).

Faced with all these uncertainties,  experts have doubts about the wisdom of 'immune passports', 'herd immunity' and several other things people are proposing.

Learning from history: Why History Urges Caution on Immunity Testing

Q: Can the systematic study of any subject be called science?

Now you need to validate and see whether what you studied and observed agrees with natural or universal scientific principles or not. Whether it works or not. Whether the results are reproducible or not.

Because of the complexity of human nature, many psychology studies are not reproducible making the main stream scientists questioning psychology’s claim that it is science. The same applies to ‘social sciences’ too.

We have pseudo-sciences too that claim to be highly systematic like astrology, homeopathy, DMIT, …

The definition of science is getting changed. We now have very stringent rules to identify genuine science.

So don’t try to call everything you can study systematically ‘science’. It is not! Not according to modern definition.

Q: What is a preprint?

Krishna: Preprint is one term of art for an academic paper that hasn’t been peer reviewed or published yet. Medical research often involves questions of life or death that presumably deserve more pre-publication scrutiny. Peer-reviewing and publication of papers take a very long time. To speed up things, especially in a critical situation like global pandemic COVID 19, more and more researchers are going for preprints to help one another and spreading knowledge at a fast rate.

The Cold Spring Harbor Laboratory on Long Island, Yale University and The BMJ (formerly the British Medical Journal) started a new “preprint server” for medical research called MedRxiv, last year. Page views to the MedRxiv site are now averaging 15 million a month, up from 1 million before the pandemic. Something significant has changed in medical research.

Many of the coronavirus-related papers being posted on MedRxiv are rushed and flawed, and some are terrible. But a lot report serious research findings, some of which will eventually find their way into prestigious journals, which have been softening their stance on previously released research. Researchers are encouraging posting to preprint servers as a way to share information immediately and speed up research to help the world. Lot of  research is out there, being commented on and followed up on by other scientists, and reported on in the news media. The journals, which normally keep their content behind steep paywalls, are also offering coronavirus articles outside of it.

This is the future for scientific communication that has been predicted since the spread of the internet began to enable it in the early 1990s (and to some extent long before then), yet proved slow and fitful in its arrival. It involves more or less open access to scientific research and data, and a more-open review process with a much wider range of potential peers than the peer review offered by. It has both pitfalls as well as hightened efficiency. It depends on how you use it or misuse it. screws are also being tightened. 

BioRxiv and MedRxiv don’t accept every submission. Pure opinion pieces aren’t allowed — there has to be actual research involved. Beyond that if something goes up on BioRxiv it just means we don’t think it’s dangerous and it’s probably not crazy nonsense. While for MedRxiv there’s heightened scrutiny of potentially dangerous claims plus a checklist of conditions that any clinical research paper must satisfy. Both servers also recently began declining papers that pointed to treatments for the coronavirus based purely on computer modeling.

Earlier in 1991, physicists began sharing theirs on the internet on a server that came to be called ArXiv (pronounced “archive”). Mathematicians, astronomers, economists and scholars in a few other disciplines soon followed suit — some on ArXiv, some on other sites.
Working paper is another (art). They’ve been distributed at meetings and seminars as long as anyone can remember.

But most problems and confusion are arising because of the media picking it up, interpreting in strange ways and reporting it irresponsibly. 

That is why we have 'infodemic' along with this pandemic. 

Q: Why don't bats get diseases despite carrying deadly viruses?

Krishna: Good question. 

Coronaviruses such as MERS, Severe Acute Respiratory Syndrome (SARS), and more recently the COVID19-causing SARS-CoV-2 virus, are thought to have originated in bats. While these viruses can cause serious and often fatal disease in people, bats seem unharmed.

The bats don't get rid of the virus and yet don't get sick. The MERS virus doesn't shut down the bat immune responses as it does in humans. 

Researchers found that cells from an insect-eating brown bat can be persistently infected with MERS coronavirus for months, due to important adaptations from both the bat and the virus working together. Instead of killing bat cells as the virus does with human cells, the MERS coronavirus enters a long-term relationship with the host, maintained by the bat's unique 'super' immune system. SARS-CoV-2 is thought to operate in the same way.

Stresses on bats—such as wet markets, other diseases, and possibly habitat loss—may have a role in coronavirus spilling over to other species. When a bat experiences stress to their immune system, it disrupts this immune system-virus balance and allows the virus to multiply. The MERS coronavirus can very quickly adapt itself to a particular niche, and although we do not completely understand what is going on, this demonstrates how coronaviruses are able to jump from species to species so effortlessly.

When exposed to the MERS virus, bat cells adapt—not by producing inflammation-causing proteins that are hallmarks of getting sick, but rather by maintaining a natural antiviral response, a function which shuts down in other species, including humans. Simultaneously, the MERS virus also adapts to the bat host cells by very rapidly mutating one specific gene. Operating together, these adaptations result in the virus remaining long-term in the bat but being rendered harmless until something—such as disease or other stressors—upsets this delicate equilibrium.

And need I say, we, the human beings, are creating this stress and inviting the disaster to fall upon ourselves?

Q: What type of knowledge is science, and how is it different from other kinds of knowledge?

Krishna: Scientific way is exactly how our universe works.

Our Universe is based on and follows certain scientific principles ... that is established science. If it is not, our universe would have collapsed by now. As it is working wonderfully, the universe has clearly demarcated what is science and what is not. If your study agrees with the universal science, it is undoubtedly 'scientific'. Nobody can challenge and provide evidence contrary to that. Universal science is settled.

Modern science is the best way to study universal science as it is, and use this understanding to help the world around us. While Science is what our universe works with and a settled one at that, science is also the process with which we try to understand things. It’s about explaining the world we see, developing models that fit the data. But fitting models to data is a complex and multifaceted process. In this process the universe itself is our guide. Human mind might not be able to comprehend fully and correctly sometimes because of its limitations, but there are processes called falsifications and corrections to set things right. It is because of the human mind limitations, we most often have only the best knowledge under the present circumstances. If we get things right, and if our data fits with the universal versions, things work and there won't be any falsification and it is the ultimate knowledge.

The in built checks and balances makes science the right path to seek knowledge.

How is it different from other kinds of knowledge?

Other kinds of knowledge don’t follow the scientific method to establish facts and allow things like faith, belief, delusions, cognitive biases and fallacies and other faulty things that try to influence your thought processes to arrive at conclusions.

A faulty process leads to faulty conclusions. How can that be the right knowledge in the first place? How can that tally with the universal working?

Q: How can science explain human behavior?

Krishna: By analysing it scientifically.

Several people think science can't deal with emotions and morals. They even taunt scientists that these things are beyond science. Is this correct thinking? If I say this is wrong 'belief' based on ancient analysis promoted by anti-science people?

Want evidence? Find out here: Can science explain or deal with emotions and morals?

Q: Is advanced science and technology, without advanced morality, very dangerous?

Krishna: Advanced science and its use in technology needs critical thinking and creativity.

Who says science doesn’t deal with morality?

When it comes to questions of morality and meaning, the way we go about deciding what is right and wrong, and meaningful or not, is not the same as the way we discover what is true and false or facts. Some emotions like kindness and empathy will be involved. Controlling them is highly important to arrive at a good decision. Just because a criminal cries and acts funnily, you cannot support him. Oh yes, his brain could be differently wired! You try to analyze what could make any person behave so differently from others. On the other hand you can empathize with a poor thief when he steals food. But if you are a logical thinker you will try to understand what circumstances made him stole the food and try to correct them. Critical and scientific thinking helps here.

Anyone who knows how a nervous system works during pain processing can do no physical harm to any living being. And anyone who knows how the brain really works at the emotional level will never try to harass another living being. Any person who has seen how the scientific rules are followed universally in a given set of conditions, and understood its beauty can never think in local terms and can never come under the influence of artificially created races, castes, groups, communities or citizenships. He sees all the living beings as his own images - following universal rules of life and as citizens of this universe.

Unlike what several people think, science deals with moral ( derived from reasoning related to...empirical evidence) issues too and can be a good guide to life's journey through the checkerboard of blacks and whites!

Can science explain or deal with emotions and morals?

Good Science training also deals with morality. Don’t worry!

Q: Who evolved first egg or hen?

Read here how this happened: https://www.science.org.au/curio...

Of course there are several theories that say hen came first too. These ‘re discussed in this video which finally concludes the egg came first:

Q: What are immunological competent cell and what are their functions in male reproductive system?

Cells involved: Macrophages, B-lymphocytes, T-lymphocytes, Mast cells, Eosinophils, Dendritic cells, and Neutrophils.

Sperm are immunogenic - that is they will cause an autoimmune reaction in a different part of the same body. The likely reason for this is that sperm first mature at puberty, after immune tolerance is established, therefore the body recognizes them as foreign and mounts an immune reaction against them. Therefore, mechanisms for their protection must exist in this organ to prevent any autoimmune reaction.

The blood-testis barrier is likely to contribute to the survival of sperm. However, the blood-testis barrier cannot account for all immune suppression in the testis, due to its incompleteness at a region called the rete testis and the presence of immunogenic molecules outside the blood-testis barrier, on the surface of spermatogonia. Another mechanism which is likely to protect sperm is the suppression of immune responses in the testis. Both the suppression of immune responses and the increased survival of grafts in the testis have led to its recognition as an immunologically privileged site. Other immunologically privileged sites include the eye, brain and uterus.

Sperm are protected from autoimmune attack, which when it occurs in humans leads to infertility.

Curiously, the testis contains factors such as cytokines, which are usually only produced upon infections and tissue damage. The cytokines interleukin-1α (IL-1α), IL-6 and Activin A are found in the testis, often at high levels. In other tissues, these cytokine would promote inflammation, but here they control testis function. They regulate the development of sperm by controlling their cell division and survival.

Testicular Immunology is the study of the immune system within the testis. It includes an investigation of the effects of infection, inflamation and immune factors on testicular function. Two unique characteristics of testicular immunology are evident: (1) the testis is described as an immunologically privileged site, where suppression of immune responses occurs; and, (2) some factors which normally lead to inflammation are present at high levels in the testis, where they regulate the development of sperm instead of promoting inflammation.

Q: Should a rational person believe in pseudoscience?

Krishna: Rational Person and belief and pseudo-science? They sound oxymoronic.

If you ‘believe’ in ‘pseudo-science’, you no longer can claim you are rational.

Because both belief and pseudo-science denote irrationality.

Now choose whether you want to be rational or irrational.

Q: Scientist invented which animal doesn't need oxygen to survive?

Krishna: Scientists didn’t ‘invent’ any animal that doesn’t need oxygen.

Scientists ‘discovered’, earlier this year, that a jellyfish-like parasite doesn't have a mitochondrial genome - the first multicellular organism known to have this absence. That means it doesn't breathe; in fact, it lives its life completely free of oxygen dependency.

Salmon parasite called Henneguya salminicola, will live with the salmon for its entire life cycle, is the one.

Find more about it here: Scientists Find The First Animal That Doesn't Need Oxygen to Survive

Q: How does water reach the leaves for synthesising food?

Water helps transport nutrients throughout all parts of the plant. Water also helps support the plant by filling up the cells that make up the plant so it can stand up straight.

So how does this water absorbed by roots reach leaves?

Water travels through long, thin tubes running up from the roots through the stems and leaves called XYLEM.

Water moves up the xylem through a process called ‘Capillary action’ which allows water to be pulled through the thin tubes because the molecules of the water are attracted to the molecules that make up the tube. The water molecules at the top are pulled up the tube and the water molecules below them are pulled along because of their attraction to the water molecules above them.

When plants have more water in their leaves than they need, they get rid of this extra water through a process called transpiration. During transpiration, water evaporates from holes in the surfaces of leaves into the air. As water molecules evaporate from plant leaves, they attract the water molecules still in the plant, helping to pull water up through the stems from the roots.

This combination of transpiration and capillary action delivers the water from the bottom to the top of a plant.

Q: How can i know what ongoing projects or research ( ranging from small to big) are going on in my city , a state or India so that I can be a part of it?

There are science groups in all the major cities across India. By joining them, you can keep in touch with the latest news in the scientific arena.

There are state and central science academies. Keep in touch with them.

Then there is literature. By scanning literature, you will know what research is being done and where in the country.

The university and research lab websites too give some information on their research work.

Then the funding agencies like UGC and CSIR (DST) too give information on their sites.

Citations:

1. Rama S. Singh et al, Genes and genomes and unnecessary complexity in precision medicine, npj Genomic Medicine (2020). DOI: 10.1038/s41525-020-0128-1

2. Ling Ni et al, Detection of SARS-CoV-2-specific humoral and cellular immunity in COVID-19 convalescent individuals, Immunity (2020). DOI: 10.1016/j.immuni.2020.04.023

3. https://www.bloombergquint.com/gadfly/coronavirus-research-moves-fa...

4. https://theconversation.com/coronavirus-surprisingly-big-problems-c...

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Replies to This Discussion

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Q:Should scientists take moral responsibility, for the good and evil, applying their science leads to? But most people only look after their own interests, and morally justify their actions, after making decisions.

Krishna: Scientists discover things that already exists. How can they take moral responsibility for something that already exists?

Inventions are a different ball game altogether. If a scientist himself invents something that causes destruction, s/he will be responsible if s/he uses it for the destruction. If others uses it for the destruction, s/he will not be responsible in any way.

Some people complain that science also brings with it a few bad things like commercial GM crops, nuclear bombs etc. along with the good it does to the mankind. But according to the scientific community – science is like a knife. A knife can be used to cut throats and spill blood. It can also be used for good purposes like cutting fruits and vegetables. It depends on the person who uses it. Likewise science can also be used for the benefit of living beings as well as for their destruction. Which way it goes is in the hands of the person who uses it. The choice is definitely yours, Homo sapiens.

Choice is Yours

Each case is different. You cannot blame scientists for the mistakes you made!

Why should scientists take responsibility for the mistakes others made? In what way they are responsible? They just provided the knowledge. They never asked you to misuse it and cause destruction!

But, what about scientific inventions or technology, that is designed only to hurt people? Like nuclear, chemical, and biological weapons. And devices created for the purpose of torturing people. Whose moral responsibility is it when these technologies are used, to violate people's human rights?

If scientists and engineers want to be held responsible for the good technology they create, then they should also be held responsible for the evil technology they create. The good is more than the evil, but if you are moral, you shouldn't do any research on technology whose only purpose is to violate people's human rights.

Krishna: “What is acting like a stated fact?”

Scientists don’t create good technology or bad technology. They just create technology It is people who use it or people who take decisions. that make it good or bad. Get that right first.

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