Health Protective Benefits of Plant-Based Functional Foods (Part 2)

by:

 Nutritionist JB Lim MD PhD FRSPH FRSM 

 

Health Protective Benefits of Functional Foods (Part 2)

Earlier I wrote an article on the health protective benefits of foods here.

https://scientificlogic.blogspot.com/2024/09/heath-protective-benefits-of-functional.html

I dedicated it to Professor Dr. Vythilingam S/O Palaniandy Pillai who is a staunch vegan, and a former president of the Malaysian Vegan Society

Before I continue my essay here as Part 2,  please be informed that the health and medicinal effects of foods can only be derived from plant-based diet as practiced by vegans and strict vegetarians, not by solely meat eaters. We can fortify meat with additional health-protective ingredients such as probiotics—live beneficial bacteria—or prebiotics, which are non-digestible fibers that promote the growth of these bacteria. While probiotics can be found in fermented foods like yogurt, kefir, and sauerkraut, they are also added to other products to support gut health, which is linked to improved digestion, immunity, and even mental health.

Likewise, health-promoting benefits of omega-3 fatty acids may also be added as I wrote in Part 1 of this essay. While typically associated with fatty fish, omega-3 fatty acids are also added to some plant-based functional foods, such as fortified flaxseed or chia seed products. These essential fats have been linked to reduced inflammation, improved heart health, and better brain function.

Still, the fortification of these ingredients, no matter how much we add them into meat products, they can never supersede the tens of thousands of medicinal phytochemicals found naturally only in plant-based foods.   

Having assured that I shall now continue with some examples for Part 2 of this write up.  

Plant foods are very rich in phytochemicals. However, there are considerable differences in phytochemical contents among vegetables. For instance, onion varieties in phytochemical content vary, particularly for polyphenols, with shallots having the highest level, six times the amount found in Vidalia onions. Yellow onions have the highest total flavonoid content, an amount 11 times higher than in white onions. Red onions have considerable content of anthocyanin pigments, with at least 25 different compounds identified representing 10% of total flavonoid content.

Broccoli, cauliflower, cucumber, mushrooms, radishes, spinach, and zucchini all contain high amounts of salicylates. Vegetables from the nightshade family, like brinjal or eggplant and peppers, also contain salicylates. So are tomatoes being very high in salicylates. So are curry powders and chillies rich in salicylates

All foods rich in salicylates (aspirin) can be used as a natural emergency drug for sudden cardiovascular events such as AMI (acute myocardial infarction) or acute heart attack.  

Star Gooseberry or cekur manis in Malay, scientifically known as Sauropus androgynus contains papaverine, a drug used in the West to treat both high blood pressure and impotence in men.

Another example is garlic. Garlic, which is utilized as a spice and flavouring ingredient, is found to have fundamental nutritional components. Carbohydrates, protein, fat, minerals, water, and vitamins are all found in abundance in this plant. The plant also has a high medicinal value and is used to cure a variety of human diseases. It has anti-inflammatory, rheumatological, ulcer inhibiting, anticholinergic, analgesic, antimicrobial, antistress, antidiabetic, anticancer, liver protection, anthelmintics, antioxidants, antifungal, and wound healing properties, as well as properties that help with asthma, arthritis, chronic fever, tuberculosis, runny nose, malaria, leprosy, skin discoloration, and itching, indigestion, colic, enlarged spleen, haemorrhoids, fistula, bone fracture, gout, urinary tract disease, diabetes, kidney stones, anaemia, jaundice, epilepsy, cataract, and night blindness.

Ajoene in garlic has recently been found to have a new anti-leukaemia agent for AML therapy as shown by H T Hassan

The reputation of garlic (Allium sativum) as an effective remedy for tumours extends back to the Egyptian Codex Ebers of 1550 BC.  Several garlic compounds including allicin and its corresponding sulphide inhibit the proliferation and induce apoptosis of several human non-leukaemia malignant cells including breast, bladder, colorectal, hepatic, prostate cancer, lymphoma and skin tumour cell lines. Ajoene (4,5,9-trithiadodeca-1,6,11-triene-9-oxide) is a garlic-derived compound produced most efficiently from pure allicin and has the advantage of a greater chemical stability than allicin. Several clinical trials and in vitro studies of ajoene have demonstrated its best-known anti-thrombosis, anti-microbial and cholesterol lowering activities. Recently, topic application of ajoene has produced significant clinical response in patients with skin basal cell carcinoma. Ajoene was shown to inhibit proliferation and induce apoptosis of several human leukaemia CD34-negative cells including HL-60, U937, HEL and OCIM-1. Also, ajoene induces 30% apoptosis in myeloblasts from chronic myeloid leukaemia patients in a blast crisis. 

More significantly, ajoene profoundly enhanced the apoptotic effect of the two chemotherapeutic drugs: cytarabine and fludarabine in human CD34-positive resistant myeloid leukaemia cells through enhancing their bcl-2 inhibitory and caspase-3 activation activities. The two key anti-leukaemia biological actions of ajoene were the inhibition of proliferation and the induction of apoptosis. Studies have shown the anti-proliferation activity of ajoene to be associated with a block in the G2/M phase of cell cycle in human myeloid leukaemia cells. The apoptosis inducing activity of ajoene is via the mitochondria-dependent caspase cascade through a significant reduction of the anti-apoptotic bcl-2 that results in release of cytochrome c and the activation of caspase-3. 

Since acute myeloid leukaemia (AML) is a heterogeneous malignant disease in which disease progression at the level of CD34-positive cells has a major impact on resistance to chemotherapy and relapse and the inability to undergo apoptosis is a crucial mechanism of multi-drug resistance in AML patients. The recent findings of the potent enhancing activity of ajoene on chemotherapy-induced apoptosis in CD34-positive resistant human myeloid leukaemia cells suggest a novel promising role for the treatment of refractory and/or relapsed AML patients as well as elderly AML patients. Further studies are warranted to evaluate similar enhancing effects for ajoene in blast cells from AML patients in primary cultures before its introduction in pilot clinical study.

So is Madagascar Periwinkle (Catharanthus roseus) although not used as a food. This plant containing alkaloids have been used in the treatment of leukaemia, Hodgkin disease, malignant lymphomas, neuroblastoma, Wilms tumour, Kaposi sarcoma, mycosis fungoides, to improve cerebral blood flow, and treat high blood pressure. Madagascar periwinkle produces over 120 such alkaloids, including vincristine and vinblastine.

The Madagascar periwinkle has been used for centuries as a folk remedy for diabetes, and this led to studies investigating its use as a medicine. These studies showed little effectiveness in treating diabetes, but great potential in stopping the division of rapidly dividing cells, leading to its use in anti-cancer therapies, particularly for treating childhood leukaemia

 Allow me as a former research nutritionist and clinician to quote just one more example how celery among hundreds of thousands of other plant-based foods can be used as a medicine

3-n-Butylphthalide (NBP) is a compound found in celery, and its potential therapeutic value in various disorders has been suggested. Celery, and its potential therapeutic value in various disorders has been suggested as one of them.

dl-3-n-butylphthalide (dl-NBP) is also a powerful antioxidant compound with profound neuroprotective effects in stroke and brain injury. However, its role in Parkinson's disease (PD) is not well known. Traumatic brain injury (TBI) is one of the key factors in precipitating PD like symptoms in civilians and particularly in military personnel, car accident victims and others suffering from traumatic head injuries.  Thus, it would be interesting to explore the possible neuroprotective effects of NBP in PD following concussive head injury (CHI). 

Oxidative stress may also play an important role in diabetic related diseases. 3-N-butylphthalide and its derivatives serve as a potential treatment option for diabetic related diseases.

3-N-Butylphthalide and its derivatives may regulate multiple cellular signalling pathways such as oxidative stress, inflammatory responses, apoptosis and autophagy.

The benefits of NBP in dementia are among the most studied. Vascular dementia presents symptoms of cognitive impairment that often originated from cerebrovascular pathological conditions. Vascular lesions and cellular damages incurred from β-amyloid (Aβ) plaques, oxidative stress, and apoptosis define the underlying pathology of vascular dementia. Over the years, studies have demonstrated the neuroprotective effects of NBP in celery via its actions in interfering with Aβ metabolism, reducing oxidative stress, and inhibiting apoptotic enzyme activity and consequent cell death. Moreover, the angiogenic effect of NBP adds to its value in vascular dementia management. Recent investigations have also looked into improving the bioavailability of NBP.

Food and nutrition scientists together with nutritionists have been exploring the mechanisms of NBP in celery,  how it exerts its neuroprotective effects and on how we may apply this vegetable's great potential as a natural food medicine to treat strokes and brain injuries.  

Let me give you just a few more examples of additional phytochemicals found in foods.

One is turmeric (Curcuma longa). The active compound is curcumin. The medicinal property of curcumin is known for its anti-inflammatory, antioxidant, and anticancer properties. It has been studied for its potential in treating conditions such as arthritis, cardiovascular diseases, and neurodegenerative disorders.

Reference: Aggarwal, B. B., & Sung, B. (2009). Pharmacological basis for the role of curcumin in chronic diseases: an age-old spice with modern targets. Trends in Pharmacological Sciences, 30(2), 85-94.

Second is green tea (Camellia sinensis). The active compound here is Epigallocatechin gallate (EGCG). The medicinal properties of EGCG is its potent antioxidant with anti-inflammatory, antidiabetic, and anticancer properties. It has been associated with reduced risk of cardiovascular disease and improved brain function.

The reference here is:

Khan, N., & Mukhtar, H. (2007). Tea polyphenols for health promotion. Life Sciences, 81(7), 519-533.

Cabrera, C., Artacho, R., & Giménez, R. (2006). Beneficial effects of green tea—a review. Journal of the American College of Nutrition, 25(2), 79-99.

Third is soybeans (Glycine max). The active compounds in soyabean are their isoflavones (Genistein, Daidzein). The medicinal properties of isoflavones are its oestrogen-like effects and are studied for their role in reducing the risk of breast cancer, prostate cancer, and osteoporosis. They are also beneficial in alleviating menopausal symptoms. May reduce menopausal symptoms, improve bone health, and have anti-cancer effects.

 The reference here is:

Messina, M., & Messina, V. (2010). The role of soy in vegetarian diets. Nutrients, 2(8), 855-888.

Messina, M. (2016). Soy and health update: evaluation of the clinical and epidemiologic literature. Nutrients, 8(12), 754.

Fourth is ginger (Zingiber officinale). The active compound in ginger is gingerol and shogaols.  Ginger medicinal properties of gingerol are its anti-inflammatory, antioxidant, and anticancer properties. It is commonly used to alleviate nausea, digestive issues, and reduce muscle pain.

White, B. (2007). Ginger: An overview. American Family Physician, 75(11), 1689-1691. The reference here is:

 Ali, B. H., Blunden, G., Tanira, M. O., & Nemmar, A. (2008). Some phytochemical, pharmacological and toxicological properties of ginger (Zingiber officinale): A review of recent research. Food and Chemical Toxicology, 46(2), 409-420.

White, B. (2007). Ginger: An overview. American Family Physician, 75(11), 1689-1691.

Fifth are grapes (Vitis vinifera) and red wine. The active compound is resveratrol. The health benefits of grapes and red wine containing resveratrol, and its antioxidant component is, it supports heart health, diabetes and may protect against certain cancers and neurodegenerative diseases, especially found in the skins of grapes that has been shown to be neuroprotective.

The reference for grapes is here:

 Baur, J. A., & Sinclair, D. A. (2006). Therapeutic potential of resveratrol: the in vivo evidence. Nature Reviews Drug Discovery, 5(6), 493-506.

Sixth, are the cruciferous vegetables (broccoli, brussels sprouts, cabbage). In these vegetables the active compounds are glucosinolates (e.g., sulforaphane).

The health benefits of these cruciferous vegetables is their detoxification enzymes induction, potential anti-cancer properties. The reference here for this is:

 Herr, I., & Büchler, M. W. (2010). Dietary constituents of broccoli and other cruciferous vegetables: implications for prevention and therapy of cancer. Cancer Treatment Reviews, 36(5), 377-383.

Seventh, are the berries (blueberries, strawberries, raspberries). These berries' active compounds are the anthocyanins, and the flavonoids. Their antioxidant properties may improve cognitive function and reduce the risk of heart disease. Here is the reference:

 Joseph, J. A., et al. (2009). Reversing the deleterious effects of aging on neuronal communication and behaviour: beneficial properties of fruit polyphenolic compounds. The American Journal of Clinical Nutrition, 81(1), 313S-316S.

Eighth are the citrus fruits (oranges, lemons, grapefruits), These fruits active compounds are hesperidin, naringenin, etc.

Citrus fruits' health benefits lie in their antioxidants. It supports vascular health, may lower cholesterol levels. The reference for this is here:

Peterson, J. J., et al. (2006). Flavanones in grapefruit, lemons, and limes: A compilation and review of the data from the analytical literature. Journal of Food Composition and Analysis, 19, S74-S80.

Nineth are the flaxseeds (Linum usitatissimum). The bioactive compounds are the lignans (Secoisolariciresinol diglucoside), and omega-3 fatty acids. These support cardiovascular health and may reduce the risk of certain cancers. The reference for this is here:

Prasad, K. (2009). Flaxseed and cardiovascular health. Journal of Cardiovascular Pharmacology, 54(5), 369-377.

Tenth is pomegranate (Punica granatum). The medicinal active compounds are punicalagins, and ellagic acid. Their health benefits lie on its antioxidant, anti-inflammatory properties that may improve heart health and combat certain cancers. The reference for this is here:

 Jurenka, J. (2008). Therapeutic applications of pomegranate (Punica granatum L.): a review. Alternative Medicine Review, 13(2), 128-144.

Elevenths are the green leafy vegetables (spinach, kale). Here the active compounds are lutein, and zeaxanthin. These compounds support eye health and may reduce the risk of cataracts and age-related macular degeneration. Here is the reference:

Ma, L., & Lin, X. M. (2010). Effects of lutein and zeaxanthin on aspects of eye health. Journal of the Science of Food and Agriculture, 90(1), 2-12.

Twelfths are the nuts (walnuts, almonds, peanuts). The active compounds in nuts are the phytosterols and polyphenols. Their health benefits are, they support heart health, may reduce inflammation and oxidative stress. Here’s the reference:

Ros, E. (2010). Health benefits of nut consumption. Nutrients, 2(7), 652-682.

Thirteenth is dark chocolate (cocoa). Dark chocolates' active compounds lie on their flavanols (epicatechin) contents. Their antioxidant content may improve blood flow, lower blood pressure, and enhance cognitive function. Here’s the reference:

Corti, R., et al. (2009). Cocoa and cardiovascular health. Circulation, 119(10), 1433-1441.

Fourteenths are the legumes (beans and lentils). Their active compounds are the saponins, and phytic acid. These bioactive compounds may lower cholesterol, stabilize blood sugar levels, and reduce the risk of heart disease. However, the presence of phytic acid may be a stumbling block in that they may inhibit the absorption of iron. The reference is here:  

Flight, I., & Clifton, P. (2006). Cereal grains and legumes in the prevention of coronary heart disease and stroke: a review of the literature. European Journal of Clinical Nutrition, 60(10), 1145-1159.

Fifthteens are the tomatoes (Solanum lycopersicum). The bioactive compound is lycopene. The antioxidant properties of lycopene may reduce the risk of prostate cancer and support heart health. Here’s the reference:

Sesso, H. D., et al.

General References on Phytochemicals

  1. Basu, A., & Rhone, M. (2006). Phytochemicals in fruits and vegetables: a review of potential health benefits. Nutrition Journal, 5(1), 1-17.

This review covers the broad health benefits of various phytochemicals found in fruits and vegetables

  2.  Liu, R. H. (2013). Health benefits of fruit and vegetables are from additive and synergistic combinations of phytochemicals. The American Journal of Clinical Nutrition, 78(3), 517S-520S.

This article discusses the combined effects of phytochemicals in promoting health.

  3.  Gupta, C., & Prakash, D. (2014). Phytonutrients as therapeutic agents. Journal of Complementary and Integrative Medicine, 11(3), 151-169.

This paper provides a comprehensive overview of the therapeutic properties of various phytonutrients.

These references will help researchers, doctors and health-conscious individuals search deeper into the subject and expand their knowledge on the medicinal properties of phytochemicals in plant-based diets.

There are tens of hundreds more I know. They are far, far too long and effort-consuming for me to continue to write here. I am already quite tired writing all night long into the eerie hours as it is already now 3:35 am into the early morning, and I don't think anyone will appreciate my efforts.  

I can only summarize for them that a plant-based diet is a holistic natural medicine for the management of obesity, diabetes, heart disease, high blood pressure, and are cancer-preventive among many, many more.

“Let Food be Thy Medicine” (Hippocrates), and never allow Big Pharma, any pharmacist, health care professional, nurse, or any doctor at all to tell you, let medicine be thy food. This last claim is criminally, scientifically, professionally and ethically wrong. Be rational and sensible, how could chemical drugs be used as our daily food?  

Hippocrates never said that. It was put there into his mouth long, long after he died. 

 

 

Heath Protective Benefits of Plant-Based Functional Foods (Part 1)

 

This article is dedicated to Professor Dr. Vythilingam S/O Palaniandy Pillai who is a staunch vegan, and a former president of the Malaysian Vegan Society

Prior to the late 1990’s we only know foods contain the proximate principles, namely, carbohydrates, fats and proteins, plus vitamins and minerals, including trace elements that would be sufficient for normal nutrition and nourishment.

Then there was new development in nutrition. Food scientists and nutritionists came out with another type of food called ‘functional foods’ that contains something else other than the normal proximate principles, vitamins and minerals that is believed to confer better health. However, the term is poorly defined. A commonly used definition is that they contain substances that have positive effects on health “beyond basic nutrition”. However, there are several problems with this definition. In many cases, healthy foods are included under the term functional foods. A new definition is proposed as follows.

Functional foods are novel foods that have been formulated so that they contain substances or live microorganisms that have a possible health-enhancing or disease-preventing value, and at a concentration that is both safe and sufficiently high to achieve the intended benefit.

The added ingredients they gave may include nutrients, dietary fiber, phytochemicals, other substances, or probiotics.

We may ask food and nutrition scientists for the benefit of practicing nutritionists as well as health-conscious individuals, in what way are these functional foods more health-protective over the normal foods we eat? What other special ingredients do they have for them to be so special over a mixture of normal food that provides a balanced diet.

The only exception I can see are fruits and vegetables that contain a lot of various types of phytochemicals. A plant-based diet may have not just different types of antioxidants, but also medicinal values and hence therapeutic properties over the subsistence of normal nourishment.

Indeed, it is appropriately said that “let food be thy medicine” and not medicine be thy food. I do not consider a meat-based diet to be classified as ‘functional foods’ because I don’t think meat has any antioxidants, phytochemicals or medicinal properties in them. The only class of foods that has health-giving and therapeutic values that deserve to be labelled as ‘functional foods’ should only be plant-based.

 After all, almost all foods must originate from the plants through photosynthesis to provide a variety of nutrients, and not from animals that depend on plants, even though some are carnivorous as they eat other animals including herbivorous animals in the first place. I don’t think animals can produce natural medicines in their flesh in the first place, only plants can do this as medicinal plants. Herbal medicines are phytochemicals that contain plant-based bioactive compounds with therapeutic properties not available from meat products. Medicinal properties can only be derived from various plant sources such as whole grains, fruits, vegetables, nuts, and herbs, and more than a thousand phytochemicals have been discovered to date. Thus, I don’t think animal flesh (meat) can produce these medicinally bio-active compounds for them to be in the category of functional foods.

My opinion on functional foods as a nutritionist brings up many important points about the distinction between plant-based and animal-based foods, especially regarding their potential health benefits beyond basic nutrition.

The concept of functional foods indeed arose from the growing recognition that certain foods or food components may have positive effects on health that go beyond providing the essential nutrients required for survival. These foods may help reduce the risk of chronic diseases, enhance physical and mental well-being, or provide other specific health benefits. But what are they? In what way functional foods have potential health benefits.

Firstly, these foods have phytochemicals and antioxidants. To the best of my knowledge in food science, and as an analytical food quality control chemist and nutritionist, only plant-based foods are rich in phytochemicals—bioactive compounds that have been shown to have various health benefits. These plant-based foods are rich in phytochemicals—bioactive compounds that have been shown to have various health benefits, including antioxidant, anti-inflammatory, and anticancer properties. These compounds, found in fruits, vegetables, whole grains, nuts, and herbs, can help neutralize free radicals, reduce inflammation, and modulate various biological processes that are crucial for disease prevention. All these compounds are naturally occurring therapeutic medicines for sure.

Then we also have the benefit of dietary fiber. Functional foods often emphasize the inclusion of dietary fiber, which is primarily found in plant-based foods. Fiber not only aids in digestion but also plays a role in regulating blood sugar levels, lowering cholesterol, and supporting a healthy gut microbiome. The latter is increasingly recognized for its impact on overall health, including immune function and mental well-being.

Some functional foods are fortified with probiotics—live beneficial bacteria—or prebiotics, which are non-digestible fibers that promote the growth of these bacteria. While probiotics can be found in fermented foods like yogurt, kefir, and sauerkraut, they are also added to other products to support gut health, which is linked to improved digestion, immunity, and even mental health.

Consider also the health-promoting benefits of omega-3 fatty acids. While typically associated with fatty fish, omega-3 fatty acids are also added to some plant-based functional foods, such as fortified flaxseed or chia seed products. These essential fats have been linked to reduced inflammation, improved heart health, and better brain function.

Let’s look at plant-based vs. animal-based functional foods

My emphasis on the unique health benefits of plant-based foods is well-supported by research. Plant-based foods, with their array of phytochemicals, antioxidants, and fibers, offer a range of health benefits that are difficult to replicate in animal-based foods. While animal products can provide essential nutrients like protein, iron, and B vitamins, they generally lack the phytochemicals and antioxidants found in plants.

There is some debate about whether animal-based products can be considered functional foods. While meat itself may not contain the phytochemicals found in plants, certain functional meat products have been developed. These may include meats fortified with omega-3 fatty acids or enriched with vitamins and minerals. However, these are often viewed as less natural or less beneficial compared to whole plant-based foods.

What would be my conclusion on the value of functional foods? The distinction between plant-based and animal-based foods in the context of functional foods is clear.  Functional foods, particularly those that are plant-based, offer potential health benefits beyond basic nutrition due to their content of phytochemicals, antioxidants, dietary fiber, and other bioactive compounds. While some fortified animal-based products may also be classified as functional foods, the intrinsic health benefits provided by plant-based foods are more robust and well-supported by scientific evidence.

My personal emphasis “let food be thy medicine" reverberates strongly with the functional food concept, especially as it applies to plant-based diets. The therapeutic potential of these foods, rooted in their natural bioactive compounds, reinforces the idea that a diet rich in fruits, vegetables, whole grains, and other plant-derived foods is foundational to good health.

I shall write on gut microbiome and their role in nutrition later for my next article 

A Brief Introduction to Molecular Biology

 

In October to November 1991, I attended the Fifth Asian Course in Tropical Epidemiology under the Southeast Asian Ministers of Education Organization (SEMEO)Technical Cooperation jointly held among the National Centre for Malaysia SEAMO Topical Medicine and Public Health Project and the Institute for Medical Research in Kuala Lumpur in collaboration with the German Agency for Technical Cooperation. It was held at the Institute for Medical Research where I worked. Prior to that I also attended another postgraduate in-service course in biotechnology and molecular biology. 

These postgraduate courses were meant for senior medical officers and senior medical researchers. They were in-service courses meant for them  

In those days, knowledge in these areas, especially in molecular biology and molecular medicine, wasn’t very advanced yet with few discoveries and their applications.

Years on I picked up on where I left to gain more knowledge on molecular biology and its applications in molecular medicine. Clinical medicine as practiced in hospitals as a standard routine is very boring to us with very slow advancement  

So today, based on what I have gained in my previous training, let me write a brief essay on molecular biology first, and separately in another essay, I shall write on how molecular biology is used and applied for the advancement of medicine in several areas, from diagnostics, development of new drugs to new treatment of diseases.

But first, let me deal with molecular biology as a springboard before we go into its application in medicine.

Molecular biology is a branch of biology that focuses on the molecular underpinnings of biological activity. It involves the study of the structure, function, and interactions of biomolecules, such as DNA, RNA, proteins, and other macromolecules, which are essential for life processes. The field intersects with genetics, biochemistry, and cell biology, and has vast applications in medicine, biotechnology, and environmental science.

What then are the key areas in the study of molecular biology?  The first fundamental area is on DNA and RNA structure and function. We can broadly divide this into 3 areas, namely, DNA replication and repair based on studies of how DNA is copied and repaired in cells. For example, research into DNA polymerase enzymes that are responsible for DNA replication has provided insights into the accuracy of genetic information transfer.

The second area we go into is transcription and translation. This focuses on how genetic information is transcribed from DNA to RNA and then translated into proteins. The central dogma of molecular biology, which describes this process, is a fundamental concept.

Then thirdly we go into gene regulation that involves our understanding how genes are turned on or off in response to different stimuli. The discovery of regulatory elements like promoters, enhancers, and silencers has deepened our understanding of gene expression.

Having understood these 3 basics, we can then go into protein structure and function. Again, there will be 3 basic ideas. The first will be on enzyme kinetics. These are studies on how enzymes catalyse biochemical reactions. The Michaelis-Menten equation is a key model used to describe enzyme kinetics. Having understood its mechanism, we can now proceed to protein folding where studies show us how proteins fold into their functional three-dimensional shapes. Misfolded proteins are linked to diseases such as Alzheimer's and Parkinson's.

Next in line is our understanding of post-translational modifications. This area examines how proteins are chemically modified after synthesis, affecting their function, localization, and interactions.

Having understood these, we proceed into genomics and proteomics. This involves genome sequencing in sequencing entire genomes to understand the genetic blueprint of organisms. The Human Genome Project was a landmark study that mapped all the genes in human DNA. Having understood this, we proceed to the study on proteomics. This study means, we focus on the large-scale study of proteins, particularly their structures and functions. Techniques like mass spectrometry are used to analyse protein composition and interactions in cells.

Having done that, we can then proceed to understand molecular genetics. In this area we study gene editing and CRISPR.  (CRISPR means “clustered regularly interspaced short palindromic repeats”).  This is a technology that research scientists use to selectively modify the DNA of living organisms. CRISPR was adapted for use in the laboratory from naturally occurring genome editing systems found in bacteria.

They explore technologies like CRISPR-Cas9 that allow precise editing of DNA sequences. This has applications in gene therapy, agriculture, and synthetic biology.

We can then begin our study on epigenetics having finished studying the above. By this I mean studies on heritable changes in gene expression that do not involve changes to the DNA sequence. DNA methylation and histone modification are key mechanisms in epigenetics.

In medicine, an area I shall write separately later, molecular biology study cell that deals with signalling pathways, signal transduction and how they automatically commit suicide or apoptosis. Signal transduction investigates how cells respond to external signals through pathways involving receptors, second messengers, and kinases. Understanding these pathways is crucial for drug development, particularly in cancer therapy. The study of programmed cell death called apoptosis is a vital process in development and disease. Dysregulation of apoptosis is linked to cancer and neurodegenerative disorders.

Let us now list the biotechnology applications when we start learning molecular biology.

First, we learn about recombinant DNA technology like I also learn when I did my postgraduate in-service course. This involves manipulating DNA to produce genetically modified organisms (GMOs), therapeutic proteins, and vaccines. Insulin production through recombinant DNA technology is a notable example.

In their application in medicine, I shall write on this separately later, but briefly mention here, we apply molecular biology in molecular diagnostics.  The use of molecular techniques like PCR and next-generation sequencing (NGS) to diagnose diseases, including genetic disorders and infectious diseases is one of them. We also have gene therapy. In this area of medical specialty, we aim to treat or prevent diseases by correcting defective genes. Recent advancements in viral vectors and CRISPR have shown promise in treating genetic diseases like muscular dystrophy and sickle cell anaemia.

What about Recent Studies and Applications in Molecular Biology?

One of them among others is the CRISPR-Cas9 Advancements. A 2020 study demonstrated the potential of CRISPR-Cas9 for correcting mutations in the DMD gene, responsible for Duchenne muscular dystrophy. This research represents a significant step toward treating genetic disorders at the molecular level.

Then we also use our knowledge for the development of COVID-19 mRNA vaccines:

The development of mRNA vaccines, such as the Pfizer-BioNTech and Moderna vaccines, is a groundbreaking application of molecular biology, but has caused a global uproar about the use of these “suicidal vaccines.” I have received far too many adverse reports about mRNA vaccines from all kinds of people including from “famous” doctors, and of course from lay people.

 But unfortunately, almost none of the untold tens of hundreds of meetings and lectures on the Covid-19  given by international experts in various fields held at the prestigious Royal Society of Medicine in London where I was admitted as a Fellow in 1993, mentioned anything about the adverse effects of these mRNA vaccines.

These vaccines use synthetic mRNA to instruct cells to produce the spike protein of the SARS-CoV-2 virus, eliciting an immune response.

Our understanding of molecular biology also brings us into cancer immunotherapy. Recent advances in CAR-T cell therapy, a form of immunotherapy, have shown promising results in treating certain types of cancer. This approach involves genetically modifying a patient's T cells to target cancer cells more effectively.

Molecular biology is an incredibly dynamic and rapidly evolving field, with new discoveries continuously pushing the boundaries of what we know about life at the molecular level.  

I have only briefly outlined molecular biology above.  I shall write more later how we apply our knowledge on this in medicine.

But if my readers want more information in this area, below are some of the references they may read for themselves.

References for Further Reading

1. Alberts, B., Johnson, A., Lewis, J., et al. (2014). Molecular Biology of the Cell (6th ed.). Garland Science.
• A comprehensive textbook covering all aspects of molecular biology, from basic concepts to advanced topics.
2. Lodish, H., Berk, A., Kaiser, C. A., et al. (2016). Molecular Cell Biology (8th ed.). W.H. Freeman and Company.
• This textbook provides a detailed exploration of cellular processes and molecular biology techniques.
3. Doudna, J. A., & Sternberg, S. H. (2017). A Crack in Creation: Gene Editing and the Unthinkable Power to Control Evolution. Houghton Mifflin Harcourt.
• A book that discusses the discovery and implications of CRISPR technology.
4. Recent Studies:

For up-to-date research articles, consider accessing journals like Nature Molecular Biology, Cell, and The Journal of Molecular Biology through databases like PubMed or ScienceDirect.

An Eternal Source of Energy from the Oceans (Part 2)

 

 

by lim ju boo 

On Monday, September 4, 2023, I penned an essay called:

An Unending Source of Energy from The Ocean here:

https://scientificlogic.blogspot.com/search?q=An+unending+source+of+energy+from+the+oceans

However, last night, 31 August 2024 a friend sent me via WhatsApp an article that China intends to build a thorium molten salt nuclear power station as the world first here:

https://www.scmp.com/news/china/science/article/3271978/china-sets-launch-date-worlds-first-thorium-molten-salt-nuclear-power-station

I shall comment on China's intentions later in another article. Bear with me. I have too many things to write 

But let me write further on my previous idea of how we can use ocean waters to produce as much energy as we want without the risk of radioactive waste using nuclear energy, whether from uranium as already done, or use thorium molten salt as China intends.

Here’s my further exploration of using hydrogen from ocean water as a renewable energy source where I addressed both the potential and the challenges of this idea with a deep understanding of the science that I know.  

Here are some further thoughts, inputs and questions I ask myself.

 What are the hydrogen production challenges?

First, I should say energy efficiency. I believe I have rightly pointed out the energy-intensive nature of electrolysis. While renewable energy sources can power this process, the overall efficiency and energy return on investment (EROI) still need to be maximized. Exploring advanced electrolysis techniques, such as high-temperature electrolysis or utilizing excess renewable energy (e.g., during periods of low grid demand), could be critical in making hydrogen production more viable.

Then we need to use catalysts in electrolysis, Recent research has shown that adding catalysts like platinum or iridium can significantly improve the efficiency of electrolysis. However, these materials are rare and expensive. The development of more affordable and abundant catalysts could revolutionize hydrogen production.

Then we also have to look at hydrogen storage solutions.  Metal hydrides are indeed a promising storage solution. Further research into lighter and more efficient materials, like complex metal hydrides or carbon-based materials, could provide breakthroughs in hydrogen storage.

We can also look at ammonia as a carrier.  Ammonia (NH₃) is another potential hydrogen carrier that is easier to transport and store than pure hydrogen. It can be synthesized from hydrogen and nitrogen (from air) and later decomposed to release hydrogen when needed. We also need to take into account environmental considerations with water usage.  

Large-scale electrolysis would require significant amounts of water, which might raise concerns about freshwater availability, especially in arid regions. Using seawater directly for electrolysis could be a solution, but it introduces challenges like corrosion and the need for desalination.

What about carbon capture then? What does that mean?  Combining hydrogen with carbon dioxide to produce synthetic fuels or chemicals is an excellent way to utilize CO₂. However, sourcing this CO₂ sustainably (e.g., capturing it from the atmosphere or industrial emissions) is crucial to ensure the process is truly carbon-neutral or even carbon-negative.

Perhaps we need technological integration using hybrid energy systems. By this I mean integrating hydrogen production with other renewable energy systems (like solar, wind, and tidal) could create a more resilient and flexible energy grid. Hydrogen could serve as a storage medium for excess renewable energy, helping to balance supply and demand. We need to consider the hydrogen economy also.  Transitioning to a hydrogen-based economy will require not just technological advancements but also significant infrastructure investments, policy support, and public acceptance. Ensuring the safety and reliability of hydrogen storage and distribution systems will be key.

What would be our future prospects? One way I have earlier mentioned is fusion energy where I touched on the challenges of creating an "artificial sun," It is worth noting that ongoing research into nuclear fusion could eventually provide a virtually limitless energy source, complementing hydrogen-based solutions.

In my proposal of ocean-based hydrogen production, I have also considered the potential of offshore hydrogen production platforms, where ocean energy (like wind or wave power) is harnessed directly to produce hydrogen on-site, minimizing the need for land-based infrastructure.

Technologically intelligent readers of mine here may agree that my vision of a hydrogen-powered future is inspiring and brings into line with global efforts to transition to clean, sustainable energy sources. While there are challenges ahead, the path I have outlined I believe is both scientifically sound and forward-thinking.

 I believe my thinking contributes meaningfully to the ongoing discourse on energy sustainability unless others disagree. In that case they need to challenge me with their very strong and valid scientific and technological reasons, not just write “I disagree”  

Forensic Science in Crime Investigation: How They are Applied?

 

On Monday, May 13, 2024, I  briefly outlined the methods scientists used in forensic science to help the police in crime investigation in this link:

What is Forensic Science?

(https://scientificlogic.blogspot.com/search?q=forensic+science)

I shall now write a bit more on forensic science. We shall answer questions like what forensic scientists use to investigate a crime scene. We shall briefly describe the procedures, investigation methods they use, and how they conduct them to come to a conclusion from the crime scene, in the lab to the courtroom.

Let’s go together with me as a tour guide, shall we?

Forensic science is the application of scientific principles and techniques to solve crimes and help the legal system. Forensic scientists play a crucial role in criminal investigations, working closely with the police, law enforcement, prosecutors, and the courts. They collect and analyse evidence and provide expert testimony. 

Let us have a look at an overview of the procedures, investigation methods, and how forensic scientists work from the crime scene to the courtroom.

The first thing is the crime scene investigation. We need to secure the crime scene. Just like rescuers in a medical emergency, they have the First Responders.  The first priority at a crime scene is to ensure safety and provide medical assistance if needed. Once the area is secure, the scene is cordoned off to prevent contamination. Then we establish a perimeter.  This area is marked with tape, and entry is restricted to authorized personnel only. This prevents evidence from being disturbed or destroyed.

Next comes documentation where detailed photos are taken from multiple angles to capture the scene exactly as it was found. Then comes sketching where crime scene sketches provide a layout of the scene, showing the locations of key evidence. Detailed notes are then taken for documenting observations, the condition of the scene, and the position of evidence.

 Evidence is then collected using systematic search. By this I mean investigators conduct a systematic search of the scene, often using methods like grid, spiral, or zone searches to ensure no evidence is missed.

Next, comes evidence handling of items like blood samples, weapons, fibres, fingerprints, and other physical evidence that are carefully collected. Each piece of evidence is placed in separate, properly labelled containers to avoid cross-contamination. A record is kept of everyone who handles the evidence from the moment it’s collected to its presentation in court. This ensures the integrity of the evidence. We call this as chain of custody

The investigators then send the samples gathered for laboratory analysis. The types of analysis are fingerprint analysis. Fingerprints are lifted from surfaces using powders, chemicals, or alternative light sources. These are then compared to known prints. 

Then the DNA analysis where biological samples like blood, hair, or saliva are analysed for DNA. Techniques like Polymerase Chain Reaction (PCR) amplify the DNA, which is then compared to known samples. We also look at toxicology where blood and tissue samples are analysed for the presence of drugs, alcohol, or poisons. We also look for ballistics such as firearms and ammunition. They are examined to determine if a particular weapon was used in a crime. This involves matching bullets or shell casings to a specific firearm. Next, are trace evidence where small pieces of evidence, like hair, fibers, glass, and paint are analyzed to link a suspect to a crime scene.

In digital forensics, electronic devices are examined for evidence such as emails, texts, or files that could be relevant to the investigation.

Having said that, what are the scientific techniques we use? First, is microscopy where high-powered microscopes are used to examine trace evidence like hair, fibers, and particles. The chemists will then use spectroscopy with techniques like mass spectrometry or infrared spectroscopy used to identify chemical compounds in samples. Chemical analysis for various chemical tests is used to identify substances like drugs, explosives, or other materials found at the crime scene.

Next, we try to interpret and reconstruct the crime scene. We call this as reconstructing events.  Forensic scientists piece together the sequence of events based on the evidence collected. This might involve determining the position of the victim, the angle of entry of a bullet, or the sequence of blows in a violent encounter.

Bloodstain pattern analysis at a crime scene can reveal information about the position of the victim, the type of weapon used, and the movement of the victim or assailant during the crime.

Let me now talk a little about insects being used in the investigation. We call this as Forensic Entomology. Let me first give ourselves an introduction to Forensic Entomology. 

Forensic entomology is the study of insects and other arthropods in a legal context. It is primarily used to estimate the time since death (post-mortem interval, or PMI) by analyzing the types and developmental stages of insects found on a decomposing body.

 Insects are attracted to decomposing bodies and colonize them in predictable sequences, making them valuable in forensic investigations. 

How are insects used in forensic investigations? First, they are used for estimating time since Death (PMI). The primary application of forensic entomology is estimating the PMI. Different species of insects are attracted to a body at different stages of decomposition. By identifying the species and their developmental stage (e.g., eggs, larvae, pupae), forensic entomologists can estimate the time elapsed since death.

Insects are also used for locating a body.  Insects can also help locate a body by their presence in unusual numbers or species in certain locations. They can determine the movement of a body.  If insects typically found in one geographic area are discovered on a body found in a different location, it may indicate that the body was moved after death. In the area of toxicology, insects that feed on a decomposing body can sometimes be analyzed for the presence of drugs or toxins, especially if the body itself is too decomposed for traditional toxicology tests.

The process is called Collection of Insect Evidence.  Insects are collected from the body and the surrounding area. This includes both the insects on the body and those in the soil or other substrates around it. Next, is the identification and analysis. The collected insects are identified, and their life stages are analyzed. This helps in determining the species and estimating the PMI.

Environmental Factors such as temperature, humidity, and environmental conditions are taken into account, as they can affect insect development and thus the accuracy of the PMI estimate.

Of course, many people have heard about DNA collection and analysis, but they have no clue this is done. Let’s go into this very briefly in a non-technical way for everybody.

First, we need to do a DNA extraction and analysis. DNA extraction requires collection of samples. Biological samples like blood, saliva, hair, or tissue are collected from the crime scene or body. In some cases, bone or teeth may be used, especially in degraded or burnt remains.

The first thing is lysis of cells.  The first step in DNA extraction is breaking open the cells in the sample to release the DNA. This is done using a lysis buffer that breaks down the cell membranes. Next, we remove proteins and contaminants.  Proteins and other cellular materials are removed using a combination of chemicals and enzymes. This leaves behind a solution containing mostly DNA.

Next, we use purification procedures.  The DNA is purified from the solution, typically using techniques like ethanol precipitation or silica-based methods, to separate the DNA from other cellular components.

Having done that, we proceed to quantification where the amount of DNA is measured to ensure there is enough for analysis. Having done that, we proceed to DNA analysis using the following:

1.      Polymerase Chain Reaction (PCR): PCR is used to amplify the DNA, making millions of copies of specific regions of the DNA. This allows even small amounts of DNA to be analyzed.

2.      Electrophoresis: The amplified DNA is separated by size using a technique called gel electrophoresis. This creates a pattern that can be visualized and compared to known samples.

3.      Short Tandem Repeats (STR) Analysis: STR analysis focuses on specific regions of DNA that are highly variable between individuals. By analyzing the number of repeats at these regions, a unique DNA profile can be created.

4. Comparison: The DNA profile is compared to profiles from known individuals or entered into a DNA database (like CODIS) to see if there is a match.

Burnt Bodies:

What happens to the DNA in burnt bodies. Good question. Let’s look at the impact of heat on DNA. There may be thermal degradation. High temperatures can degrade DNA, breaking it down into smaller fragments or destroying it altogether. The extent of degradation depends on the duration and intensity of the heat exposure. Fortunately, there are also resilient samples.  Despite the destructive power of fire, some parts of the body, like teeth and bones, are more resilient and may still contain usable DNA. Bone marrow and the dense part of teeth (dentin) can sometimes protect DNA from complete destruction.

 DNA recovery from burnt bodies includes sampling from resilient tissues. In cases where the body is burnt beyond recognition, forensic scientists focus on collecting DNA from the most protected parts of the body, such as bones or teeth.

We can also use specialized techniques for recovery.  Forensic labs may use specialized techniques to recover and amplify even the smallest fragments of DNA from these samples, often requiring more advanced and sensitive methods than standard procedures. 

For example, we can use mitochondrial DNA analysis.  Mitochondrial DNA (mtDNA) is often used when nuclear DNA is too degraded. mtDNA is more abundant in cells and more resistant to damage, making it useful in degraded or ancient samples. However, it is less unique than nuclear DNA and is inherited maternally.

What are the challenges and limitations in severe degradation?  In cases of extreme heat exposure, DNA may be too degraded for any meaningful analysis. In such cases, identification may rely on other forensic methods like dental records, medical implants, or circumstantial evidence. Sometimes only a partial DNA profile can be obtained from a burnt body. While this can still be useful, it may not provide a conclusive identification without additional evidence.

Forensic entomology, DNA extraction, and analysis are all crucial tools in the forensic scientist's toolkit, helping to solve even the most challenging cases.

Next, is the timeline establishment.  Forensic scientists help establish a timeline of events, determining things like time of death through techniques such as body temperature measurement (algor mortis), rigor mortis, and livor mortis.

The forensic scientists after all the investigations, do the reporting and testimony

Forensic scientists write detailed reports on their findings, describing the methods used, the evidence analyzed, and the conclusions drawn. Reports are written in clear, non-technical language to be understandable to non-experts, including judges, and court prosecutors.

They then give their expert testimony in a courtroom presentation.  Forensic scientists may be called to testify in court as expert witnesses. They explain their findings, the methods used, and how they arrived at their conclusions.

During cross-examination, the defence may challenge the forensic scientist’s methods or conclusions. The forensic scientist must be able to defend their work and explain it clearly.

Forensic science is a meticulous and rigorous process that requires attention to detail, scientific expertise, and the ability to communicate complex findings in a clear and understandable manner. From securing the crime scene to providing expert testimony in court, forensic scientists are vital in ensuring that justice is served by providing objective, scientific evidence to support investigations.