How Does Diet Influence Immunity

B0009442 Collage of mixed fruits and vegetables, MRIThe short answer is by very complex intelligent communication with a vast array of signals from a single layer of cells. This single intestinal epithelial cell layer makes elaborate decisions about digestion, types of diet, analysis of the effects of trillions of microbes and the types of immune cells and specialized lymph nodes. What are the mechanisms that allow one cell to understand all of the factors involved?

The barrier cells in the skin, gut and blood-brain do much more than block microbes and toxins from entering the body. These intelligent epithelial cells engage in elaborate back and forth communication with the trillions of microbes on the outside as well as many different kinds of immune cells on the inside. The communication determines which microbes are considered friendly, which are drawn nearby for protection, which are allowed to make vitamins and other factors and which are enemies that need particular immune responses.

B0003777 Villus from the human duodenumSignaling of epithelial cells with immune cells determines which types are needed and how the immune centers and factories in lymph nodes and specialized tissues are formed. See the posts on the intelligent skin cell and the intelligent intestinal epithelial cells for more information than is in this post. Perhaps, the most intelligent of all of these epithelial cells is the choroid cells that allow only very small molecules (one eighth the size of the intestinal cell) and very particular microbes and cells to enter the brain. Choroid cells determine the constitution of the cerebral spinal fluid, including responding to signals from every part of the brain and sending exact messages to attract the type of immune cell needed for any current brain region problem. (See post on intelligent choroid cell).

Recent research shows that many different micronutrients from the diet are critical parts in this decision making process. This type of signaling between epithelial and immune cells is necessary to develop immunity for babies that determine life long immunity. Micronutrients and the epithelial signaling are, also, vital in a day-to-day basis to maintain the various immune cells needed for each circumstance throughout life. Vitamins A and D have been known to be extremely important for immunity, but the mechanisms have not been clear. Recent research has discovered special receptors and cascades into the nucleus that are used by these vitamins and are needed for immunity. Along with these two vitamins, many other molecules from food trigger these vital pathways and interact in the nucleus through additional special nuclear receptors. Micronutrients in fruits and vegetables are just being discovered and the mechanisms are extremely complex.  

This post will describe recently discovered mechanisms of signaling in the gut epithelial cells that determine the unique lymphocytes and lymph tissues needed to fight infections throughout life. As more is learned, this line of research will map the extremely complex relationship of diet and life long immunity, which is completely dependent on intelligent communications between these cells.

Intestinal Epithelial Cell

B0006124 Goblet cellThe very intelligent intestinal epithelial cell was discussed in a previous post. This section is a brief summary of material in that post. The gut has been considered a second brain with the largest semi autonomous nervous system outside of the brain. Much of this activity is coordinated in this one layer of epithelial cells.

In most areas, microbes trigger vigorous immune responses. In the intestine, epithelial cells play a critical role in deciding whether a modified response or no response should occur, instead. Cascades of molecules that trigger genetic networks are involved in making the decision to produce graded immune responses. Friendly microbes signal for protection from infection and tissue damage, but this friendly signaling can increase cancer creation. The epithelial cell must balance digestion, protection against dangerous microbes, support of friendly microbes, modulation of inflammation and avoiding cancer. Different responses occur in different parts of the bipolar shaped cell.

Epithelial cells are in constant communication with immune cells, such as phagocytes that present antigens to T cells. These signals either increase or decrease the amount of dendritic cells and macrophages that will tolerate friendly bacteria. In fact, there are a wide variety of different kinds of phagocytes that travel to the various lymph nodes with microbe antigens–both live bacteria and pieces of microbes. Because they hang out at the barrier lamina, some of these macrophages already understand tolerance to some microbes.

PD FEATURE WIK 800px-SalmonellaNIAIDMessages from the barrier epithelial cells instruct traveling T cells to be tolerant or not. The macrophage can signal with cytokines that loosen the tight junctions and allow them to stick their long arms through to the lumen to grab particular antigens to be analyzed, defeated or helped. In fact, the epithelial cell initiates the signals to the tight junction. Other functions are:

  • Interacting positively and negatively with trillions of microbes using thousands of cytokine signals
  • Modulating the immune system to accommodate thousands of different microbe communities
  • Determining multiple attributes of digestion of food and production of vitamin
  • Influencing the human immune system development and normal function through thousands of cytokines
  • Signaling in complex ways to many types of cells with thousands of cytokines
  • Maintaining order by building and supporting the barrier that separates the microbes from the body
  • Producing enzymes to help or hurt microbes
  • Producing mucous that creates a barrier region for friendly microbes

Exposure to the Environment

VillusExposure to the environment is a double-edged sword for organisms. They need the nourishment and must avoid toxins, dangerous microbes and assault. The immune system is the first responder for invasion by microbes and toxins and the response to injury. The immune system consists of a very large number of different types of cells that are called upon for a vast amount of different tasks (including the vast number of different bacteria and viruses). These cells are unique in particular organs. At the skin (see post), intestinal (see post) and respiratory epithelium, a conversation occurs between the outside world of trillions of microbes and inside world of necessary types of immune cells. The external influences are part of this conversation and influence how immune cells and their lymph structures develop and perform. Perhaps, the most significant influence from the environment is the food and drink that are necessarily taken in. In this way, specific nutrients, such as vitamin A, can have many varied effects in different locations. This research is the new frontier of diet influencing inflammation.

Crop IEC summary from NatureSignaling at the epithelial lining is perhaps the most sophisticated of any in the body. A wide variety of signals back and forth help determine which microbes will be supported as friends and which will be fought as enemies. The signals involve both cytokines and neurotransmitters. There are a variety of microbes that are absolutely necessary for production of needed materials and vitamins. It is known that diet affects immunity and general health (research in poor countries), but only recently has the particular molecular events been understood. It affects diabetes, heart disease and cancer. Recent research shows elaborate signaling from microbes and many parts of the body.

Because of the constant assault by toxins, situations are closely observed by the travelling and tissue resident immune cells. Toxins and dangerous microbes are identified by receptors on T and B-lymphocytes in the lymph tissues near these gateway organs, especially the GI tract.

Specialized immune cells in the small intestine include two types of intraepithelial lymphocytes (IELs). They have T cell receptors (TCRs) and can rapidly respond to danger, but meanwhile, maintain the barrier and the tissue. They produce IFN-γ, which rapidly kills enemy cells, but can’t produce IL-17. They are present at birth helping to deal with the very first microbes. They can suddenly change to become memory T cells.

Further below the entrance at the epithelial cell, there are many other different types of immune cells including many distinct T helper cells, which can produce IL-17 to protect against fungus. These unique cells don’t occur in other places in the body. But, this cytokine is implicated in multiple sclerosis, rheumatoid arthritis and lupus. Sodium chloride levels can influence this cytokine. (See post on Intelligent T Cells.)

Lymph Tissue is the Home Base and School for Lymphocytes

From Nephron

From Nephron

Peyer’s patches, which are large lymph tissues exposed to the outside world, and internal lymph nodes are the places where lymphocytes identify and start reacting to specific molecules (antigens) by producing new specialized types of cells. They must identify the good bacteria and molecules from the organism (self molecules) and keep the organism tolerant, that is, avoid a destructive reaction to them. If they don’t function well, they can become a place where viruses can live chronically. Because these systems develop in the fetus, factors from the environment can begin their influence before birth, by producing particular kinds of lymph structures.

After birth, a unique type of small lymph structure (cryptopatche) appears in the intestine just under the crypts of Lieberkun, where villi are formed. When they are exposed to microbes, they become adult isolated lymphoid follicles (ILFs) that produce lymphoid tissue initiator cells (LTin cells) and lymphoid tissue inducer cells (LTi cells). As these cells respond to more and more microbes and other materials, the cryptopatches mature.

Early Diet is Very Important

AS0000091FE23 Child, eating fruit, vegetables, balanced dietStudies of poor countries have found that nutrition is critical for the proper response to vaccinations. Studies now show that response to micronutrients includes both the central thymus organ and other lymph nodes. Specific nutrients are necessary for the fetus to develop good immune structures and cells. Also, specific diet is necessary after birth for the cryptopatches to develop normally. In particular, vitamin A influences the size of fetus lymph nodes and Peyer’s patches in mice through the vitamin A receptor—retinoic acid receptor (RAR alpha). Stimulating this receptor is essential for immune function later in life, particularly against viruses. This influence appears to be from the LTi cells, not B and T-lymphocytes and cannot be reversed later in life.

There is still little information on exactly what type of nutrition is absolutely necessary at certain points in development. It comes from various foods and involves a lot more than the known vitamins. In fact, impairments that occur in the immune response to vaccines are dependent on micronutrients. These problems with the strength of vaccinations cannot be reversed later. Mothers who are undernourished have less immunoglobulin A.

In cultures where the quality of nutrition is tied to the harvest cycle, those born at the time of harvest have less mortality from infections as adults. Exposure to sunlight and vitamin D contributes to better immunity. These factors influence the number and size of lymph nodes that develop, including Peyer’s patches in the gut, just below the epithelial cell. The immune cells in the nodes benefit from some of the microbe products from the lymph and blood flow. The LTi cells start building the nodes before birth, when vitamin A is critical. The cryopatches appear at birth and grow based on signals from the epithelial cells, immune cells and microbes.

Vitamin A

PD Vitamin_AVitamin A comes from animal and plant food and is only rare in poor countries, where children develop night blindness as an early symptom of vitamin A deficiency. Plants have an inactive molecule (beta-carotene) that is oxidized by enzymes to retinol, which is taken into cells. Enzymes in the epithelial cells then makes trans-retinoic acid and 9-cis-retinoic acid. Animals have an active form of vitamin A in fat that can be built up to toxic levels. Retinoic acid is fat-soluble and diffuses easily. Also, epithelial and intestinal immune cells, dendritic cells make retinoic acid, as well as directing lymphocytes.

Children from poor countries with poor diets that have low weight have many more infections from a poorly developed immune system. It is still a big problem in Asia and Africa despite programs to increase vitamin A for pregnant women. By the time, the children are born it is too late for vitamin A to reverse the life long immune problems. Even increased amounts after birth did not help reverse the problems, even though it is absolutely necessary for survival.

W0030906 Dietary sources of vitamin AAs well as helping to develop appropriate lymph tissue in the fetus, vitamin A has important effects in maintaining appropriate lymphocytes and other immune cells (TCRs) in the intestines. The size of the stem cell pool that makes the special lymphocytes sitting in the intestinal epithelium appears to be determined in the fetus and stays poor throughout life, if it is deficient at birth. It also limits the other lymph organs. It is not yet known exactly where the IELs, lymphocytes that sit in the intestinal epithelium, are made.

Vitamin A is also critical to T cells and their functions in general. It appears to be critical for special T regulator cells to form all through the body. Vitamin A stabilizes some T cells when they are fighting infections. It stops them from becoming the negative type of T cell. This means that Vitamin A is critical in the fetus but all through life, as well. Vitamin A is used differently when there are different sets of nutrients being ingested.

The Aryl Hydrocarbon Receptor

Cells regulate immunity pictureThere are a variety of receptors discovered for vitamin A and D as well as other micronutrients.

Recently, a very important receptor family was discovered—the arylhydrocarbon receptors AhRs. These are critical in the response to the environment and respond to many different substances in different ways. One receptor picks up toxins like dioxin, which has negative effects on the immune system including the thymus. Others respond to products from apples (quercetin), resveratrol in grapes and curcumin with positive effects. This process is important for LTi cells to stimulate the proper cryopatches and mature isolated lymphoid patches ILFs. Animals, not fed these vegetables, did not have enough immune function to fight off infections. The research is not conclusive yet that these factors cannot reverse some of the immune problems later.

B0008745 RaspberryAhRs are important in T regulator cells in the regions below the epithelial cells. Stimulating these AhRs from the diet factors is necessary to have the cytokine IL-22 that is critical for the epithelial cells to prosper. These AhRs are also critical for the lymphocytes that live in between the epithelial cells. In fact, without AhR stimulation there are very few of them.

AhR is a critical receptor in many different immune cells; it was first identified in several types of T cells. It is important for the stimulation of the cytokines IL-17 and IL-22 cytokines. There are many different chemicals that can stimulate these receptors in various ways. These AhR receptors have evolved over time to be able to respond to even modern totally new chemicals. Some immune cells have the inability to function without these receptors. Without these receptors there is more dangerous inflammation and less of the critical lymphocytes in the intestine.

AhR receptors also exist in the epithelial cells of the intestine where they respond to a wide range of products from microbes and appear to be one of the main ways that epithelial cells deal with microbes. In this role they increase the immune functions of cells that may not even be traditional immune cells.

N0033005 Bowl of blueberriesIn diets fed to mice with all known micronutrients and vitamins, but no natural fruits and vegetables with their unique compounds, the number of lymphocytes in the total intestine was decreased (but not in the epithelial cells). But, if they were given a product indole I3C that exists in broccoli, Brussels sprouts, kale and cabbage they were maintained. This product doesn’t trigger AhRs itself but instead makes a variety of other active molecules that do (such as diindolylmethane or DIM).

AhRs and Response to Inflammation

From Jacopo Werther

From Jacopo Werther

There is still little known about the human AhR receptors and what food products stimulate them, even though it is clear that green vegetables and some microbes do. Without AhRs, mice develop colitis and other infections with many inflammation related changes. These changes include increased cytokines, scarring and microbes.

Studies show that irritable bowel syndrome among twins is related to high fat Western diet. A diet with fewer vegetables is correlated with Crohn’s inflammatory bowel disease. These patients have less AhRs and altered IL-22. If AhRs were present, they showed much stronger immune response. It is not yet known whether fruits and vegetables are the major factors stimulating AhRs, but they seem to be. This could well be the mechanism that allows fruits and vegetables to help the ability of the intestine epithelial cells to keep microbes out.

Signaling Cascades from Micronutrients Meet and Interact in the Nucleus

PD How_proteins_are_made_NSFAll of these active ingredients—vitamins and other micronutrients from food—have cascades of molecules that meet in the nucleus. The interactions between them are extremely complex and just being discovered. They involve the receptors that trigger cascades to the nucleus and, also, special receptors in the nucleus itself. They all interact in extremely complex ways to trigger genetic networks and immune functions. Vitamin D and A are known to be part of this with their own nuclear receptors receptors.

Nutrients are taken in by the intestinal epithelial cells and sent in the blood. Some are altered in the in the liver and kidneys to become important active molecules. The nutrients enter the cells and stimulate receptors inside, which travel to the nucleus, which along with many other factors stimulate genetic networks. Vitamin A binds to the retinoic acid receptor (RAR) and forms the complex retinoic X receptor RXR. This receptor is in the nucleus and affects how retinoids stimulate genetic networks. Each of these have many forms and subunits. These nuclear receptors are varied in different kinds of cells and produce a variety of “response elements” (RAREs).

B0009427 Human skin section, histologyVitamin D from skin that has been modified by the sun goes to the liver and kidney creating active molecules (especially 1,25-(OH)2D3), which stimulate vitamin D receptor (VDR) and complexes with RXR making the vitamin D response elements (VDREs).

Arylhydrocarbons, such as DIM from food and microbes stimulate the AhR receptors. These cascade to the nucleus making other response elements (XREs). Arylhydrocarbons include molecules from plants such as flavonoids, plypheolics, and indoles. They include man made molecules such as synthetic polycyclic aromatic hydrocarbons and substances like dioxin.

All of these receptors utilize very complex nuclear mechanisms involving epigenetic histone tags, transcription factors and many different DNA activators and repressors.

Vitamin D and Immune Cells

From Jatlas wik

From Jatlas wik

Vitamin D is uniquely critical for intestinal lymphocytes (IELs), which are maintained on a daily basis by them. Vitamin D influences the thymus (the center of the T cell development – the critical organizer of the immune system). Vitamin D3 (the active ingredient) interacts closely with Vitamin A in the nucleus. It is critical for the IELs of the intestinal lining and the maintenance of control of the microbes there.

Vitamin D is actually an entire group of different molecules called calciferols, which come from diet in small amount and skin cells stimulated by the sun in larger amount, metabolized from cholesterol. Both D2 and D3 come from food and the distinction between them is not yet totally clear. Animals bring 25 hydroxyvitamin D3. This is inactive and has to be altered (as vitamin A) in the liver and kidney. Also, immune cells can make these active metabolites. Calcitriol, from D3, is the active molecule. D2, or ergocalciferol, is processed to 25-hydroxyergocalciferol. Immune dendritic cells and macrophages have the enzymes to do this, but how they make it is not clear. It is not enough to help the immune cells at the skin. Vitamin D metabolism has critical effects on calcium and phosphorus metabolism and bone. Many people do not have enough Vitamin D in the winter.

Inflammation, Vitamin D and Vitamin A

From Arcadian

From Arcadian

Inflammatory bowel diseases (IBD) are affected by genes (30%) and environment. Both microbes and nutrients play a big role. Both vitamin D and A are important. Without enough vitamin D people can develop asthma, diabetes, autoimmunity and infections. These produce altered T cell activity. There are many different types of T cells that are produced in different circumstances at the skin and intestine. The complex T regulatory cells are produced locally for special conditions and respond to a wide variety of cytokines from human cells and microbes.

Short chain fatty acids from diet (butyrate) are critical for the development of these special T cells. They are clearly related to specific dietary factors, but the research is very complex and not well understood at this moment.

Diet affects health in every way, both stimulating healthy responses and causing disease (obesity, heart disease, cancer and diabetes). These nutrients affect immune cells in complex ways including the development of the critical lymph tissues that create the wide variety of different cells. Microbe products are, also, critical and influence micronutrients and at the same time, microbes are influenced by the diet.

Special types of microbes exist with different diets. Recently, it was found that eating red meat attracts particular microbes that like to eat the meat’s carnitine, which creates a byproduct. This byproduct is absorbed and changed into a substance that produces plaque and clots in the blood vessels causing heart disease. Vegetarians have different kinds of microbes. (See post Five Secrets of Brain Health). One problem with the complexity of this research is the unique responses in the human gut from other research animals.

How Does Diet Influence Immunity

БИОлогиня Commensals_vs_pathogens_mechanismThe extremely complex ways that ingested foods and products made by microbes affect our immunity is just being discovered. The intelligent signaling of epithelial structural cells at the barriers of skin and gut determine the outcome of immune function. These cells make a vast amount of decisions about friendly and non-friendly microbes, as well as calling for and training the exact immune cells that are needed. Through signaling they inform the immune cells whether to react or not to situations and how to build the specialized lymph nodes that deal with unique types of inflammation.They, also, make decisions about digestion.

This back and forth communication is very elaborate. Is it possible to think that these processes are random? How can anyone not see the incredible intelligent work and decision making being done by this one layer of cells? This intelligent communication and decision making between cells is vital for our function at every level?

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  • the_professeur

    A great article and timely to some studying I am doing presently. I do wish you could revert to how you earlier handled graphics in your articles as the reduced size in your current articles don’t able me to make out some of the finer detail.

  • If you are interested in a somewhat more technical representation of the facts Dr. Lieff just presented, please also see examples of the links from atoms to ecosystems in my 2013 review:

    Nutrient-dependent/pheromone-controlled adaptive evolution: a model http://www.ncbi.nlm.nih.gov/pubmed/24693353

    • Also, this was reported today:

      A multitool for cells http://phys.org/news/2015-12-multitool-cells.html and it links cellular intelligence across all cell types via their nutrient-dependent RNA-mediated differentiation: Not by mutations. Not by natural selection. Not by evolution.

      Serious scientists and Jon Lieff link atoms to ecosystems. Theorists wish they could do that, but they won’t take the time to learn how cell type differentiation occurs.

      • Roy Niles

        Not by mutations? Not by natural selection? Not by evolution?
        Here’s your purported explanation of cellular intelligence:

        “CONCLUSION:
        An environmental drive evolved from that of nutrient ingestion in unicellular organisms to that of pheromone-controlled socialization in insects. In mammals, food odors and pheromones cause changes in hormones such as LH, which has developmental affects on pheromone-controlled sexual behavior in nutrient-dependent reproductively fit individuals across species of vertebrates.”

        So pheromones are intelligently controlling sexual behaviors.
        Ask Jon Lieff if he agrees.

        • I don’t care who agrees. If they do not have a model that links atoms to ecosystems for comparison, they are theorists.

          Jon Lieff is not a theorist. See also: http://jonlieffmd.com/blog/alternative-rna-splicing-in-evolution

          • Roy Niles

            Of course he’s a theorist. All good scientists are theorists. All of them are open to learning more about their fields and are especially open to learning from their inevitable mistakes to revise their theories.
            If you were an actual scientist, you’d be eager to ask him whether or not he agrees that pheromones are intelligently controlling sexual behaviors.

            Linking atoms to ecosystems for comparison? Is that supposed to be a model for linking pheromonal intelligence to evolution? Well in the sense that atoms exist in pheromones, there’s apparently a purpose involved for them to be there. But it’s a bit of a stretch if you’re implying that the purpose is to add intelligence to the pheromone.
            OK, so of course you’re not implying that because purposes have never been a part of your “scientific” calculations.

          • Roy Niles. Stop it! You cannot understand anything about what serious scientists understand and you are mocking us all.

            See Kohl, James V. (2014): Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems. https://dx.doi.org/10.6084/m9.figshare.994281

            Ask questions about the model. If Jon Lieff did not understand it, that’s what he would do. That’s what all intelligent people do.

          • Roy Niles

            You’re not a serious scientist, Kohl. You don’t have legitimate scientific training and you have no university degrees to show for it. I on the other hand have a degree in both psychology and philosophy from UC Berkeley, and worked for over twenty years doing psychological assessment work in counterintelligence for the Feds during the cold war..
            And I note that again you’ve ducked the question as to whether or not your pheromones can act intelligently. Afraid to ask Dr. Lieff? Apparently so.

          • I worked as a medical laboratory scientist for 39 years and am still credentialed by the American Society for Clinical Pathology. But, you’re right. I could not think slowly enough to get a university degree, and decided not to waste any more money trying to be like most Berkeley grads.

          • Roy Niles

            You were a lab assistant, not a scientist. But yes, you obviously can’t think slowly enough to deal with the hard and harder questions that scientists deal with on much higher levels of abstract analysis.

          • For most of my career, I was a medical laboratory manager. For your entire life, it appears that you have been nothing more than a moron who attacks others with invented claims that are not supported. Simply put, you are a liar.

          • Roy Niles

            You were not a scientist, and you are lying when you say you are. I have invented no claims, so you’re the liar there as well, and I’ve caught you at it every time we have these exchanges.
            For my entire life I’ve contributed work of value to my fellow citizens – you’ve contributed nothing but a scam.

          • My ASCP member ID is 25331607 and my Certificate number is 232572. It is issued to me as a Medical Laboratory Scientist and must be renewed every three years after completion of continuing education credits.

            What kind of investigator claims I am not who and what I say I am and continues to denigrate my works? What kind of person does that?

            A Berkeley grad? Of course.

            The biology department at Berkeley does not seem to be teaching students the difference between a mutation and an amino acid substitution.

            See http://evolution.berkeley.edu/evolibrary/glossary/glossary.php?start=g&end=m

            amino acid
            A building block of proteins.
            There are about 20 amino acids and protein-coding DNA tells the
            cellular machinery which amino acids to use to build a particular
            protein.

            mutation
            A change in a DNA sequence, usually occurring because of errors in replication or repair. Mutation is the ultimate source of genetic variation.

            All serious scientists know that ecological variation is the source of genetic variation and they known how to link atoms to ecosystems. Berkeley is still teaching students to become biologically uninformed science idiots who believe in neo-Darwinian nonsense.

          • My ASCP member ID is 25331607 and my Certificate number is 232572. It is issued to me as a Medical Laboratory Scientist and must be renewed every three years after completion of continuing education credits.

            What kind of investigator claims I am not who and what I say I am and continues to denigrate my works? What kind of person does that?

            A Berkeley grad? Of course.

            The biology department at Berkeley does not seem to be teaching students the difference between a mutation and an amino acid substitution.

            See http://evolution.berkeley.edu/evolibrary/glossary/glossary.php?start=g&end=m

            amino acid
            A building block of proteins.
            There are about 20 amino acids and protein-coding DNA tells the
            cellular machinery which amino acids to use to build a particular
            protein.

            mutation
            A change in a DNA sequence, usually occurring because of errors in replication or repair. Mutation is the ultimate source of genetic variation.

            All serious scientists know that ecological variation is the source of genetic variation and they known how to link atoms to ecosystems. Berkeley is still teaching students to become biologically uninformed science idiots who believe in neo-Darwinian nonsense.

          • My Mensa membership number is1072386

            Thank God, I was intelligent enough to not let anyone teach me to become a biologically uninformed science idiot.

          • Roy Niles

            Wow, how desperate can you get, trying to prove that since you’ve joined Mensa, you’re immune from being seen as what very well may be a successful psychopath.

          • Why are you so desperate to continue characterizing me as a psychopath despite my refutations of all your ridiculous claims about my background, expertise, and intelligence?

            Is it because you are the psychopath, Roy Niles? Alternatively, is it because you are the most biologically uninformed science idiot that most people will ever encounter?

          • Roy Niles

            You’re a refutation expert only in your own mind. And by the way, I’ve never made a claim about your intelligence, per se. I’m not the one here that calls everyone that disagrees with him an idiot. A very unintelligent response to criticism for one who claims to have put their intelligence to much better use than credentialed scientists have.

          • I am a credentialed scientist and a member of Mensa, Roy Niles. I call you an idiot because you refuse to learn. Others are merely biologically uninformed, but you take it to the next level. Those who are biologically uninformed and refuse to learn must be called biologically uninformed science idiots to distinguish between them and intelligent people.

          • Roy Niles

            You are NOT a credentialed scientist, even though you want us to believe that an association you belonged to gave you a piece of paper awarding you that designation. As to being a member of Mensa, that’s a joke, unless you’re not intelligent enough to know that having an above average IQ is no guarantee that you will have the capacity for the abstract thought that analytical science requires.
            You have repeatedly demonstrated here that you don’t have the capacity to “explain” anything about the theories that you are claiming to have intelligently proposed.
            And you have proven this repeatedly by, among many other attempts to avoid any intelligent explanations, your continued refusal to present your “intelligent pheromone” theory to Dr.Lieff for his examination.

          • Roy Niles

            With that, I think I’m done with you, unless of course you feel you’re not done with me.

          • I can’t resist responding to your ridiculous claims because they exemplify what others might also believe. You are showing serious scientists and non-scientists alike how much damage has been done by those who tout neo-Darwinian pseudoscientific nonsense.

            Most people may not realize how much ignorance there is among those who believe that de Vries definition of mutation and assumptions about how long it might take accumulated mutations to lead to evolution of a new species have some sort of explanatory power.

            Can you imagine what might happen if a medical laboratory scientist reported test results based on definitions and assumptions about biologically-based cause and effect?

          • Roy Niles

            And you continue to pretend that I must be a neo-Darwinist when I specifically told you that I’m a follower of James A Shapiro’s theories of adaptive mutation – also referred to by some as a self-engineering or self-adaptive process. Proving that as usual, you’re either incurably ignorant or a patent liar.

            As to de Vries, although I’ve never mentioned him in anything I’ve written on the subject, he was instrumental in discovering what we now refer to as mutations, and when you state that “how long it might take accumulated mutations to lead to evolution of a new species” does NOT have some sort of explanatory power, you show how deep your ignorance of the subject goes.

            As to having a lab assistant that based test results on what would be correct assumptions as to biologically based cause and effect, that’s the one I’d want to keep.
            And yet instead, they gave you the prize for discovering somehow that pheromones were causatively effective?

          • I received two awards. The first for publication of “Human pheromones: integrating neuroendocrinology and ethology” (with co-authors) http://www.nel.edu/22_5/NEL220501R01_Review.htm

            The second for a review that was concurrently published as a book chapter in the Handbook of the Evolution of Human Sexuality. — author’s copy here: “The Mind’s Eyes: Human pheromones, neuroscience, and male sexual preferences” http://www.sexarchive.info/BIB/kohl.htm

            Both award-winning reviews linked the accurate representations we made in our 1996 review

            From Fertilization to Adult Sexual Behavior http://www.hawaii.edu/PCSS/biblio/articles/1961to1999/1996-from-fertilization.html to RNA-mediated nutrient-dependent pheromone-controlled behavior in species from microbes to humans without any pseudoscientific nonsense about mutations and evolution.

            That’s why Roy Niles has been an ongoing, insulting antagonist. He wants to continue to believe in Shapiro’s nonsense about adaptive mutations like all other biologically uninformed science idiots want to do. Has he made that perfectly clear to everyone?

            We linked everything what is known about

          • Roy Niles

            Yes, I HAVE tried to make it perfectly clear as well that you are NOT a believer in adaptive mutation, and the reason you don’t consult Dr. Lieff about the evolutionary purposes of pheromones is because he IS a supporter of those that belong to what I’d like to call the Shapiro school.
            Aren’t you glad we’ve got that straightened out?

          • Now, you’re going to tell others what Jon Lieff believes.

            Viruses perturb nutrient-dependent RNA-mediated DNA repair, which is why they can readily be linked from accumulated mutations to all pathology. Claims that mutations are adaptive mutations can only be associated with pseudoscientific nonsense that does not link atoms to ecosystems.

          • Roy Niles

            You keep digging that grave deeper, don’t you.
            Explain, if you can, HOW evolutionary purposes are fulfilled by some newly intelligent way that atoms link to the ecosystems that in my old fashioned view wouldn’t exist at at were it not for atoms.
            Or have you discovered some newly active atoms to go along with those newly active pheromones?

          • What purposes are you claiming are “evolutionary purposes?” How do you link atoms to ecosystems via “evolutionary purposes?” How did Shapiro do it?

          • Roy Niles

            Evolution does not operate by pure accident, as every change that is selected by the organism as so far being beneficial to its survival was selected for that exploratory purpose. Selected BY the organism and not by the accident. Chosen as an optional trial by the organism and not by the accident.
            A true neo-Darwinist will tell you that the accidents themselves are responsible for the selections and that deaths that can be attributed to a bad selection will not allow the selectees to evolve. Nice, except that non-intelligent accidents can’t select intelligent results.
            Sorry if this is getting too complicated for a Mensa member, but I just can’t seem to make it any simpler.
            And since nobody that I know of understands what you mean by having atoms linking to ecosystems when it’s the ecosystems that could not have evolved without the use of their atomic structures, I don’t know how you think about them in some other operative way that has not been obvious to anyone who is actually in the evolutionary sciences business, including the microbiologist, James A Shapiro, who is, believe it or not, really and truly an actual evolutionary scientist.

          • Every serious scientist I know links atoms to ecosystems via hydrogen-atom transfer in DNA base pairs. Perhaps Shapiro really is just an evolutionary scientist who knows nothing about the biophysically constrained chemistry of nutrient-dependent RNA-mediated protein folding in the context of the physiology of reproduction in all living genera. Or perhaps you know nothing about Shapiro, too.

          • Roy Niles

            It seems that since you clearly have never understood the adaptive mutation process, you’re clinging to some cockamamie process that, as you seem to believe, cannot have a purpose, but even so manages with consistent force (which is what is meant by constrained ) to operate contrarily by accident to somehow help or cause (but not to gather or select) nutrients to allow RNA to fold protein, which doesn’t need to be explained further since the folding is plainly being done in the context of the physiology of reproduction.
            Weasel wording to the max is all a real biological scientist can say about that “explanation.”
            You really don’t know the purposes for protein folding, do you. And if you don’t think Shapiro knows either, we’re at an impasse.
            A good scientist is open to learning something new, and trusts that someone like Shapiro might have something new to teach. A self anointed scientist is less willing to have his opinions changed, for fear that his whole theory will go down the drain of uselessness.
            Another reason, perhaps, that you won’t consult with Dr. Lieff on any of the “theories” that you’ve publicly proclaimed to be certainties. Especially as you’ve apparently taught yourself that for economic purposes you must really and continuosly tell yourself that you believe in them.

          • Many years before he published, we detailed RNA-mediated cell type differentiation in our 1996 review and in 1995 I included the links across species in a co-authored book for a general audience. You are twisting my words into something of your own making, which is ridiculous.

            If Shapiro is not using the weasel words of evolutionary theory, you should simply explain how he linked atoms to ecosystems via perturbed protein folding in the context of the nutrient-dependent physiology of reproduction. Otherwise, the only conclusion that can be reached here is that you are a moron.

          • Roy Niles

            Hah, like many of the internet provocateurs, who have no valid arguments available, you resort to an insult as a substitute for your missing argument.
            But you seem to have hesitated to call Shapiro a moron as well for letting me believe his “weasel word” theory as opposed to believing yours.
            And thus the logical opposing conclusion would have to be that you are a moron for resorting to the form of argument where a cogent explanation by you, as the theorist, is impossible to be arrived at all.
            So your dodge as usual is that you co-authored a book in the past that explained then what you are continuing to fail to explain in the present. And I see that protein folding now, in the brightness of your Mensa mind, involves perturbation rather than, or in addition to, constraint. No explanation needed there as well.

            You have the floor now to continue with your insults. Anything, I suppose, to avoid consulting on these matters with Dr. Lieff.

          • Hopefully, Dr. Lieff is nearly finished writing his next article on nutrient-dependent RNA-mediated links from atoms to ecosystems via the immune system and physiology of reproduction.

            This week’s issues of “Science” and “Nature” extend the information about diet and immunity to differences in human morphological and behavioral phenotypes. It is clear that the differences in modern humans are linked to protection against virus-driven entropy, which links everything known to serious scientists about physics, chemistry, and molecular biology to RNA-mediated DNA repair during the past 6000 years.

          • Roy Niles

            There’s nothing in those articles that allow you to logically jump from evolving differences in human “morphological and behavioral phenotypes” to a “clear” determination that differences in modern humans are “linked” in any causative sense at all to protection against “virus-driven entropy”- a meaningless phrase that only you have been known to use, without explanation, and mainly in your own “research” and in your repetitively incomprehensible Science and Nature comments.

            And now you claim that any explanations of your RNA-mediated links from atoms to ecosystems will be explained by Dr. Lieff, or so you hope. Your theory being, I expect, based on the philosophical conjecture that everything in nature must be linked in some way to every other thing. But wait, that theory would require some grasp of inductive logic to explain the proposition, yet for which the factual evidence you’ve been logically required to present as proof of concept has been completely lacking.

            So I’m confident you will find another way to stall the necessity for any use of logic as an explanation for anything, but then again it’s my prediction that you’ll never prove your pudding’s for the eating even if some day you might in the end decide, logically and/or experimentally, to even try.

          • Dr. Lieff will continue to link “Alternative RNA Splicing in Evolution” to the morphological and behavioral diversity of “The Uniquely Talented and Intelligent Octopus” via what is known to serious scientists about nutrient-dependent-pheromone-controlled cell type differentiation in the context of links from atoms to ecosystems.

            All serious scientists are doing that, and he is helping us by reporting results in a format that more people can understand. Serious scientists may also want to see: Role of olfaction in Octopus vulgaris reproduction http://www.ncbi.nlm.nih.gov/pubmed/25449183

            Excerpt: Future work on O. vulgaris olfaction must also consider how animals acquire the odours detected by the olfactory organ and what kind of odour the olfactory organ perceives. The OL acting as control centre may be target organ for metabolic hormones such as leptin like and insulin like peptides, and olfactory organ could exert regulatory action on the OL via epigenetic effects of nutrients and pheromones on gene expression (Kohl, 2013; Elekonich and Robinson, 2000). — p. 61

            Kohl (2013) is my review

            Nutrient-dependent/pheromone-controlled adaptive evolution: a model http://www.ncbi.nlm.nih.gov/pubmed/24693353

            I am grateful to Dr. Lieff for helping others to learn about the works of serious scientists and my model.

            I wonder what attracts psychopaths like Roy Niles to blog sites designed for discussion of epigenetically effected top-down causation, but the behavior of psychopaths remains a mystery and no effective treatment is available so far as I know.

          • Dr. Lieff will continue to link “Alternative RNA Splicing in Evolution” to the morphological and behavioral diversity of “The Uniquely Talented and Intelligent Octopus” via what is known to serious scientists about nutrient-dependent-pheromone-controlled cell type differentiation in the context of links from atoms to ecosystems.

            All serious scientists are doing that, and he is helping us by reporting results in a format that more people can understand. Serious scientists may also want to see: Role of olfaction in Octopus vulgaris reproduction http://www.ncbi.nlm.nih.gov/pubmed/25449183

            Excerpt: Future work on O. vulgaris olfaction must also consider how animals acquire the odours detected by the olfactory organ and what kind of odour the olfactory organ perceives. The OL acting as control centre may be target organ for metabolic hormones such as leptin like and insulin like peptides, and olfactory organ could exert regulatory action on the OL via epigenetic effects of nutrients and pheromones on gene expression (Kohl, 2013; Elekonich and Robinson, 2000). — p. 61

            Kohl (2013) is my review

            Nutrient-dependent/pheromone-controlled adaptive evolution: a model http://www.ncbi.nlm.nih.gov/pubmed/24693353

            I am grateful to Dr. Lieff for helping others to learn about the works of serious scientists and my model.

            I wonder what attracts psychopaths like Roy Niles to blog sites designed for discussion of epigenetically effected top-down causation, but the behavior of psychopaths remains a mystery and no effective treatment is available so far as I know.

          • See: http://jonlieffmd.com/blog/alternative-rna-splicing-in-evolution

            On 10/27/13 Jon Lieff wrote:
            I very much appreciate your comments on pheromone communication and its rapid and critical link to the olfactory brain. I look forward to any current references and future work to help understand the immune brain connection as well as communication in general.

          • Re: Roy Niles claim about “…protection against “virus-driven entropy”- a meaningless phrase that only you have been known to use, without explanation…”

            See also: http://medicalxpress.com/news/2015-01-reveals-cancer-causing-virus-blocks-human.html Viral microRNAs are known to prevent host cell death, promote host cell growth and dampen the host cell’s viral defenses. “I was actually surprised that all these different viruses had converged on the same mechanism for blocking the body’s defenses,” said Sullivan. “As a biologist, this is evolutionary gold.”

            Evolution of Intelligent Viruses and Jumping Genes
            http://jonlieffmd.com/blog/evolution-intelligent-viruses-jumping-genes

          • Roy Niles

            Where does that say “virus-driven entropy”?

            Also, don’t forget to ask Dr. Lieff if he shares your poor opinion of what you referred to as the weasel worded science of James A Shapiro and the adaptive mutation theories that he supports.

          • Roy Niles

            That was in 2013. What has Dr. Lieff written since, and will he confirm your contentions sometime in 2016 that pheromones are functionally designed to give intelligent meaning to their messages?

          • Roy Niles

            Just like the usual con artistry, you’ve stuck in this totally irrelevant conjecture, “The OL acting as control centre may be target organ for metabolic hormones such as leptin like and insulin like peptides, and olfactory organ could exert regulatory action on the OL via epigenetic effects of nutrients and pheromones on gene expression (Kohl, 2013; Elekonich and Robinson, 2000),” which has nothing to do with your previous “promise” that RNA-mediated links from atoms to ecosystems will be explained by Dr. Lieff, or so you hope. Evidently you don’t hope that anymore.
            You can keep using these deceptive tactics to fool some of the people some of the time, but once you mentioned your association with Mensa you may have sealed your doom, as you are certainly not giving them anything to help their reputation for filtering out the nutcases as prospective members.

          • Roy Niles

            There’s nothing in those articles that allow you to logically jump from evolving differences in human “morphological and behavioral phenotypes” to a “clear” determination that differences in modern humans are “linked” in any causative sense at all to protection against “virus-driven entropy”- a meaningless phrase that only you have been known to use, without explanation, and mainly in your own “research” and in your repetitively incomprehensible Science and Nature comments.

            And now you claim that any explanations of your RNA-mediated links from atoms to ecosystems will be explained by Dr. Lieff, or so you hope. Your theory being, I expect, based on the philosophical conjecture that everything in nature must be linked in some way to every other thing. But wait, that theory would require some grasp of inductive logic to explain the proposition, yet for which the factual evidence you’ve been logically required to present as proof of concept has been completely lacking.

            So I’m confident you will find another way to stall the necessity for any use of logic as an explanation for anything, but then again it’s my prediction that you’ll never prove your pudding’s for the eating even if some day you might in the end decide, logically and/or experimentally, to even try.

          • Every serious scientist I know links atoms to ecosystems via hydrogen-atom transfer in DNA base pairs. Perhaps Shapiro really is just an evolutionary scientist who knows nothing about the biophysically constrained chemistry of nutrient-dependent RNA-mediated protein folding in the context of the physiology of reproduction in all living genera. Or perhaps you know nothing about Shapiro, too.

          • Roy Niles

            Evolution does not operate by pure accident, as every change that is selected by the organism as so far being beneficial to its survival was selected for that exploratory purpose. Selected BY the organism and not by the accident. Chosen as an optional trial by the organism and not by the accident.
            A true neo-Darwinist will tell you that the accidents themselves are responsible for the selections and that deaths that can be attributed to a bad selection will not allow the selectees to evolve. Nice, except that non-intelligent accidents can’t select intelligent results.
            Sorry if this is getting too complicated for a Mensa member, but I just can’t seem to make it any simpler.
            And since nobody that I know of understands what you mean by having atoms linking to ecosystems when it’s the ecosystems that could not have evolved without the use of their atomic structures, I don’t know how you think about them in some other operative way that has not been obvious to anyone who is actually in the evolutionary sciences business, including the microbiologist, James A Shapiro, who is, believe it or not, really and truly an actual evolutionary scientist.

          • RE: You are NOT a credentialed scientist, even though you want us to believe that an association you belonged to gave you a piece of paper awarding you that designation.

            I do not care what anyone believes, Roy Niles. Stop denigrating all the members of my profession with your ignorant claims about me.

            See: http://www.ascp.org/About-the-ASCP
            The American Society for Clinical Pathology (ASCP) is the world’s largest professional membership organization for pathologists and laboratory professionals. Our mission is to provide excellence in education, certification and advocacy on behalf of patients,
            pathologists and laboratory professionals across the globe. With more than 100,000 members, the society’s influence has guided the application and evolution of the pathology and laboratory medicine specialty since 1922.

            Certification
            The ASCP Board of Certification (BOC), with accreditation from the American National Standards Institute, is the oldest and largest certification agency for pathologists and laboratory professionals. Administratively independent of the ASCP, the BOC has certified more
            than 450,000 people since it was founded in 1928 and represents the gold standard for certification of pathologists’ assistants and laboratory professionals.

          • Roy Niles

            So now you’re claiming to be a certified pathologist, that is nevertheless writing papers about biological science? Do they call you Doctor Kohl at the ASCP? Will wonders never cease?
            And pheromones actually evolve to think?

          • No, Roy Niles. Now you are claiming that I am “…claiming to be a certified pathologist…” because you are a certifiable lunatic with some sort of known or unknown pathology that causes you to misrepresent two decades of my published works as if I had ever claimed that pheromones evolved to think.

          • Roy Niles

            Actually you have claimed that pheromones cause various and sundry biological entities to evolve. So are you now conceding that they don’t actually “cause” the evolving changes that you have appeared to argue that they do? Or do you just simply not understand the intricacies of biological cause and effect? Hell, they taught me that in high school.

          • Roy Niles

            Try door number three, where you’ll find someone who has learned all the ways that psychopaths will try to trick the average person, and especially how they feign indignation when they are actually emotionally unequipped to feel what real indignation is triggered by.

          • the_professeur

            Thank you, Roy, I hadn’t considered Kohl might be a psychopath, but it makes sense now that you say it.

            I had dismissed his emotional name-calling as part of protecting his income stream.

            He uses a very limited number of unintelligible responses with you just as he did with me. They are almost like a religious mantra they way he throws them out there assuming only idiots don’t know the imaginary significance he has built up around the word salads he serves up.

            Meanwhile, I am enjoying the clear and well thought out articles by Jon Lieff, and I hope you are as well.

          • Roy Niles

            Thanks. You’ve aptly compared the sublime here to the ridiculous.!

          • Roy Niles

            A scientist is defined as a person who is studying or has expert knowledge of one or more of the natural or physical sciences. You have exhibited no expert knowledge in anything except to repeat the mantra over and over regarding nutrient-dependent RNA. And you refuse to deal with the question of your pheromones and their allegedly intelligent activities.

            As to my being a neo-Darwinist, it’s unfortunate that Berkeley still teaches courses that support that version of evolutionary science. Their only excuse would be that most other universities, none of which you’ve ever attended of course, still preach the same doctrine. I happen to be a follower of James A Shapiro at Univ. of Chicago, who introduced me to adaptive mutation years ago.. He hasn’t yet told me that pheromones can think, however.
            Hey, maybe you can ask them to do better job at helping you to carry out your evolutionarily active perfume sales scam!

          • You need only search for “RNA mediated” to be confronted with my expert knowledge of physics, chemistry, and molecular mechanism. which link atoms to ecosystems.

            If Shapiro thinks mutations are adaptive, he has not learned enough about thermodynamic cycles of protein biosynthesis and degradation or virus-driven genomic entropy.

            His 2011 book section on “Signaling from the cell surface to the genome: pheromone response in the sexually aroused yeast cell” could readily have come from our 1996 Hormones and Review — but we provided more details in our section on molecular epigenetics.

            http://www.hawaii.edu/PCSS/biblio/articles/1961to1999/1996-from-fertilization.html

          • Roy Niles

            You can’t help but repeat the same rote memory recitation about molecular mechanisms which link atoms to ecosystems. And worse, the meaninglessly repeated pronouncement about thermodynamic cycles of protein biosynthesis and degradation of virus driven genomic entropy.
            You couldn’t explain what any of that is supposed to mean to a real scientist, and have no real grasp of what you seem to hope we’ll think it means.
            Yes, Shapiro wrote about the uses of pheromones for signaling purposes. But whatever details you’ve allegedly provided re molecular epigenetics, something seems to have prevented you from discussing them with Dr. Lieff.

          • Dr. Lieff probably knows as much or more about alternative splicings and the chromosomal rearrangements that link atoms to ecosystems in species from microbes to humans — as anyone else I have encountered.

            I’m not sure what he knows about the thermodynamic cycles of protein biosynthesis and degradation. I only know that no one can be as ignorant about so many things as you are, Roy Niles.

            http://youtu.be/DbH_Rj9U524

            Thermodynamically “futile” cycles of RNA transcription and degradation (Yap & Makeyev, 2013) may also be responsible for changes in pheromone production that enable accelerated changes in nutrient-dependent adaptive evolution controlled by the microRNA/messenger RNA (miRNA/mRNA) balance (see for review Meunier et al., 2013). Environmental cues, like those that signal the availability of glucose, appear to cause changes in the miRNA/mRNA balance that enable gene expression during developmental transitions required for successful nutrient-dependent reproduction in species from microbes (Park et al., 2010) to man (Jobe, McQuate, & Zhao, 2012).

          • Roy Niles

            Derived from your “summer institute” ramblings: “Mutations do not lead to the evolution of new species because the nutrient-dependent chemistry of protein folding is biophysically constrained by the physiology of reproduction, which enables fixation of the RNA-mediated amino acid substitutions that differentiate all cell types in all individuals of all species during their life history transitions.”

            Did you really write that? It’s absolutely meaningless. The nutrient dependant chemistry of protein folding? That’s an “explanation” of absolutely nothing. Do you have any inkling as to what the purposes for that folding are? A real scientist would be concerned with that, but you can’t seem to grasp why these changes are being made at all. Amino acid substitutes? What are those substitutes accomplishing?
            The irony here is that you have non-intelligent pheromones somehow doing intelligent duties while the amino acid “substitutes” that are actually doing the intelligent work are somehow “differentiating cell types” without a thought.
            You’re the PT Barnum of the biological science world. Fooling some of the people all of the time beats not fooling all of the people some of the time.

            And you still haven’t asked Dr. Lieff what he thinks about your intelligently productive chromosomes, have you? Even though you pretended in that same lecture series that he was one of your main supporters in your search for the transitional truth.

          • Re: Amino acid substitutes?

            NO, you brain-dead MORON. Amino acid substitutions. They stabilize the organized genomes of all living genera via the conserved molecular mechanisms we detailed in our 1996 Hormones and Behavior review.

          • Roy Niles

            The usual Kohl argument by insult when you can’t otherwise explain your “theories.”
            “They stabilize the organized genomes of all living genera via the conserved molecular mechanisms we detailed, etc.” is simply a repeated example of a meaningless bit of garble which you can’t explain intelligently, and didn’t do so either in that 1996 review, because you couldn’t.
            And yes, my spell checker wrote substitutes for substitutions, giving you what you pretend to be an out in that “conserved molecular mechanism” babble when I doubt that you know what a conserved mechanism actually is.
            And you especially don’t know how or why amino acids “stabilize” anything or you’d say so without continuing to duck the question.

          • For most of my career, I was a medical laboratory manager. For your entire life, it appears that you have been nothing more than a moron who attacks others with invented claims that are not supported. Simply put, you are a liar.

          • Roy Niles

            Of course he’s a theorist. All good scientists are theorists. All of them are open to learning more about their fields and are especially open to learning from their inevitable mistakes to revise their theories.
            If you were an actual scientist, you’d be eager to ask him whether or not he agrees that pheromones are intelligently controlling sexual behaviors.

            Linking atoms to ecosystems for comparison? Is that supposed to be a model for linking pheromonal intelligence to evolution? Well in the sense that atoms exist in pheromones, there’s apparently a purpose involved for them to be there. But it’s a bit of a stretch if you’re implying that the purpose is to add intelligence to the pheromone.
            OK, so of course you’re not implying that because purposes have never been a part of your “scientific” calculations.

      • IntelligentAnimation

        jvk, if mutations are not involved, why do they say the following under the heading “An important foundation stone”?:

        “We were then able to confirm this hypothesis experimentally through mutations and using the fluorescence microscope”.
        Are mutations coding for the necessary proteins to carry out the functions of sensing a scent, extending an arm toward that scent and/or stopping the extension? If not, why did they use the word “mutations”?

        • Thanks for asking. Stress-induced mutagenesis experiments were used. They show the need for nutrient-dependent RNA-mediated DNA repair. Repair occurs in the context of links from atoms to ecosystems. Amino acid substitutions stabilize supercoiled DNA in the organized genomes of all living genera. The substitutions are fixed in the context of the physiology of reproduction.

    • Roy Niles

      Note this commentary at Pharyngula on Kohl and his pseudo-scientific grasp of adaptive evolution by the pheromonal smelling of how and why who do which and what:
      http://freethoughtblogs.com/pharyngula/2014/01/06/one-crank-dies-another-rises-to-take-his-place/comment-page-1/
      Also note this comment at: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4049134/#CIT0007
      “Based on his writings, both published and unpublished, James Kohl presents an unsupported challenge to modern evolutionary theory and misrepresentations of established scientific terms and others’ research. It was a mistake to let such a sloppy review through to be published.”

      Somewhat more technical than than what Dr. Lieff has just presented? What’s that I smell?

      • Note this comment at the Science Magazine site and the attempts to discuss what is known to all serious scientists about the links from atoms to ecosystems in the context of the nutrient-dependent support of the innate immune system and RNA-mediated cell type differentiation in all living genera. Bipolar drug turns foraging ants into scouts. http://news.sciencemag.org/biology/2015/12/bipolar-drug-turns-foraging-ants-scouts

        • PZ Myers (at Pharyngula) has a habit of ignoring everything known to serious scientists after he attacks them. See what happens when I ask him to explain why he has continued to ignore the role of chromosomal rearrangements in ecological speciation.
          http://scienceblogs.com/pharyngula/2015/08/14/i-repeat-octopuses-are-not-aliens/

          • Roy Niles

            I see that he ignores those who are only serious scientists in their your minds.

          • For the links from all invertebrates to all vertebrates, see: http://www.ncbi.nlm.nih.gov/pubmed/25449183

            Excerpt: Future work on O. vulgaris olfaction must also consider how animals acquire the odours detected by the olfactory organ and what kind of odour the olfactory organ perceives. The OL acting as control centre may be target organ for metabolic hormones such as leptin like and insulin like peptides, and olfactory organ could exert regulatory action on the OL via epigenetic effects of nutrients and pheromones on gene expression (Kohl, 2013; Elekonich and Robinson, 2000). — p. 61

            Kohl (2013) is my review. http://www.ncbi.nlm.nih.gov/pubmed/24693353

          • Roy Niles

            Pheromones are not olfactory organs. They don’t have a function! It won’t surprise me if the next thing you do is write a paper about the epigenetic effects of farts. Purposeful farting, right?

          • You are both crass and ignorant Roy Niles. Why do you follow me around only to demonstrate that fact?

            For comparison, I cited two published reviews — and both contain many citations to works you know nothing about.

          • Roy Niles

            Tell us then how pheromones act as olfactory organs. You’ve never done that nor cited any “reviews” that you or anyone else have published that scientifically explains that.

            As to following you around, it’s more of the opposite, where I’m offended to find that reputable sites that are devoted to good science are being invaded by pseudo scientific parasites such as you.

          • …how pheromones act as olfactory organs. = IGNORANCE

            …pseudo scientific parasites such as you. = CRASS

          • Roy Niles

            Please elucidate. Show us that you’re not a parasite.

          • Roy Niles

            Please elucidate. Show us that you’re not a parasite.

          • …how pheromones act as olfactory organs. = IGNORANCE

            …pseudo scientific parasites such as you. = CRASS

          • Roy Niles

            Tell us then how pheromones act as olfactory organs. You’ve never done that nor cited any “reviews” that you or anyone else have published that scientifically explains that.

            As to following you around, it’s more of the opposite, where I’m offended to find that reputable sites that are devoted to good science are being invaded by pseudo scientific parasites such as you.

          • Roy Niles

            I see that he ignores those who are only serious scientists in their own minds.

        • Roy Niles

          There was nothing in that comment that supported your theory that your pheromones played a functional role in ant behavior. Ants use smells. Smells don’t use ants.

      • IntelligentAnimation

        Roy, are you kidding me? Kohl presented a scientific paper, replete with supporting experimentation, published in a reputable scientific journal and funded by the National Institute of Health no less, plus he supported it with further NIH papers. You have a BLOG entry from PZ Myers, a Darwinian with an atheism evangelist agenda, on a forum that does NOT allow contrary opinions. (Its “freethought” only if you agree with Myers.)
        And you suppose you hold the higher ground here?

        • Roy Niles

          Note the rest of what I made reference to there, and then check Google for the various sites where Kohl is called out as a fraud. He’s not a scientist, and the closest he came to that was to work as an assistant in an alternative science lab, and most of the scientific papers cited by Kohl were actually written by him to promote his perfume sales business.
          Yes PZ Myers is a Darwinist, but even though I disagree with him on that scale, he’s not a fraud.
          What an atheist evangelist is, I have no idea.

    • PZ Myers inadvertently linked what is known about nutrient-dependent pheromone-controlled life history transitions in octopuses from RNA-mediated cell type differentiation via what is known about supercoiled DNA and chromosomal rearrangements.

      http://scienceblogs.com/pharyngula/2016/01/08/friday-cephalopod-baby-done-growed-up/#comment-845133