Morgellons : A Working Hypothesis
Neural, Thyroid, Liver, Oxygen, Protein and Iron Disruption
(Link to Parts I, II, III – Click Here)
Clifford E Carnicom
Dec 18 2013
Note: I am not offering any medical advice or diagnosis with the presentation of this information. I am acting solely as an independent researcher providing the results of extended observation and analysis of unusual biological conditions that are evident. Each individual must work with their own health professional to establish any appropriate course of action and any health related comments in this paper are solely for informational purposes and they are from my own perspective.
This paper seeks to identify a host of organic compounds that are likely to comprise the core physical structure of biologically produced filaments characteristic of the Morgellons condition. A biological oral filament sample will be analyzed for the presence of candidate organic functional groups using the methods of infrared spectrophotometry. Potential health impacts from these same core structures are examined and compared to the observed , reported and documented symptoms (in part) of this same condition. Potential mitigating strategies, from a research perspective only, are discussed.
A body of evidence, accumulated over a period of several years, reveals that the Morgellons condition is likely characterized by a host of serious physiological and metabolic imbalances. These imbalances are caused by the disruption of a variety of major body processes including, as a minimum, the regulation of metabolism by the thyroid, potential liver enlargement, a decrease of oxygen in the circulatory system, the utilization of amino acids important to the body, the oxidation of iron and a potential impact to neural pathways. The impact of this degradation to human health can be concluded to be serious, debilitating and potentially lethal in the cumulative sense; the reports of those who suffer from the condition are in alignment with these conclusions. This paper will summarize the body of work and chronology which leads to this more comprehensive hypothesis.
The health, medical and governmental communities will again be invited to offer their expertise and contributions , as well as to assume their role of responsibility and the obligations of their professions to serve the public.
This paper will be divided into three parts:
I. Identification of the functional groups / components
II. Potential health impacts of the various functional groups identified.
III. Potential mitigating strategies (research-based)
The infra-red spectrum of the Morgellons oral filament sample in Nujol (mineral oil) on a KCl Real Crystal(TM) card and the interpretation/annotation (working notes) of its fundamental molecular and chemical composition.
It is now understood, to a relatively high level of confidence, the essential molecular and chemical composition of the Morgellons biological filamentous material. This knowledge is a prerequisite to understanding at least a portion of the impact to the body and human health. It now appears, from all available research, that this determined molecular composition can be summarized in the following complex phrase:
The structure of the filament form appears to be, based upon the best available information to date, primarily that of an “polycyclic organo-metallic halogenated aromatic amine”. Substantial evidence also exists for the coupling of a iron-amino acid (cysteine and histidine dipeptide complex). The implications of such a compound and structure upon human health are profound.
The recently acquired spectrum that is shown above, along with all previous research to date, will be important in supporting the conclusions that are presented here. Before we begin with the detailed analysis of this infrared spectrum, let us recall briefly what has already been established with respect to the growth of the structure.
It has been established, through rather painstaking processes over a period of several years, that primary constituents of the growth form are comprised of both iron and amino acids. The methods to achieve this have been described in detail on previous reports. The essence of impact to health has also been discussed at length, namely, that if these elements are used by the organism for its own growth then those same nutrients are being denied to the human host that supports the invasive growth. Your iron is at the core of your respiration and hence of all energy transfer within your body; proteins are the structural framework that allows your body to exist and grow. The absconding of both iron and amino acids (i.e., proteins) from the human body is by itself of sufficient damage to warrant a full and dedicated allocation of resources to this problem; this has not happened to date. This information has, however, been very useful to develop an entire host of strategies to mitigate this damage and these have been discussed on this site. There remains much to do.
Unfortunately, the information that is now gleaned from the use of infrared spectrometry only makes the situation more serious and compelling. There is, however, great value from two standpoints with our current discussion. First, a more comprehensive portrait of the actual structure of the growth form is now established. This is an absolute necessity to understand the expected impacts upon human health, and this problem remains unfinished until the full complement of investigative resources, equipment and personnel are aptly dedicated to this problem, i.e, the “Morgellons” problem. Second, and of even greater importance, is that the primary mechanisms of compromise and damage to human health are now identifiable to a greater extent. Armed with this knowledge, there is every reason to think that more effective strategies of alleviating suffering and improving health are at hand. This has been and remains a primary pursuit of this researcher. The health and medical communities are required to assume their role to evaluate the veracity of this information and to implement any potential benefits that might result from this work.
We now transition to the powers of infrared spectrophotometry, and what it can teach us about the current situation. To begin that process, let us devote a few words to the generalities of spectroscopy. One could easily devote a career to the study of this discipline alone; the history, the literature and the science itself is detailed and extensive. This speaks of the utility, value and importance of the methods. I will make no claim to being an expert in the field but I have applied myself in this, as well as dozens of other disciplines, to get certain questions answered in the face of urgency and need. An understanding of at least the basic science is in order.
Spectrometry, in general, is the response of matter to electromagnetic energy. Spectrophotometry, in particular, is the reaction of matter to light waves, i.e., a specific and limited window within the electromagnetic spectrum. Furthermore, this light energy can be broken down into ultraviolet, visible and infrared light sections. When matter is subjected to the energy of the light source, it gets excited or vibrates. Depending upon the portion of the spectrum involved (i.e., visible, UV, IR) this excitement or vibration occurs in different forms. Carnicom Institute now owns both a modern visible light spectrophotometer and an infrared spectrophotometer (albeit aged but functional) and the public is to be commended for that accomplishment. Our focus within this paper is specifically infrared spectrophotometry (IR).
Infrared spectroscopy is an absolute core and stalwart of biochemical study for the following simple reason : it can be used to identify organic molecules, i.e., the stuff of life (natural or engineered, for that matter..). Visible light spectroscopy is useful if whatever you are looking at has color; in practice it will be found that this has serious limitations. The majority of organic molecules are transparent and have no color; you can not see them with your eye. This correspondingly makes the process of identification inherently difficult. What happens in the infrared spectrum is that molecules vibrate in characteristic ways that are known, understood and catalogued and this is helpful in identifying what are called “functional groups” in the discipline of biochemistry. Functional groups are combinations of molecules within biology that have identifiable characteristics and behavior. As has been mentioned, infrared spectrometry can be a lifelong pursuit of study in its own right; there is no magic single button that gives one a printout of what something is made of. The “building blocks” of a biological structure can be identified with the use of IR, but it is unrealistic to expect complete and total knowledge of detailed molecular composition. There are databases built into modern equipment that can radically accelerate the problems and details of IR interpretation, but even these will not address many of the problems at hand. This is especially the case if we are dealing with unknown, newly synthetic or engineered substances or complexes. There is both art and science in the practice of IR spectroscopy and those expert in the field are to be commended for their own dedication to the subject. The work that I offer here will, hopefully, point us in the right direction and allow us to anticipate what we are trying to see at the end of the tunnel. There are a host of other technologies (including additional spectroscopy methods) and instrumentation which could give us the level of knowledge and detail that is to our benefit and need; Carnicom Institute has no such access to what is truly needed at this time.
Now we must dig a little deeper, and into the thick of it. For those willing to expand your study of the discipline I encourage you to do so. For those that have the knowledge already, it is time to bring our best foot forward and make the analysis. It is time to study the spectrum presented above.
The instrument in use is a Perkin-Elmer 1320 Infrared Spectrophotometer, a dual beam dispersive IR instrument. The sample substrate being used is that potassium chloride (KCl) in an International Crystal Laboratories Real Crystal IR Sample Card (TM). Considerable time has been spent with study of numerous reference spectra and the oral sample spectrum using a polyethylene substrate; the advantages of uniform transparency to IR with KCl are immediately apparent as they have recently become available. KCl is highly preferred in many respects as, for example, it is free from the interference of Nujol and polyethylene absorbances and the transmittance in the IR spectrum is also extremely high and uniform across the range of 4000 to 600 cm-1. This substrate form is also unique in that it will handle a certain level of water in the preparation of the sample on the salt crystal.
Reference spectra of KCL and Nujol on KCl plates to address any questions of interference in the spectral interpretation:
Example of the uniform transmittance of the reference KCl crystal as a sample substrate; an ideal IR material without interference absorption.
Reference IR spectrum of Nujol (mineral oil) on KCL plates. Nujol is a useful substrate for solid samples. Notice the only significant interference absorption peaks will be at approximately 2900 cm-1 and 2850 cm-1.
In the case here, the oral sample is collected and thoroughly rinsed and the moisture evaporated from the sample. The sample is then ground to a fine powder with mortar and pestle and mixed with Nujol (mineral oil) to a uniform consistency. A drop of the compound is then placed on a KCl Real Crystal (TM) along with a KCl cover slip. Any and all moisture must be completely driven from the sample before proceeding to avoid contamination of the spectrum with water; this is accomplished by evaporating the sample under mild heat to completion. The tools of analysis and cross-referencing applied to the interpretation of the absorption peaks will be as follows:
1. Infrared Absorption Spectroscopy – Practical, Koji Nakanishi.1
2. Reprint of Colthrup Chart of Characteristic Group Absorptions in Modern Methods of Chemical Analysis, Pecsok.2
3. IR Pal Software 2.0, , A Table Driven Infrared Application, Dr. Wolf van Heeswjik.3
4. Spectral Database for Organic Compounds (SDBS), National Association of Advanced Industrial Science and Technology (AIST), Japan.4
The initial method of analysis will focus on the use of IR Pal and correlated Nakanishi. The work will progress through a series of iterations: the first stage will identify candidate functional groups, a second stage will examine the candidates from a geometric-graphical perspective, and a third stage will examine cross-correlations between the candidate functional groups. The final stage will form from a composite of all three approaches, as well as integration of knowledge gained from previous research. The end goal will be to create a more comprehensive assessment of the expected structural-chemical composition of the growth form. A leading discussion into potential health implications will be initiated along with the call for continued research under urgent conditions.
The Candidate Stage:
The first absorbance peak, occurring in the functional group region, is at approximately 3390 cm-1. The 3390 cm-1 absorption peak (transmittance minimum) leads us to the following candidates:
IR Pal : 3390 cm-1 candidates
The functional group candidates here will therefore be carboxylic acids and aromatic phenols.
Our next absorption peak is at approx. 3150 cm-1. The candidates are:
The candidates list is restricted to carboxylic acid functional groups in this case.
Next we have a major absorption peak in the range of 2850-2950 cm-1. The candidate list is:
Our list of functional groups at the broad absorption peak includes alkanes and carboxylic acids.
Our next absorption peak is a minor peak at 2730 cm-1:
This introduces an aldehyde functional group for consideration.
Another minor peak absorption at approximately 2680 cm-1:
which leads to the consideration of a phosphoric acid group.
Our next absorption peak (i.e., transmittance minimum) is at approximately 2360 cm-1:
This now includes consideration of the miscellaneous categories of a phosphine and a silane. Next we see a minor absorption peak at approximately 1730 cm-1:
This minor peak introduces the consideration of both aldehydes and esters. We also note the reference to the 6-ring structure, i.e., the possibility of aromatic structure appearance.
Our next absorption peak is at approximately 1625 cm-1:
This search lists amides, amines, alkenes (notice aromatic reference again) and a C=N double bond structure.
The next absorption peak is at 1430 cm-1:
Our candidates here are a sulfate ester and, once again, an aromatic structure.
The next absorption peak is at approximately 1360 cm-1:
Here we have the following entries: an aromatic amine, sulfonyl chloride, sulfate ester, an alkane group and an N-O (nitrogen oxygen single bond).
The next absorption peak is at 1140 cm-1:
Numerous candidate groups appear here: alkyl halides, ethers, amines, thiocarbonyl, sulfone, phospine, phosphine oxide, phosphate, carboxylic acids and esters.
The next absorption peak (minor) is at approximately 1025 cm-1:
Here we have a listing of alkyl halides, phosphine, P-OR esters, Si-OR, carboxylic acids and esters.
Our next absorption peak is at approximately 920 cm-1:
This set includes a P-OR ester and a carboxylic acid group.
Lastly, we have a strong absorption peak at approximately 710 cm-1:
This final candidate list shows an alkene, a strong presence of aromatics, a S-OR ester and an amine.
We are still at the early stage of analysis of the spectrum. It is of interest, however, even at this early stage to identify groups or combinations that are showing an increased relative frequency within the tabular listings. It will be found that such groups, terms or combinations such as:
sulfur (or derivatives)
phosphorus (or derivatives)
are present at a relatively increased level. We will keep these terms in mind, along with others, as we continue in the analysis below:
Our next phase of work is to begin screening, or filtering , the data that we have to work with as it can be a bit daunting at this stage of collection. We must be careful in this process, however, not to lose critical data along the way. The approach taken will be to look at cross-correlations in the data and to look for some of the patterns that may be stronger than others within the data set. Correlations identified will tend to strengthen the case for the existence of the group; they will be identified as weak, moderate or strong respectively. IR Pal infrared tabular software excels at this approach, and is to be commended as highly valuable software for assisting in infrared spectral analysis. Let us begin, and once again take each candidate absorption peak individually.
Begin with the absorption peak at 3390 cm-1.
With the first carboxylic acid group, correlations are suggested at approximately 1710 cm-1. Our closest peak here is at 1730 cm-1. The 1730 cm-1 peak is also listed as strong. This correlation would appear reasonably weak at this point, and this rating will be assigned tentatively at this time.
The second carboxyl acid group shows a possible relation at 1690 cm-1, also listed as a strong peak. This correlation is also determined to be weak at this time. This same carboxylic acid shows correlations with alkenes at 3020, 1660, 725-675, 1675, 970 cm-1 respectively. Of this set, the 725-675 cm-1 of medium strength is of strongest interest, and will be assigned a strong rating. The remaining peaks do not indicate correlation with the 3390 cm-1 absorption peak.
The phenol group indicates a correlation with an alkane expected at 3000-2850 cm-1. This will be rated as a strong correlation because of the observed broad and strong absorption peak at approximately 2950-2850 cm-1.
Correlation Summary : 3390 cm-1:
Carboxylic Acid > Alkene (725-675)
Phenol > Alkane (3000-2850)
Carboxylic Acid > Carboxylic Acid (1730)
Carboxylic Acid > Carboxylic Acid (1690)
Our next correlation search is at 3150 cm-1:
It will be seen that the discussion for the carboxylic acid group here is identical to that discussed for the case at 3390 cm-1 so the appropriate correlations are listed below:
Correlation Summary : 3150 cm-1:
Carboxylic Acid > Alkene (725-675)
Carboxylic Acid > Carboxylic Acid (1730)
Carboxylic Acid > Carboxylic Acid (1690)
Our next correlation search is at 2850-2950 cm-1:
The correlations of interest from the initial alkane group will be all subsidiary alkane groups shown, at moderate to strong levels. Continuing with the second carboxylic acid group:
A weak relationship may or may not exist with the carboxylic group at 1710 cm-1.
Correlations of the carboxylic acid group with the alkene at 1660 cm-1 is rated as weak. The correlation at 725-625 cm-1 is strong. The correlation at 1675 cm-1 is weak. The correlation in the range from 3400 – 2800 cm-1 is strong, and the correlation at 1690 cm-1 is weak to marginal.
Correlation Summary : 2950-2850 cm-1:
Alkane > Alkane (722, 1360)
Carboxylic Acid > Alkene (725-675)
Carboxylic Acid > Carboxylic Acid (3400 – 2800)
Alkane > Alkane (1375)
Alkane > Alkane (1460, 1375)
Carboxylic Acid > Carboxylic Acid (1710, 1690)
Carboxylic Acid > Alkene (1710, 1675)
Our next correlation search is at 2730 cm-1:
The correlation of the aldehyde candidate with the potentially associated aldehydes at 1725 cm-1 and 2820 cm-1 are rated as strong. In summary:
Aldehyde > Aldehyde (1725, 2820)
Our next correlation search is at 2680 cm-1:
No correlations are identified with the candidate phosphoric acid group.
Our next correlation search is at 2360 cm-1:
The phosphine candidate has a weak prospective correlation with the phospine group ranging from 1250 to 950 cm-1, based upon the observed absorption peaks at 1140 cm-1 and 920 cm-1. Notice the character of these latter peaks is listed as weak, however, and this is especially questionable with regard to the observed peak at 1140 cm-1.
No additional correlation opportunities are listed for the silane candidate.
The next search is at 1730 cm-1:
The first aldehyde group has potential correlation to the aldehydes at 2720 cm-1 and 2820 cm-1, rated as strong.
The ester group at 1735 cm-1 has potential correlation to the strong ester peak between 1320 cm-1 and 1000 cm-1, rated as moderate at this point with consideration of the sharp observed peak at 1140 cm-1.
The second ester group at 1735 cm-1 has the same relationship as the prior case. We do note, however, that this ester is a 6-ring structure. This is to be kept in mind with respect to any aromatic structural discovery. In summary:
Ester > Ester, Ester (6-ring) (1320-1000)
The next search is at 1625 cm-1:
The amide group candidate shows no correlations of significance.
The amine group candidate shows amine correlations at 3400 cm-1, 1640-1560 cm-1, 1230-1030 cm-1 and 910-665 cm-1. These correlations are rated as strong.
The aromatic alkene candidate group shows correlations to the meta-disubstituted aromatic at 700 cm-1, the 1,2,3 trisubstituted aromatic at 745-705 cm-1, and the 1,3,5 trisubstituted aromatic at 730-675 cm-1. These are rated as strong from the observed absorption peak at 710 cm-1.
and lastly for this segment at 1625 cm-1:
Here we have no correlations shown for the carbon-nitrogen double bond.
Amines > Amines (3400, 1640-1560, 1230-1030, and 910-665.)
Aromatic Alkene > meta distributed aromatic (700)
Aromatic Alkene > 1,2,3, trisubstituted aromatic (745-705)
Aromatic Alkene > 1, 3, 5 trisubstituted aromatic (730-675)
Next, we investigate any correlations at 1430 cm-1:
We see that no additional correlations exist for the sulfate.
The aromatic group also does not present any correlations of note.
We proceed now to correlation examination at 1360 cm-1:
The amine group (aromatic) shows strong correlation to the monsubstituted aromatic at 700 cm-1, to the meta-disubstituted aromatic at 700 cm-1 and to the 1,3,5 trisubstituted aromatic at 730-675 cm-1. Moderate correlation to the ortho-disubstituted aromatic exists at 770-735 cm-1.
The sulfonyl chloride does not show any significant correlations; the observed peak at 1140 cm-1 is expected to be outside of the 1190-1170 cm-1 range and beyond the errors of observation.
Similarly, the sulfate group shows no correlations present.
The alkane group shows alkane correlation at 3000-2850 cm-1 at a strong level. The correlation at 1460 cm-1 is rated at the weak level. The correlations at 1375 cm-1 and 722 cm-1 are rated at the moderate level.
The N-O single bond shows N-O moderate correlation at 1380 cm-1 and at 1350 cm-1.
Correlation Summary : 1360 cm-1:
Alkane > Alkane (3000-2850)
Amine (Aromatic) > mono-substituted Aromatic (700)
Amine (Aromatic) > meta-disubstituted Aromatic (700)
Amine (Aromatic) > 1,3,5 tri-substituted Aromatic (730-675)
Alkane > Alkane (1375, 722)
N-O > N-O (1380, 1350)
Amine (Aromatic) > ortho di-substituted Aromatic (730-675)
Alkane > Alkane (1460)
The next examination is at 1140 cm-1:
The alky halide shows correlation rated as moderate at 1300-1150 cm-1.
The ether shows no correlation.
The first amine group shows strong correlation to amines at 3400 cm-1, 1640-1560 cm-1, 1230-1030 and at 910-635 cm-1.
The second amine group shows strong amine correlations at 1230-1030 cm-1 and at 910-665 cm-1.
The thiocarbonyl shows no correlations.
The sulfone shows moderate correlation to the sulfone at 1350-1300 cm-1.
The phospine shows strong correlation in the 2440-2280 cm-1 range.
The phosphine oxide shows no additional correlations.
The phosphate shows no additional correlations.
The carboxylic acid shows strong correlation at 3400 cm-1. The carboxylic acid shows moderate correlation at 1760 cm-1. The carboxylic acid shows strong correlation in the 3400-2800 cm-1 range. The carboxylic acid shows moderate correlation at 1710 cm-1.
The ester shows no correlations.
Correlation Summary : 1140 cm-1:
Phospine > Phospine (2440-2280)
Carboxylic Acid > Carboxylic Acid (3400, 3400-2800)
Amine > Amine (3400)
Amine > Amine (1640-1560)
Amine > Amine (1230-1030)
Alkyl Halide > Alkyl Halide (1300-1150)
Sulfone > Sulfone (1350-1300)
Carboxylic Acid > Carboxylic Acid (1760, 1710)
The next search is at 920 cm-1:
No additional correlations for the ester is found.
No additional correlations for the carboxylic acid are found.
Summary: No correlations found.
The last in the series of this correlation analysis will be at 710 cm-1:
In the case of alkenes, we have a weak correlation at 1660 cm-1 with the alkenes.
The mono-substituted aromatic has a moderate correlation with a mono-substituted aromatic at 770-730 cm-1. We also have a moderate correlation with the aromatic at 1592 cm-1. We also have a strong correlation with the aromatic at 1500-1400 cm-1.
The meta-substituted aromatic shows moderate correlation to the aromatic at 1592 cm-1. It also shows strong correlation to the aromatic at 1500-1400 cm-1.
The 1,2,3 tri-substituted aromatic shows moderate correlations to the aromatic at 1592 cm-1 and strong correlation to the aromatic at 1500-1400 cm-1.
The 1,3,5 tri-substituted aromatic shows moderate correlation to the aromatic at 1592 cm-1 and strong correlation to the aromatic at 1500-1400 cm-1.
The S-OR ester shows no additional correlations.
The amine group shows strong correlation to the amine group at 3400 cm-1, 1640-1560 cm-1, 1230-1030 cm-1 (RNH2) and 1230-1030 cm-1 (R2NH).
Correlation Summary : 710 cm-1:
mono-substituted Aromatic > Aromatic (1500-1400)
meta-substituted Aromatic > Aromatic (1500-1400)
1,2,3 tri-substituted Aromatic > Arromatic (1500-1400)
1,3,5 tri-substituted Aromatic > Aromatic (1500-1400)
Amine > Amine (3400)
Amine > Amine (1640-1560)
Amine > Amine (1230-1030) (RNH2)
Amine > Amine (1230-1030) (R2NH)
mono-substituted Aromatic > mono-substituted Aromatic (770-730)
mono-substituted Aromatic > Aromatic (1592)
meta-substituted Aromatic > Aromatic (1592)
1,2,3 tri-substituted Aromatic > Aromatic (1592)
1,3,5 tri-substituted Aromatic > Aromatic (1592)
Alkene > Alkene (1660)
We are now in a position to start collating the information that we have acquired. The goal is to identify the candidates that are most likely to be structural components of the oral sample under investigation. We now have three primary data points available to use in the approach that will be developed:
1. The functional group candidates themselves, as identified with the tabular data from IR Pal as well as additional tables or sources as needed (e.g., Nakanishi).
2. The position of the absorption peaks within the graphical ranges that have been shown above and that accompany these same tabular listings.
3. The extensive correlation analysis that is presented above. In addition to having these three sources of information available, a strategy to use them in a sensible fashion will need to be developed. In general, a linear combination of graphical and correlative rankings will be used to integrate and combine this data.
Spreadsheet to evaluate the graphical and correlative weighted contributions to the expected structural composition of the oral filament sample.
The rankings of the contributions of the various functional groups can now be made. We have the following relative contributions of the functional groups or structures, from the greatest likelihood to the less likely:
It is the position of this researcher that the above chart reveals, along with the amino acids and iron content previously disclosed, the most probable structural features of the “Morgellons” oral filament sample material. The job remaining before us is to form a more composite picture of this structural whole and the likely and expected health impacts from this same characteristic structure. The culminating discussion is then to bring into consideration various strategies that may be beneficial in mitigating these health impacts and to once again invite the health and medical communities to investigate the veracity of this accumulated research. These issues, to the degree appropriate and possible here, will be pursued.
The next step in our work is to investigate the general nature and characteristics of the functional groups that are indicated, at least to the level of probability appropriate to the means and equipment. This basic knowledge of functional group characteristics will be necessary in understanding the assemblage that is to come further down the road in this report. We will progress from the most prevalent to the least prevalent groups.
Let us start with the amines. The amines are a functional group that contains nitrogen, and they are derivatives of ammonia, whereby the hydrogens of ammonia (NH3) are replaced by various organic groups. A primary amine has one hydrogen replaced and has the formula NH2. Secondary amines replace two of the hydrogens and tertiary amines replace three of the hydrogens, respectively.5 Amines can react with acids due to their basic nature; the basicity varies over a fairly wide range6. The chemistry of amines is dominated by the presence of a lone pair of electrons on nitrogen 7(this is in the ammonia form). They are produced by the decomposition of organic matter.8 Amines are a fundamental constituent of amino acids (i.e., proteins). Some of the important reactions that take place with amines includes interactions with alkyl halides, aldehydes, ketones, acid chlorides and nitrous acid.9 Amines are the most important biological bases.10 Amines often have a “fishy” odor and many drugs, such as quinine, codeine, caffeine and amphetamine, are amines.11
Our next group of significance is carboxylic acids. Carboxylic acids are one the most important biological acids. They react with bases (such as amines) to produce salts. These salts contain an ammonium ion from the amine and a carboxylate ion from the acid.12 They are most acidic of the common functional groups13. The carboxyl group the formula COOH, i.e, a carbonyl group attached to a hydroxyl group. Many long-chain carboxylic acids occur as esters in fats and oils, and are known as “fatty acids”.14 Carboxylic acids are the largest group of organic acids. As more electronegative atoms in the acid increases, the strength of the acid increases. For example, if the hydrogen atoms in the acid (acetic acid, for example) are replaced with fluorine ( a halogen) to produce trifluoroacetic acid, the increase in acidity is quite large. Amino acids, by definition, contain combine both an amine group and a carboxyl group, and a “R” group (i.e., variable group). Amino acids can act as both acids and bases, because of the combination of the amine (basic) and the carboxyl group (acidic), separated by the R group.15 Some common examples of carboxylic acids are acetic acid, oxalic acid and formic acid. Carboxylic acids are amongst the most useful building blocks for synthesizing other molecules, both naturally and in the laboratory.16
The next category of interest is that of an aromatic-alkene complex. Let us begin with an introduction of the importance of the presence of aromatics in the structure identification:
Aromatics are an extremely important branch of organic chemistry, with many ramifications to follow. Organic chemistry can be divided into two main structural forms, that of aliphatic and aromatic organic chemistry. Aliphatic, in a very general sense refers to a chain-like structure and aromatics, in a general fashion, refer to ring based structures. This division is significant, especially with respect to stability and expected chemical reactions to take place. Examples of aliphatics are alkanes, alkenes and alkynes (basically carbon-hydrogen bonds in a chain-like structure)17. An example of an aromatic compound is benzene, a classic six carbon ring structure that many of us have some familiarity with. It is of interest that our category of an aromatic alkane is the next on our list. This alone informs us that we are likely dealing with a combination of both aliphatic and aromatic form, which alone would allow for infinite chemical flexibility from an organic chemistry perspective. For now, our focus will remain on the aromatic aspect of discovery that has taken place.
Let us discuss aromatic chemistry in a general fashion. Aromaticity, in general, is used to refer to benzene and its structural relatives. Although this may conjure up an image of a fixed six-ring carbon structure, this level of restriction is not at all appropriate in our understanding of aromatic chemistry. A more formal definition of aromatic is that of a “cyclic conjugated molecule containing 4n+2 pi electrons.”18 We will make some headway into that rather intimidating phrase as we go along, but for now let us work with the classical ring structure in mind and some of the general chemical characteristics of that same benzene structural form.
A couple of the more important characteristics of aromatics (or with benzene as a typical example) is that of its cyclic, or ring structure and its physical and chemical stability. These features go hand in hand because of the structural nature involved; a hexagon is one of the most stable structures of nature (e.g., the honeycomb). Here is an image of benzene to begin this visualization process:
A typical aromatic structure – Benzene
Another feature characteristic of the aromatic is its “conjugated” nature. Conjugation refers to the alternation between single and double bonds in a chemical structure. Conjugation, in general, has the effect of lowering the energy of the molecule and of increasing its stability, an important complementing feature to this same stability mentioned earlier. Benzene is only one example of an aromatic structure; there are an infinite number of variations on this basic theme that will lead to the individual chemistry, i.e., biochemistry, of the form that is under investigation. Benzene by itself is toxic; it leads to bone marrow depression and lowered white cell counts. On the other hand, there are some amino acids in the body that contain aromatic structures (e.g., phenylalanine, tryptophan, tyrosine19). Other examples of aromatic compounds include natural fragrances, steroid hormones, and many drugs such as valium and morphine. The fact that a structure is aromatic is, therefore, not sufficient to characterize its general chemical influence upon the body. We must know more. The presence of an aromatic structure, nevertheless, is one of monumental significance in understanding the expected influences and impact upon human health. The rub will be in knowing how the aromatic structure is modified so that its impact can be more likely assessed with fairness. The identification of aliphatic compounds (that of alkenes in our case, to be discussed separately) in combination with an aromatic structure leaves us with plenty of room for further important discoveries.
To begin that process of discovery, we must now look at the types of reactions that are known to occur with aromatic compounds; this is our key to further progress In essence, the use of infrared spectroscopy has opened a very important puzzle for us to solve, and deeper we must now go into this unsolved mystery.
The most common chemical reaction with aromatics is that of electrophilic aromatic substitution. What this means, in the most basic sense, is that one of the carbon atoms on the ring gets replaced by “something else.” The nature of the “something else” is crucial to an understanding of the expected chemical and biochemical impact of the filament structure upon human health and biology in general. In response to this need, let us introduce the definition of an electrophile and a nucleophile, respectively.
An electrophile is something (i.e., ion or molecule) that is deficient in electrons and that can accept electrons. Electrophiles are positively charged, and examples include the positive ion of NO2+ and the electron deficient SO3 atom. Electrophiles are reducing agents and act as what is known as a Lewis acid. A nucleophile, in contrast, is an ion or molecule that has an excess of electrons and that can donate them. Nucleophiles are oxidizing agents and act as Lewis bases. Examples of nucleophiles are the Chlorine ion (Cl–) and ammonia (NH3)20. Here is a picture of the general process:
In this diagram, E+ is the electrophile. The electrophile reacts with one of the hydrogens on the aromatic ring and substitutes itself on the ring.
It is now sensible to introduce the types of aromatic electrophilic substitution reactions that occur. These are as follows21:
1. Halogenation :
The substitution of a halogen for one of the hydrogens.
2. Nitration :
The substitution of a nitro group (NO2) for one of the hydrogens.
The substitution of a sulfonic acid group (SO3H) for one of the hydrogens.
The substitution of an alkyl group for one of the hydrogens. An alkyl group is formed when one of the hydrogens is removed from an alkane group. An example of an alkyl is a methyl group (CH3-), which is formed from methane (CH4). Alkanes are saturated hydrocarbons with the general formula CnH2n+2. Examples of alkanes are methane (CH4), propane(C3H8) and butane(C4H10). Saturation refers to molecules that have only single bonds, i.e., no double or triple bonds. Alkanes contain only carbon and hydrogen, and all the bonds between atoms are single bonds22. A common term for alkanes is that of paraffins.
The substitution of an acyl group for one of the hydrogens. An acyl group has the form RCO-, where R is any organic group. An example of an acyl is the acetyl group, CH3O-. Another variation of an acyl is the case of acyl halides, which has the form RCOX, where X is a halogen, such as acyl chloride (RCOCl)23.
Each of these reactions requires certain reagents or catalysts to be present to take place. In human biochemistry, some of these reactions are more likely to be able to occur than others. Let us examine these groups and determine which reactions in the body are less likely to occur than others, thereby simplifying and restricting our scope of probable structural composition.
In the description of aromatic nitration24, it will be found that this requires the presence of a mixture of concentrated nitric and sulfuric acids. Since this combination is not likely to be found within the human body, the process will be excluded further from our structural investigation. A similar situation will be found for that of sulfonation25, which can occur in the presence of fuming sulfuric acid. Sulfonation will also be consequently diminished in our further consideration in this investigation, however, we must remain alert to alternative catalysts or pathways whereby a reaction might occur. Aklylation, acylaton and halogenation are expected to occur fairly readily within human biochemistry, and remain under full consideration in our structural analysis. Considerable discussion on the halogenation substitution reactions will take place.
Since the group identified most recently within this discussion is that of an alkene aromatic, we must introduce this addition as well. The alkene is an unsaturated hydrocarbon that contains one or more double carbon bonds. The general formula of an alkene is CnH2n and examples include propene and butene. A common term used for alkenes is olefins or olefines.
Studying our list of probabilistically ranked functional groups further, the next item mentioned is again that of amines, with an important addition. The presence of the aromatics, this time in combination with the amines in addition to that previously noted for alkenes, must be recognized. This strengthens the case considerably for aromatic biochemistry within our structure. The importance of halogenation substitution within the aromatic group will also be further developed in our discussion as we proceed.
We next see the alkanes introduced, and they have already been discussed to some extent. They are a very common organic functional group to be found within organic compounds. They are saturated, single bond hydrocarbons with the general formula CnH2n+2. Alkanes are within the branch of aliphatic organic chemistry, which serves as a chain structure that links many different types of organic compounds together.
The carboxylic acids, the alkenes, the alkanes and the amines all repeat themselves subsequently on the list of functional group candidates. This further strengthens their consideration in our structural analysis that is in progress.
The next addition on our list is an aldehyde. The aldehyde group has the structure -CHO and can be visualized as follows: The simplest example of an aldehyde is also shown below, that of formaldehyde.
The aldehyde group. The R represents any generic organic structure, i.e., an organic variable.
An example of an aldehyde, i.e., formaldehyde. We see here that the R group has been occupied by a hydrogen atom.
Aldehydes are a reactive group and they readily polymerize26. Polymerization is the joining of molecules to form a series of repeating units. They are formed by the oxidation of alcohols, and further oxidation yields carboxylic acids (mentioned previously). Aldehydes can also be halogenated by reactions with chlorine, bromine or iodine in an acidic solution27. An example of halogenation (bromination) of an aldehyde, in this case with the use of acetic acid, is as follows:
Notice also the combination of an aromatic structure, and aldehyde and halogenation occurring in the presence of an organic acid in the above example of an aldehyde reaction.
Our next entries are those of aromatics and substituted aromatics, once again. This continues to reinforce the expected importance of aromatics and electrophilic substations in our future discussion of the composite structural portrait that continues to develop within this paper.
We next have the introduction of a phenol group, once again in combination with an aromatic form. A phenol, by definition, is the existence of a hydroxyl group (OH) that binds directly to a carbon atom on a benzene ring28. Hydroxyl groups normally indicate an alcohol, but in the case of the phenol, the structure is acidic because of the influence of the benzene ring. A diagram of the phenol structure is as follows:
The phenol group
Source : commons.wikipedia.org
One of the interesting structures involving the phenol group that has arisen within this investigation is that of dopamine. It will be noticed that dopamine is composed primarily of an aromatic ring, a couple of phenol groups attached, and an amine structure at the end of a carbon chain. Dopamine may well have to do primarily with the motivation and drive of an individual; see Eric Matzer’s article : Dopamine is Not About Pleasure Anymore and How Science Evolves. What is of interest here is the importance of the role the relatively simple phenol group can play in the behavior and neural functioning of an individual. The role of Parkinson’s disease in relation to dopamine will also be worthy of our examination. Lastly, in the future we will examine how a slight tinkering of this molecule can lead to the development of neurotoxins that can easily be expected to seriously interfere with the neural functioning of an individual. More on this issue later.
We are approaching the end of the functional group ranking list, at least to the level that we can have a greater confidence in. The lack of repetition of functional groups that is developing is a signal that we should begin to exercise caution in extrapolating our results beyond an expected level of significance. Brief mention will be made of the finalizing set of groups to consider at this time, which includes phosphine, a repeat of carboxylic acids, a nitrogen-oxygen group, and an alkyl halide. Phosphine (PH3) is a highly toxic gas formed by heating white phosphorus in concentrated sodium hydroxide. There is no particular reason to expect this particular compound in human biochemistry and notice no repetition of occurrence of the compound. Carboxylic acids have been mentioned previously and they remain as a primary candidate. Nitro compounds can also not be emphasized in this investigation due to the lack of repetition.
The alkyl halides do provoke a level of interest, due to the previous discussion of both alkyls and halogens. An alkyl halide (also known as a haloalkane) is a organic compound whereby one of the hydrogen atoms of an alkane has been substituted with a halogen. Alkyl halides can be formed by a combination of alkanes, halogens and ultraviolet light, in addition to reactions between alcohols and an halogenating agent. One example of an alkyl halide is dibromoethane, CH2BrCH2Br. Many alkyl halides are major pollutants or toxins. They are widely used in flame retardants, refrigerants, pesticides, propellants, solvents and pharmaceuticals. Most alkyl halides are synthetic, but natural sources do exist and they are produced by some bacteria, fungi and algae. We also note an additional minor absorption peak at 1025 cm-1 that corresponds to the alkyl halides and that increases our interest in this particular group.
This completes our list of functional groups that are to be considered in this analysis. The next stage in this project is to collect the information that now besets us, both from previous work and from this current work. Infrared spectrometry will not allow us to define a single finite structure, but it will serve to identify some of the building blocks. These building blocks along with some understanding of the expected biochemistry will end up serving us well for the effort that has been spent.
To begin with, let us recall what has been learned from previous work and from alternative methods. We know from previous papers entitled, Morgellons : A Thesis (Oct 2011) and Amino Acids Verified (Nov 2012), that iron and amino acids are core constituents of the biological filaments. These are crucial and important discoveries in their own right. Please be aware, however, that it has taken several years of work to arrive at a point that could have easily been understood and attained within a matter of months with the proper support and resources.
It is also of benefit, at this stage, to recall the beginnings of structural analysis that was taking place at the terminus of the papers mentioned immediately above. This work took place using primarily the methods of column chromatography, electrolysis, ninhydrin analysis and visible light spectrometry. The work was protracted, tedious and took well over a year to accomplish. An initial iron-amino acid complex molecular model (shown below) was developed to open this door which we are now entering more deeply:
Proposed Model of Histidine-Cysteine Proteinaceous Dipeptide Complex
Please see Amino Acids Verified, CE Carnicom, (Nov 2012) for additional information on the work leading to the above model. This model depicts an amino acid-iron complex.
As with all nutrients that are redirected to support a parasitic or diseased relationship between living forms, this loss of nutrients and energy will be done at the expense of the host. Let us be clear that the human being is the host here, and there can be no expectation other than that of suffering to some degree. In many cases, the suffering is extreme and we all pay the price for this with each day that we allow this situation to pass unchallenged.
Next, let us collect the probabilistic list from the current work. Understand that nothing is definite here. All work here is evolutionary with highly limited resources and is subject to errors; I will, however, do my best to establish a path that others hopefully will assist in. This current paper based upon infrared spectrophotometry proposes the following additions to now incorporate into our structural analysis:
Aromatic substituted Alkenes
Aromatic substituted Amines
Time has been spent on discussing the general features and characteristics of each of these functional groups. We must use this information to attempt to create a greater composite picture of our structure involved, and its subsequent expected biochemistry and impact upon human health.
For the sake of consolidation and simplification, let us now repeat the candidate list in total and in combination, along with some relevant imagery:
Amino Acids – General
Specific Amino Acid: Cysteine
Specific Amino Acid : Histidine
Aromatic substituted Alkenes
Aromatic substituted Amines
Previously Proposed : Iron – Cysteine- Histidine – Amino Acid Complex Model (Nov 2012)
Table of Candidate Components – Functional Groups of Morgellons Oral Filament Sample :
Analyzed by Infrared Spectrophotometry, Chromatography, Electrolysis, Ninhydrin Tests and Visual Light Spectrophotometry
END OF PART I
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7. Ibid., McMurray.
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12. Ibid., Moore.
13. Ibid., Hathaway.
14. Ibid., Oxford.
15. Ibid., Brown.
16. Ibid., McMurray.
17. Ibid., Oxford.
18. Ibid., McMurray.
19. Principles of Biochemistry, H. Robert Horton, Prentice Hall, 1993.
20. Ibid., Oxford.
21. Ibid., McMurray.
22. Ibid., Hathaway.
23. Ibid., Oxford.
24, 25. Ibid., McMurray.
26. Ibid., Oxford
27. Ibid., McMurry
28. Ibid., Oxford.
29. Morgellons : A Thesis, Clifford E Carnicom, Oct 2011, www.carnicominstitute.org.
30. Morgellons Research Project : Scientific Study of the Morgellons Condition, Carnicom Institute.
31. Free Radicals in Biology and Medicine, Dr. P.K. Joseph
32. Iron Deficiency, Wikipedia, wikipedia.org.
34. Amino Acid Chart, Dr. Guy Wilson, www.1choicevitamins.com.
35. Ibid., McMurray.
36. Principles of Biochemistry, Albert L. Lehninger, Worth Publishers, 1982.
37. ATSDR – Medical Management Guidelines : aniline, U.S. Department of Health and Human Services, CDC.
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44. Ibid., McMurray
45. Ibid., Morgellons : A Thesis, Carnicom
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48. Oxidopamine, wikipedia.org
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56. Desipramine attenuates working memory impairments induced by partial loss of catecholamines in the rat medial prefrontal cortex, SM Clinton, National Institutes of Health.
57. Ibid., Cotran.
58. Ibid., Cotran.
60. Morgellons, The Breaking of Bonds and the Reduction of Iron, Clifford E Carnicom, Nov 2012, www.carnicominstitute.org
61. Ibid., Morgellons : A Thesis, Carnicom
63. Ibid., Risk of Iron Supplements
64.The role of vitamin C in iron absorption, L. Hallberg, National Institutes of Health.
65. Ibid, Morgellons, The Breaking of Bonds and the Reduction of Iron, Carnicom.
66. Ibid., Morgellons : A Thesis, Carnicom
67. Ibid., Amino Acids Verified, Carnicom.
68. N-acetylcysteine (NAC), David Wheldon.
70. Ibid., Morgellons : A Thesis, Carnicom
71. Ibid., Morgellons : A Thesis, Carnicom
73. Ibid., Cotran.
74. Ibid., A Discovery and A Proposal, Carnicom.
75. Free radicals, antioxidants, and human disease curiosity, cause, or consequence?, Barry Halliwell, Lancet, Sept 10, 1994 v344 n8924 p721(4), published at auraresearch.com.
76. Ibid., Cotran.
77. Oxidative Stress and Neurodegenerative Diseases: A Review of Upstream and Downstream Antioxidant Therapeutic Options, Current Neuropharmacology, Mar. 2009, Bayani Utara, National Institutes of Health.
79. Alcohol, Oxidative Stress and Free Radical Damage, Defeng Wu, PhD, Alcohol Research & Health, National Institues of Health.
80. Ibid., A Discovery and A Proposal, Carnicom
81. Ibid., Cotran.
82. Ibid., Cadenas.
84. Structure and reactivity of radical species, University of California at Davis., www.chemwiki.ucdavis.edu
85. Diradical Chemistry, The Chemogenesis., www.meta-synthesis.com
86. Magnetic Liquid Oxygen, University of Illionois, Chemistry Department.
88. Ibid., Cadenas.
89. Ibid., Pharmaceutical Field.
90. Ibid., Pharmaceutical Field.
91. Ibid., Pharmaceutical Field.
92. Free Radicals and Reactive Oxygen, Colorado State University, Biomedical Hypertexts.
93. Ibid., Colorado State University.
94. Ibid., Morgellons, The Breaking of Bonds and the Reduction of Iron, Carnicom.
95. Morgellon’s : The Role of Atmospheric Aerosolized Biological Nano-Particulates, An Anonymous Physician.
96. Ibid., Morgellons, The Breaking of Bonds and the Reduction of Iron, Carnicom.
96d. How Do Anioxidants Work Anyway?, Kristy Russ, www.antioxidants-make-you-healthy.com
98. Ibid., Wikipedia
102. Acid-Base Tutorial, Dr. Alan Ggrogono, , www.acid-base.com.
103. Ibid., A Discovery and A Proposal, Carnicom, Feb. 2010.
105. Ibid., Morgellons : A Thesis, Carnicom
107. Sugars and dental caries, Riva Touger, The American Journal of Clinical Nutrition.
108. Urine and Saliva pH Testing, Michael Biamonte, C.C.N, www.health-truth.com
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110. Dr. Henry G. Bieler, Wikipedia.
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111. Lactic Acidosis, Wikipedia.
114. Ibid, Weatherby.
116. Thyroid Balance, Dr. Glenn Rothfeld, MD, Amaranth, 2003.
118. Ibid., Weatherby.
120. Tincture of Iodine, Wikipedia
121. Povidone Iodine, Wikipedia
122. Toxicity Profile, Polyvinylpyrrolidone, legacy.library.ucsf.edu.
123. Medline Plus : Iodine, National Institutes of Health
124. The Great Iodine Debate, www.westonaprice.org
125. Ibid., Cotran.
126. Oxidative stress and neurological disorders in relation to blood lead levels in children, M Ahamed, National Institutes of Health.
127. Naton Gadoth, Oxidative Stress and Free Radical Damage in Neurology, Springer, 2011.
128. Oxidative Stress in Neurodegeneration, Varsha Shukla, Hindawi Publishing Corporation, 2011.
129. Katlid Rahman, Studies on free radicals, antioxidants, and co-factors, National Institutes of Health.
131. Ibid., Wylde.
132.James A. Joseph, Nutrition and Brain Function, U.S. Department of Agriculture.
133. Enhancing Memory and Mental Functioning , NYU Langone Medical Center, www.med.nyu.edu.