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[biologydictionary]

Essential Amino Acids

Definition

Essential amino acids (EAAs) make up a group of nine amino acids that cannot be produced inside the body (de novo) but must be ingested as dietary protein. The building blocks of proteins, amino acids are bound together to produce polymer chain or folded proteins with a huge array of functions. There are three groups of amino acids: essential, non-essential, and conditional.

Essential amino acid L-lysine

List of 9 Essential Acids

This list of 9 essential acids briefly describes the role of each within the human body. Histidine Histidine is an essential amino acid in children; however, this is not the case in adults unless kidney function is affected. Histidine is necessary for human growth. It is also important in maintaining the nervous system and is a metabolite of the neurotransmitter histamine. The most important role of histidine is to metabolize and regulate heavy metals including iron, copper, molybdenum, zinc, and manganese. A body low in histidine but high in trace metals quickly depletes any histidine stores, causing mineral-enzyme deficiencies.

Histidine Isoleucine Isoleucine is known for its use in supplements for endurance athletes. The three essential amino acids isoleucine, leucine, and valine constitute up to 70% of all human proteins. Isoleucine plays a role in tissue repair, hemoglobin synthesis, and regulating blood glucose and energy levels. Isoleucine can also be safely consumed in relatively large amounts making it a popular ingredient in sports supplements.

Isoleucine Leucine Leucine is one of the three branch-chain amino acids. Leucine, isoleucine, and valine make up the BCAA group of essential amino acids. Leucine aids in fat metabolism without reducing muscle mass. For this reason, leucine is often used as a weight-loss supplement but works best in combination with vigorous exercise. Vegans tend to have low leucine levels as this amino acid is mainly found in meat and dairy products.

Leucine Lysine Lysine is necessary for calcium absorption and therefore essential for healthy muscle and nervous system function. Lysine additionally assists in collagen and carnitine production. Vegans and vegetarians can find sources of lysine in legumes. Lysine deficiency can lead to symptoms such as slow growth, fatigue, nausea, dizziness, and infertility. It can be used to lower the number of seizure events in neurological patients; however lysine-restricted diets are recommended in pyridoxine dependent epilepsy.

Lysine Methionine Methionine is found in meat, dairy, and whole-grain foods and is, therefore, not necessarily required in supplement form. The improper conversion of methionine can lead to atherosclerosis as this essential amino acid plays a role in lipid and fatty acid biosynthesis. Methionine is one of two amino acids that contain the element sulfur – the other is cysteine. Sulfur plays an important role in the synthesis of anti-oxidants. Methionine supplements either in dietary or powder form are beneficial for women and men suffering from estrogen dominance or people suffering from liver disease. However, recent studies into the positive effects of low methionine diets to improve cancer outcomes and cell longevity may throw a spanner in the methionine supplement works. Vegans and vegetarians need not worry as their diet is naturally low in this essential amino acid.

Methionine Phenylalanine Phenylalanine is a precursor of tyrosine, adrenaline, and noradrenaline, the latter of which increases mental alertness and memory, improves mood, and suppresses appetite. Phenylketonuria refers to the lack of an enzyme that allows the body to use phenylalanine. This inability to utilize phenylalanine causes high levels of this amino acid to circulate in the body and no way to use it. The result is severe, irreversible mental retardation if this disorder is left untreated after the first three weeks of life. Threonine Threonine works together with aspartic acid and methionine to promote fat metabolism in the liver and avoid fatty liver (steatosis). In the CT image below, a healthy liver is shown above and under it a scan of a fatty liver. This essential amino acid is also integral to nervous system health and supplements are often taken by multiple sclerosis and Lou Gehrig’s disease patients. Threonine is necessary for the synthesis of glycine and serine and so assists in collagen, elastin, and muscle tissue production. More recent research is looking into its use as a colitis therapy.

Liver steatosis - bottom image Tryptophan Tryptophan is one of the most recognized of amino acid supplements and a mainstay ingredient in health store supplements that improve energy levels and mood. The reason tryptophan has become so popular in this area of the health industry is due to its role as a precursor to serotonin; it is also precursor to melatonin, enzymes and structural proteins and low levels are perhaps partially responsible for the occurrence of migraine. With recent studies looking into the role of gut-produced serotonin and the blood-brain barrier, tryptophan’s role is judged to be a very significant one. It is currently used to successfully treat menopausal depressive conditions, calm children diagnosed with ADHD, reduce anxiety, and alleviate the symptoms of restless leg syndrome. Valine Valine, leucine, and isoleucine form a group of branched-chain amino acids (BCAAs) that show a different structure than other amino acid types and are often sold as a group package in the dietary supplement industry. It is one of the essential amino acids most easily available to vegans and vegetarians and found in sufficient quantities in green, leafy vegetables and kidney beans. Valine plays multiple positive roles within the human body. Its effect upon the nervous system calms during moments of stress and improves sleep quality. Cognitive function may also be improved. Valine aids in all types of muscle tissue recovery, repair and growth and is therefore often used by endurance athletes. Shown to decrease the appetite, it is also an ingredient in many weight loss supplements.

Valine

Non Essential Amino Acids

12 nonessential amino acids are produced within the body, although many believe in providing further sources by way of amino acid supplements or high-protein diets. Humans are able to synthesize alanine, arginine, asparagine, aspartate, cysteine, glutamate, glutamine, glycine, proline, serine, taurine, and tyrosine. Inborn deficiencies of non essential amino acids and their catalyzing enzymes may cause abnormal phenotypes caused by a genetic inability to form certain proteins. This can be seen in low or nonexistent arginine and glycine amidinotransferase production that leads to mental retardation and muscular abnormalities. A lack of glutathione synthetase, even in the presence of plentiful non essential amino acids, causes sufferers to exhibit signs of oxidative stress, progressive neurologic disorders, hemolytic anemia, and metabolic acidosis.

Conditional Amino Acids

Six amino acids are conditionally essential in the human diet. This means that under certain conditions, the human body’s ability to produce them is limited. This does not concern genetic disorders or disease but natural, temporary physiological states such as in babies born preterm or extreme stress conditions with associated physiology. The six conditional amino acids are arginine, cysteine, glycine, glutamine, proline, and tyrosine. Arginine is on occasion included in essential amino acid lists, as preterm babies are unable to synthesize it. Read the full article

[biologydictionary]

Rigor Mortis

Definition

Rigor mortis is one of the stages of death in which chemical changes that affect muscle fiber elasticity cause the muscles to stiffen. An indication of the time of death in forensic science, rigor mortis usually initiates at two to three hours after death and presents according to the position of the body at rigor mortis onset.

How Long Does Rigor Mortis Last?

How long rigor mortis lasts is of extreme importance to forensic scientists looking for a time of death or postmortem interval (PMI) when studying the body or the autopsy report. This is because the usual pattern of rigor mortis is possible to trace in time. Yet, certain factors such as the cause of death, temperature of the body or its environment, previous levels of fitness and muscle mass, drug abuse, infection, and availability of nutrients and ATP immediately previous to death can drastically shorten or lengthen these times. One medical report revealed rigor mortis onset and not cadaveric spasm as mentioned later on in this article, to occur within two minutes of cardiorespiratory arrest. Most textbooks report that most cases of rigor mortis commence between two to three hours after death. Over the following twelve hours, rigor mortis set in, developing as myofibril chemical changes spread throughout every muscle. All muscle types – cardiac, skeletal and smooth – contain actin and myosin and all are therefore affected during the stage of rigor mortis. Maximum rigor mortis can continue for anywhere between 18 and 36 hours. As the next hours pass – sometimes days -  these effects wear off. Muscles lose rigidity in the same order that they appear over the course of the next 24 – 50 hours. Rigor mortis becomes even more pronounced if this natural course is broken. If, for example, a body is moved from its original position during the natural development of rigor mortis more significant rigidity may be the result. This is a very useful indication for forensic scientists looking for evidence of homicide or manslaughter where a body has possibly been moved from the scene after death.

Popular on TV: Forensic examination In subjects who pass away when in a very low physical condition - usually very underweight and malnourished individuals - rigor mortis can set in much more rapidly. Muscle elasticity is dependent upon a source of energy in the form of adenosine triphosphate (ATP) but the amount of ATP stored in the muscles is only able to sustain a few seconds of muscle contraction. Once death has taken place, ATP synthesis halts but available resources continue to be consumed. Where low levels of ATP are present, either through time or absence of ATP, ATP non-availability and the acidic environment of a dead body due to lactic acid production cause the muscle-contracting proteins actin and myosin to bind together, forming a gel-like substance. Rigor mortis initiates when ATP levels are approximately 85% of a normal, healthy level. In subjects who, previous to death, were unable to produce normal levels of ATP either through malnutrition or other disorders such as Huntingdon’s disease, rigor mortis will develop at a more rapid rate. In those with high muscle mass or high ATP production and transfer rates such as the active obese, rates can usually be expected to slow down. Adenosine triphosphate levels of  15% indicate maximum rigor. It has been suggested that some bodies do not go through the process of rigor mortis at all. This idea is due to reports of lack of stiffness during the hours where rigor mortis is expected. As the chemical breakdown of actin and myosin is unavoidable after death, these reports are not accepted as proof of the absence of rigor mortis. Instead, it has been shown that the subjects in these reports were often very young children and babies with extremely low muscle mass. Rigor mortis would have been present in these individuals but the tactile method of measuring postmortem stiffness – manually bending the joints and evaluating the levels of resistance – gave results that did not point to a rigor mortis state. In other words, young limbs could be bent with little to no resistance due to low muscle mass. The claims of rigor mortis absence are therefore not accepted in the scientific community.

Rigor Mortis Stages

The stage of rigor mortis is third in an ordered group of postmortem phases known as the stages of death. The timescale a body needs to fully decompose depends on its pre-death anatomy, physiology, and the surrounding environment both at the time of death and after. Rigor mortis follows stages pallor mortis and algor mortis respectively and precedes livor mortis. A full description of these stages continues below.

The Stages of Death

The stages of death often overlap. Pallor mortis is usually achieved within thirty minutes of death. Body cooling (algor mortis) initiates within this time and continues until the body is the same temperature as the ambient air – anywhere up to six hours postmortem. Muscle stiffening (rigor mortis) usually begins within one to two hours after a person has died and will continue for a number of days. Livor mortis begins at around the same time and requires approximately eight hours to progress to a maximum state. Autolyze or cell death also commences from the moment cell death occurs and continues throughout the fresh stage of decomposition; other early stages of decomposition are also present. All of these timescales depend heavily on the physiology and anatomy of the person and their immediate environment. Pallor Mortis Pallor mortis or postmortem paleness is the result of the lack of capillary circulation once death has taken place and occurs almost immediately. This means pallor mortis is not a good indication of the time of death as bodies are often discovered at a later period. The process of death begins upon what is known as somatic death. This is the cessation of cardiopulmonary activity and subsequent brain death. Once somatic death has taken place the supply of oxygen runs out and all cells die. This is called cellular death. Pallor mortis accompanies cardiopulmonary activity cessation and brain death. However, one of the earliest indications of death in a clinical setting is the appearance of retinal vascular segmentation upon ophthalmoscopy where the cessation of circulation within the retina occurs at the start of the last stages of the dying process. This explains pre-death blindness. A degree of pallor mortis is distinguishable whatever the skin color. The darker the skin, the weaker the effect but skin tone becomes paler in any newly dead organism. In the picture below, the difference between a normal hand and the hand of a person with anemia gives a good idea of what the color of skin in the stage of pallor mortis might look like.

Hand skin-color comparison Algor Mortis The second stage of death is algor mortis or the cooling of the body. A body will naturally cool over the following two to three hours, although the variables relating to how slowly or how quickly a body cools down are multiple. The body remains pale. This occurs because of a lack of blood circulation but blood pooling can begin to give a slightly darker tinge to the skin of the lowest points of the body in relation to gravitational forces. During algor mortis the body temperature lowers to match that of the surrounding environment and continues for approximately six hours postmortem. The rate of cooling is dependent upon the difference in body temperature and ambient temperature. This rate is increased in water, where a body is naked, and in the absence of high quantities of fat tissue. This means an obese, clothed body will cool down at a slower rate than a naked, thin body in a similar environment. Rigor Mortis Rigor mortis, as already mentioned, is postmortem rigidity due to ATP depletion and lactic acid build-ups that form gel-like actin myosis bonds and keep the body in a certain position for up to fifty hours after death. Previous to rigor mortis, muscles are flaccid. This flaccidity returns after the rigor mortis phase has ended. The first muscles visibly affected by rigor mortis are the eyelid, facial and jaw muscles. These are smaller muscles than those in the arms, legs, and trunk. Eventually, the breakdown by enzymes of actin and myosin binding sites during the last hours of rigor mortis initiates secondary, permanent muscle flaccidity. Livor Mortis Livor mortis or postmortem hypostasis indicates the pooling of blood in the blood vessels according to the forces of gravity. This results in darker skin in the lowest positioned tissues, usually the back of the head, shoulders, rump, and limbs when death occurs in a supine position. Livor mortis begins approximately one-hour post mortem and develops over the course of three to four hours. By eight hours postmortem, livor mortis has progressed to its maximum state. Livor mortis is of extreme use to forensic scientists as lividity – skin changes associated with the pooling of blood once circulation has stopped – is a fixed entity. Even upon repositioning or relocation of the body, indications of its original position will remain. Decomposition Decomposition involves two different processes – autolysis and putrefaction. Autolysis begins immediately after cell death when cells begin to leak enzymes. This process is not visible to the eye and therefore often forgotten in death phase lists, replaced by the visible decomposition process of putrefaction. Decomposition follows an order of stages, too. These are fresh, bloated, decay, post-decay and dry. An agreed group of decomposition stages has not yet been agreed upon in the world of scientific research. It is also impossible to take into account the range of intrinsic and extrinsic factors that affect the rates and appearance of decomposition. Autolysis is present during the fresh stage of decomposition that begins upon cell death. Fresh decomposition lasts until around two hours postmortem as cells, starved of oxygen, die and lose their structure – a mechanism that occurs because of the build-up of lactic acid in the tissues. When the cell structure breaks down, its enzymes leak into surrounding tissues. Inside the digestive tract, still-living bacteria begin to consume the soft organs. After autolysis comes putrefaction which describes the bloated, decay and dry stages of decomposition. The bloating period begins after dead cells have broken down and is one of the first visible signs of the decomposition process. The bacteria within the body produce gases which the non-breathing corpse cannot diffuse. The tongue and eyes may protrude and the smell of death becomes noticeable. Bloating usually begins around the second-day postmortem and continues for a further five to six days. The decay phase continues on from the end of the bloating phase and lasts for approximately eleven days. Bacteria-produced gases escape creating a strong, putrid smell that is attractive to decomposers. The corpse takes on a wet appearance as fluids drain via orifices and pores. Inside the body, organs are well decomposed, helping to produce the aforementioned fluids. Post decay begins at around the tenth to twelfth-day postmortem. Where insects, fungi, and bacteria are present, such as in or on the soil, most of the flesh will have been consumed or is decomposed by this point. This is why this stage is sometimes referred to as skeletonization. Finally, dry stage decomposition that begins at about three to four weeks after death involves the decomposition of dry remains, usually bones, cartilage, and dehydrated skin. Some products such as adipocere or ‘corpse wax’ composed of fatty acids may need considerable time to break down.

What Causes Rigor Mortis?

Rigor mortis causes require an understanding of muscle contraction mechanisms in the living organism. When action potentials sent via the nerves reach their target muscles, calcium ions are released from muscle transverse tubules which make up a part of the sarcoplasmic reticulum. The sarcoplasmic reticulum that surrounds each myofibril within a muscle fiber is responsible for calcium ion concentration in the muscle fiber. In a resting muscle fiber, the cytosol is practically free of calcium ions as the sarcoplasmic reticulum ‘sequesters’ them away, binding them to a protein called calsequestrin. There is more calsequestrin in fast-contracting muscle fibers than in slow-contracting fibers. When an impulse is sent by the nervous system to ask a muscle fiber to contract, the transverse tubules that travel from the surface of each fiber forward this impulse whenever the tubules come close to the sarcoplasmic reticulum. In the presence of such a signal, any area of the sarcoplasmic reticulum close to the transverse tubule will release calcium ions. The released calcium ions cause troponin and tropomyosin to move along the muscle filament; this action initiates muscle contraction. After the muscle has contracted (and in the absence of further signals from the nervous system) the leftover signaling neurotransmitter, acetylcholine, is broken down by acetylcholinesterase. The SERCA pump (sarcoplasmic endoplasmic reticular calcium ATPase pump) stops releasing calcium ions and sequesters them off to quarantine areas within the sarcoplasmic reticulum. The lack of available calcium ions blocks the movement of myosin and the muscle is able to relax. Only constant nervous system signals can keep a muscle contracted for any length of time in the living body. In the dead, no nervous system signals are present due to brain death and muscle contraction is then solely the result of chemical imbalance. As its full name suggests, a SERCA pump requires plentiful ATP. After death, all metabolic activity ceases to function and ATP is no longer produced. This leads to permanently elevated calcium ion levels within the sarcomere and no sequestering mechanism. The SERCA pump is, therefore, unable to remove them. The result of this is sustained contraction or rigor mortis.

What is Cadaveric Spasm?

A cadaveric spasm is quite rare. When rigor mortis commences at an extremely accelerated rate it is renamed cadaveric spasm, instant rigor, postmortem spasm or cataleptic rigidity. The cadaveric spasm occurs in the absence of primary muscle flaccidity and is most commonly encountered in deaths that involve serious physical and/or emotional stress. A cadaveric spasm usually affects a single group of muscles such as those of one limb or hand. Cadaveric spasm is probably the result of the combination of neurogenic mechanisms and high muscular exertion immediately prior to death. Examples include dead bodies tightly gripping weapons or objects of defense, blades of grass, and precious possessions. Cadaveric spasms are most common in violent situations such as war and brawl scenarios, and modes of death like falling, drowning, and plane crashes.

Quiz

1. A very obese, well-nourished body is usually expected to: A. Show earlier signs of rigor mortis B. Show earlier signs of algor mortis C. Show later signs of rigor mortis D. Show no signs of algor mortis 2. Which is the correct order of these four death stages? A. Algor mortis, rigor mortis, pallor mortis, livor mortis B. Pallor mortis, rigor mortis, livor mortis, algor mortis C. Algor mortis, livor mortis, rigor mortis, pallor mortis D. Pallor mortis, algor mortis, rigor mortis, livor mortis 3. SERCA stands for: A. Sarcoplasmic endoplasmic reticular calcium ATP B. Sarcoplasmic endoreticular calcium ATPase C. Sarcoplasmic endothelial reticular calcium ATP D. Sarcoplasmic endoplasmic reticular calcium ATPase 4. Which of the following is a binding protein found in the endoplasmic reticulum A. Calsequestrin B. Calsyntenin C. Synaptotagmin D. Calretinin 5. Which acid is responsible for the low pH of a cadaver? A. Acetic acid B. Lactic acid C. Gastric acid D. Glutamic acid Read the full article

[biologydictionary]

Treponema Pallidum

Definition

Treponema pallidum subsp. pallidum is a subspecies of the Treponema genus and a microaerophilic bacterium that belongs to the spirochetal order. It is characterized by a thick phospholipid membrane and a very slow rate of metabolism, requiring approximately thirty hours to multiply; even so, T. pallidum is a difficult-to-eradicate pathogen and responsible for the sexually-transmitted disease, syphilis.

Treponema pallidum

What is Syphilis?

Syphilis is a chronic human disease and the result of either sexual transmission or transmission from mother to baby during its progression along the birth canal. Known as ‘The Great Pretender’ has a differential diagnosis is always possible, the first potentially visible sign of syphilis is the chancre, a small, round and hard ulcer or lesion found at the site of primary infection. As this site is often inside the vagina, mouth, throat or anus, a chancre is rarely detected immediately unless is it visible – on the lips or penis. Most internal primary lesions are observed at a later date during general screening activities in clinical settings. Poorer populations with low access to medical care are more likely to continue in sexual activity (and subsequent childbearing) without the benefit of diagnostics and treatment. A chancre also heals without treatment after approximately one month. This is another reason why those without immediate access to medical care may ignore a primary syphilis lesion or discontinue antibiotic therapy. However, it is very important that treatment commences at the primary phase to prevent a syphilis infection from reaching the secondary phase.

Syphilis hand rash The secondary stage of syphilis is characterized by a rough red or brownish rash usually on the soles of the feet and the palms of the hands, although the location can be elsewhere on the body. Another secondary syphilis symptom is the appearance of larger lesions in moist areas such as armpits, mouth, and groin. These lesions are known as condyloma lata. Again, if treatment is ignored, the secondary phase of syphilis will progress to a further stage. Additional worrying symptoms associated with the secondary stage include hair loss, swollen glands, headaches, and fatigue. Consultation with medical professionals is, therefore, more common during this phase.

Syphilis hand rash The next stage of syphilis development is the latent stage. It presents without symptoms and its name – latent – refers to a dormant period; however, Treponema pallidum is still present within the body and the person in question remains highly infectious when taking part in sexual activities with one or more partners. This is also possible when an infected female gives birth to a baby without a caesarian section. The latent stage can last for many years but the latent stage’s symptom-free characteristics discourage carriers to seek out medical help. Without treatment, the latent stage of syphilis eventually passes into a potentially fatal tertiary syphilis. Colonization of T. pallidum in various areas of the anatomy will cause serious damage. Diagnosis often names a tertiary stage according to the area of damage, in particular neurosyphilis, cardiovascular syphilis, and ocular syphilis. Other areas of damage are the liver, bones, and joints. Lesions and open sores progress over the body. It is because of this tertiary stage that the disease was given its name as ‘The Great Pretender’; multiple diagnoses exist for the symptoms also produced by a T. pallidum infection of the tertiary stage. Upon initial contact with this spirochete, infected humans develop specific immune responses that do not have the capacity to wipe out large populations of treponemes from syphilis sites. Usually, T-cell-mediated delayed-type hypersensitivity responses involve the infiltration of T-cells into Treponema inoculation sites and activate macrophages to remove these treponemes via phagocytosis. However, T. pallidum bacteria can avoid this hypersensitivity response thanks to a number of factors.

Treponema Pallidum Immunity Factors

Treponema pallidum immunity factors are a complicated affair that has made it very difficult to develop a vaccine. A lack of knowledge pertaining to the occurrence of multiple reinfections in humans, even after a strong immune response during the first infection, means a cure has not yet been found. Recent research into the protective mechanisms of these so-called stealth pathogens is, however, a hot topic; new discoveries are regularly published in scientific journals. T. pallidum transmits syphilis through vaginal, anogenital, and orogenital contact. This bacterium has an extremely small genome and lacks genes that encode the classic virulence factors of more aggressive and resistant bacteria. This means that treatment with penicillin is very effective. However, current ideology regarding an antibiotic-resistance crisis, the increasing number of allergic reactions to penicillin in the human population, and the rapid reappearance of syphilis around the globe cause concern.

How antibiotic resistance happens Studying Treponema pallidum subsp. pallidum is made more difficult through the susceptibility of these bacteria to in-vitro settings; it is very hard to reproduce colonies in a laboratory. A more recent understanding of T. pallidum subsp. pallidum metabolism is now enabling some researchers to succeed where others have failed. The combination of small genome, very slow metabolism and thick phospholipid membrane makes this spirochete a power-packed disease carrier in an extremely basic package that has been grouped into a small group of difficult to immunologically recognize and remove microorganisms known as stealth pathogens. Treponema can survive quietly in the human body for years and at the same time remain highly infectious. Treponema Pallidum: Stealth Pathogen IgG Treponema pallidum protection in the form of immunoglobulin G antibodies – the most common type of antibody in human blood and other extracellular fluids - is a later response to infiltration by a foreign organism or material than IgM (immunoglobulin M antibodies). In the case of T. pallidum subsp. pallidum, primary infection of a previously non-infected human occurs during sexual activity or natural birth. T. pallidum bacteria pass from an infected person into a new human host and slowly multiply. In order to understand T. pallidum’s identification as a ‘stealth pathogen’, it is first important to understand the mechanisms involved in its recognition as a hostile protein and the body’s inefficiency in removing it. The Treponema Reduced Immune Response A protein foreign to the body is referred to as an antigen. The majority of bacteria, viruses and other pathogens produce antigens on their surface membranes which are usually instantly recognized as foreign. In the case of T. pallidum, the thick phospholipid membrane holds the majority of these antigens hidden under its surface. Furthermore, the membrane lacks lipopolysaccharide (LPS) glycolipids. LPS’s cause inflammatory Gram-negative bacteria reactions that either alert the immune system to act or cause symptoms that bring the infected person to request medical help. This combination of features means that Treponema pallidum enters the body without attracting much attention and, even though it multiplies slowly, is given the time to disseminate (spread) with little resistance. The chancre is, therefore, a sign that the innate mechanism of active immunity has detected a foreign presence and proceeded to attack it. Macrophages that recognize the few Treponema surface proteins as hostile begin to remove them via phagocytosis (see below). As foreign bacteria are broken down, large amounts of inflammatory cytokines are produced. The result of this initial inflammatory reaction is the chancre. This initial response is quite late and the body is by now the host of T. pallidum spirochete colonies.

Innate immunity - phagocytosis Macrophages show the results of their work to B lymphocytes or plasma B cells that begin the process of somatic hypermutation in the adaptive (or humoral) immune system - a process that allows the B cell to set up a code for a new antibody. This code is featured on the antigen as a Treponema pallidum-specific binding site (Antigen Binding Site or ABS). Immunoglobulin M is one of the first-produced antibody types; immunoglobulin G is the most commonly formed. The new antibodies circulate and recognize the coded T. pallidum bacteria surface proteins wherever these are visible and set to work destroying the bacteria. How effective this action is may have an effect upon the length of the latent stage of syphilis and the appearance and severity of tertiary symptoms.

Adaptive or humoral immunity More recent data, however, complicates this later recognition process. Forms of T. pallidum are heterogeneous, meaning diverse types exist within a single subspecies. For bacteria with one of the smallest genomes known to man, this is no small feat. While one form of the hostile bacteria will bind with the antigens produced by the adaptive immune system, another form will not. Additionally, the antigen-to-antibody binding process is significantly slow, almost keeping the immune system distracted and leaving non-binding versions to multiply and spread. The inflammation resulting from the destruction of binding T. pallidum causes secondary symptoms such as palm and sole rash and condyloma lata. The energy required to keep populations of spirochetes under control leads to fatigue. The theory that spirochetes may colonize hair follicles may be pertinent to hair loss in secondary syphilis. Treponema Pallidum and IgM Treponema pallidum IgM response at initial infection is, as has already been described, slow and hindered through a difficult to recognize bacterial membrane. This means that IgG responses very quickly follow that of IgM; testing solely for IgM antibodies as a method of detecting early Treponema infection is of little diagnostic value. Instead, blood serum testing for syphilis by way of an antibody test is carried out with Total Antibodies (IgG and IgM) testing.

Testing Treponema Pallidum Antibodies

To test Treponema pallidum antibodies, all that is needed is a few milliliters of blood collected in a tube that separates blood serum from the cell mass. The antibody test known as Syphilis Total Antibodies has relatively recently taken over the pole position of an older test known as RPR or Rapid Plasma Reagin. Previously, RPR was advised as an initial test to determine the presence of cardiolipin, cholesterol, and lecithin in blood plasma. These are non-specific antibodies produced when a body is fighting certain sorts of bacterial or viral infection via adaptive immunity. A doctor would, therefore, have to first observe syphilis symptoms or consider a person at risk of syphilis before justifying such a generic test. Only if the result of an RPR came back positive in an at-risk patient or one showing symptoms would a Syphilis Total Antibodies (STA) test be requested. The table has since been turned. The first test is now the Syphilis Total Antibodies (STA) test. If this comes back negative, there is little need for the RPR. If the physician is not convinced or if more results are requested, the RPR can provide further proof of antibody activity. If there is a discrepancy between STA and RPR results, a further test called T. pallidum particle agglutination (TPPA) will confirm a positive or negative result.

First STA, then RPR

Quiz

1. In which order would you carry out the following tests? A. RPR, TPPA, STA B. IgM, IgG, RPR C. ABS, RPR, STA D. STA, RPR, TPPA 2. Which of the following is not a symptom of secondary syphilis? A. Rash on palms and soles B. Chancre C. Condyloma lata D. Fatigue 3. Which of the following products found on Gram-negative membranes cause inflammatory reactions? A. T-cells B. ABS C. LPS D. IgM Read the full article

[biologydictionary]

The Dark Side of the Genome

Did you know that only 2% of the human genome actually creates proteins? Scientists are still not sure what the other 98% does, exactly. A new paper about fruit fly genetics sheds some light on how researchers can begin to look into this “Dark Side” of the genome. To fully understand this study, you need a little background on the basics of DNA:

DNA → RNA → Proteins

In the form of DNA most widely taught in high schools, there is a “mantra”. DNA makes RNA which in turn creates Proteins. Proteins are the cellular machines that carry out all the functions of a cell, from copying the DNA to creating and maintaining a cellular membrane. This is essentially what allows cells to survive and reproduce. Ultimately, this form of storing information in the genome allows the forces of natural selection to work on the genome, selecting only the mutations that allow an organism to survive or reproduce more efficiently.

At the molecular level, DNA is a massive and complex molecule, much of which we know little about. More specifically, the DNA is broken up into exons and introns. Exons hold the actual information of each protein. The information is stored in “codons” - sets of three nucleotides that specify each amino acid in a protein. The order of amino acids is extremely important to protein function. If an amino acid is missing or is in the wrong order, the function of the protein can be completely altered. So, we know a lot about exons and about how they create proteins. But, we know a lot less about introns….

DNA doesn’t always make Protein…

Just because introns don’t make proteins does not mean they are not important. Researchers have discovered many uses for introns. Some are used to bind to histones - important structural proteins that allow DNA to be stored in chromosomes. Other introns affect the transcription of DNA by attracting transcription proteins. Introns are also sometimes transcribed into RNA, though these RNA sequences do not go on to become proteins. In the study, researchers used high-throughput RNA tests (similar to the tests 23andMe and other DNA testing companies use) in order to understand which types of fruit flies were producing which networks of RNA. Researchers found that there was much higher variation within introns than they expected. Their new method, which essentially “reads” the RNA sequences present in a cell or organism, allows the researchers to fully understand which of the DNA introns are being expressed into RNA sequences. While the exons of the fruit fly are well studied, science still knows very little about the much larger and more complex spaces between them. Hopefully, this new method of scanning and documenting RNA sequences can help us build a big picture of how they influence genetics. Read the full article

[biologydictionary]

Scientists Just Found The World's Smallest Dinosaur

We all know that T. rex is the king of the dinosaurs. Fossils of T. rex show that it was huge, had sharp claws and teeth, and likely few predators. Now, scientists are exploring the opposite end of the spectrum: The world’s smallest dinosaur fossil, no bigger than the world’s smallest living bird: the Bee Hummingbird.

The Bee Hummingbird, which is the same size as the world's smallest dinosaur! This newly found specimen, dubbed “Oculudentavis khaungraae,” represents the smallest dinosaur currently known to science. To fully understand how and why this tiny dinosaur came to be and was ultimately discovered by science, we have to take a look at a few biological concepts!

Miniaturization

Essentially, size can be a huge factor when it comes to reproductive success. The blue whale, the world’s largest animal (even bigger than dinosaurs), has evolved to be large to escape predation from large sharks. At the other end of the spectrum, many other animals find more success as tiny creatures. These creatures, being so small, are able to occupy niches unavailable to larger animals. Miniaturization is a process that has taken place across many different evolutionary lines. The process involves a species rapidly decreasing in size, often to fill a niche newly available to the population. There are many, many examples of this in nature. Fennec foxes have gotten smaller to deal with the harsh desert conditions they live in. Pygmy marmosets eat small insects in the Amazon rainforest, allowing them to occupy the same region as other primates that eat fruit. Even the Bee Hummingbird (pictured above) has evolved as the world’s smallest bird to gain access to nectar in flowers unavailable to larger birds. Interestingly, this process typically takes place on islands. Islands, because they are separated from the ecosystem of the mainland, often develop their own ecosystem. When a full-sized group of organisms colonizes the island, they are subject to the rules of the new ecosystem. Oftentimes, their preferred niche is no longer available, so they must adapt. Sometimes, this adaptation comes in the form of getting much smaller. This gives the population access to new nutrients and resources. Unsurprisingly, researchers found the smallest dinosaur ever among fossil deposits that are thought to have originated on an island. But, the tiny creature faced one more enormous challenge in actually being discovered by scientists: fossilization.

Fossilization

Typically, fossilization occurs when the remains of a dead animal are covered in mud, tar, or another oxygen-depleted substance. This stops the process of decomposition, which would otherwise devour the dead animal and recycle it as nutrients in the environment. Small organisms have a much harder time at becoming fossilized because they are simply more fragile and more likely to break down over time. Fortunately for these scientists, this particular minuscule dinosaur was a fan of tree sap. Tree sap, the same stick stuff that you can find leaking out of your neighborhood tree, has been a consistent feature of trees for millions of years. Fortunately for scientists, some trees put off a tremendous amount of sap. Small animals, like the newly discovered dinosaur, accidentally get stuck in the sap. This could have happened before the dinosaur died, or the sap could have flowed around the animal after its death. Either way, the sap contains very little air - stopping the action of decomposers. After millions of years, the sap hardens to become amber. Amber has yielded some truly amazing fossil discoveries, such as this frog, completely intact millions of years after its death:

A fossilized frog, well preserved in amber. So, it was lucky that this little, bird-like dinosaur found its way into a flow of sap. Otherwise, we might have never known that it existed! Read the full article

[biologydictionary]

Turtles and Plastic Don’t Mix

If you haven’t heard - Plastics are ruining many ecosystems. A recent study of sea turtles shows the problem explicitly.

Turtles suffer from plastic waste in many ways. In this study, researchers observed the food-seeking behaviors of loggerhead sea turtles when exposed to different smells. When the smell of food was pumped into the enclosure, the turtles would lift their head above the water for several minutes. This allows them to track the food, so they can swim in the right direction, find the food, and eat it. The most eye-popping result from the study was that sea turtles had this exact same reaction to plastics covered in the smell of food. These plastics have absolutely no nutritional value, cannot be digested, and often cause blockages in the turtle’s digestive system that can easily lead to death! To fully understand why turtles can be so easily confused by plastics, we have to look at some biological concepts to find an explanation.

Sea Turtle Diet

Sea turtles eat a wide variety of other ocean creatures, including shrimp, small fish, jellyfish, and even sponges. Some sea turtles have even evolved to be able to handle the powerful toxins that some of these creatures produce! So, it seems shocking that plastics are so harmful to a creature that seemingly has an “iron gut”. Plastics are not necessarily toxic, but they do something to the turtles that can essentially starve them to death - plastics do not break down. Normally, when a sea turtle eats a toxic sponge or a stinging jellyfish, the material goes into the stomach where it is broken down to its chemical level. Nutrients are released, absorbed into the bloodstream, and any left-over waste products pass easily through the turtle’s intestines. The waste products are excreted as feces, allowing the turtle to continue eating and passing food through its guts. Plastics block this process because they do not break down in the stomach or intestine. While turtles have spent millions of years evolving to eat the toxins present in jellyfish and sponges, plastics have been around for less than 100 years. And, considering how much plastic is already in the environment, it is unlikely that turtles will be able to adapt before they go extinct.

Plastic Pollution

Plastics have been mass-produced for over 50 years, and until now there has never been any concern about plastic pollution. But, scientists all over the globe are finding very high levels of plastic in almost every natural environment. Oceans are getting the brunt of plastic pollution, mostly because all freshwater leads to the ocean. This carries a torrent of plastic waste into the ocean, where it circles around relentlessly in ocean currents. This map shows just how bad the plastic problem is.

Map of plastics found in the ocean (red = higher plastic density). This map measures microplastics - tiny pieces of plastic - in the world’s oceans. The red areas show where the plastics are accumulating. Unfortunately for turtles and other wildlife, currents are building up these plastics in many tropical areas, near coral reefs, and in the feeding grounds for many organisms. While turtles are beloved by many and can help rally support for ending plastic pollution, there are many other animals at risk for ingesting plastic and dying. In fact, one report estimates that up to 99% of sea birds have ingested plastic. In the next decade, this could absolutely reak havoc on global ecosystems and completely break-down the entire marine food web. Tell your friends - Stop Plastic Pollution Now! Read the full article

[biologydictionary]

Baby Bees and Pesticides: Bad News for the Environment

It has long been known that all sorts of animals suffer from the use of commercial pesticides. In the 1950s, scientists created the pesticide DDT. DDT was widely used on crops, as a personal pesticide, and as a way to combat disease-carrying mosquitos. However, in 1962 Rachel Carson published the book Silent Spring, bringing to light all of the terrible effects DDT has on the environment. It was quickly found that DDT actually weakens the shells of bird eggs, leading to a massive decline in the populations of many predatory birds. DDT was banned for many uses by the newly formed Environmental Protection Agency in the 1970s, but the general use of other pesticides was continued. Now, researchers are bringing more negative effects of many other pesticides to light. A new study, published in Proceedings of the Royal Society B, shows just how drastically even the smallest amount of pesticide can affect bees and other pollinators. To fully understand why pesticides are harmful, we have to look at a couple of important biological concepts.

Brain Development

When you were a fetus in your mother’s womb, your brain started developing. You started with a small cluster of nerves - cells that have specialized in transferring chemicals and electric signals. These cells then multiplied and spread throughout your developing body. These nerves extend to all parts of your body. In your skull, your brain begins forming. Your brain is like the central processing system for your entire body. Though your brain starts as only a few cells, it quickly replicates to become nearly 100 BILLION different cells. These cells each connect to tens of thousands of other brain cells, forming a neural network that contains TRILLIONS of connections. In order for your brain to function properly, these connections must be specific and well-formed when you are finally born. Pregnant women are told to avoid a large number of toxins - such as alcohol and tobacco - because these substances can cause delays and deformities during brain development. A bee brain forms in a similar way. After an egg is laid in a cell within the hive, it hatches into a small larva. This larva eats honey, a substance created as bees eat and regurgitate the nectar they find in flowers. Their brain develops during this time, finally forming the adult brain in the pupa stage. You can see the whole bee lifecycle below:

The Life Cycle of a Honeybee When bees bring back nectar that has pesticides in it, the pesticides may not kill the adult bees. But, they are transferred directly to the developing larva. Pesticides cause major disruption in brain development, leading to serious performance declines later in life. To understand why this can be so devastating, it’s important to understand a bee’s role in an ecosystem.

Pollinators in the Ecosystem

Pollinators are organisms that transfer plant pollen from one plant to another. Pollen is essentially plant sperm, and it is used to fertilize plant eggs found deep within a flower. After a flower is fertilized, it can produce fruits, nuts, and seeds. Therefore, pollinators are responsible for much of the food production throughout the world.

The process of pollination transfers pollen between flowers. In this study, researchers showed that bees with pesticide-ridden brains do not function well as adults. In fact, they found that these bees essentially had major brain damage and could not perform their essential “bee tasks”, such as creating and maintaining the hive, communicating with other bees, and collecting nectar. If pesticides get to all the larva in a hive, the hive will quickly die because these bees will not be able to complete basic hive upkeep tasks. If we keep poising bees and other pollinators with pesticides, they could eventually die off completely. That’s bad news for farmers! While pesticides can help protect their crops from crop-eating insects, the same pesticides are slowly destroying insects that are necessary to produce fruits, vegetables, nuts, and seeds. Without bees and other pollinators, the entire agricultural industry would collapse in on itself like a dying star. Read the full article

[biologydictionary]

Glowing Frogs? You Bet!

A brand new article in Nature reveals a new truth about amphibians: many of them glow. While we can normally not see this glowing light radiating from their skin, a new technique is revealing the hidden truth.

A frog showing biofluorescence. This frog, and many other amphibian species explored in the study, glow with fluorescence when they are hit by certain wavelengths of light. To fully understand why amphibians glow under certain lights, we have to understand some basic biology concepts.

Biofluorescence

There are many substances in nature that emit fluorescence. Fluorescence is caused by a fairly simple physical phenomenon. When energy-loaded light photons hit certain types of molecules, the molecules absorb some of the energy. Then, the excess energy moves through the molecule until it escapes. When the energy escapes, it is emitted as new photons. However, because of the shape, size, and chemical properties of the molecule they are emitted from, these photons come off in a specific frequency (or color). In amphibians, the photons emitted are mostly within the green spectrum, giving the amphibians a green glow under the right conditions. These amphibians have molecules created by their bodies that can create this fluorescence. This is considered “biofluorescence” because it is a molecule produced by biology that creates the glowing light.

Animal Perception

When we start seeing fluorescence in animals, we have to ask: what is the purpose? While this question is still being answered, scientists have uncovered a myriad of uses that animals use fluorescence for. Salamanders are known to signal to each other by flashing their stomachs, areas that are full of biofluorescent molecules. This is thought to be a territorial threat display. Fish also display a wide variety of fluorescence, and scientists theorize that these patterns may also be for communication and territorial purposes.

A variety of fish that show biofluorescence However, the presence of fluorescence is not likely to be arbitrary. It is assumed that if animals show and use this fluorescence that they can also perceive the fluorescence. In other words, not only do amphibians show this coloring, but they can probably see it without the use of filters, special cameras, and the other scientific equipment that humans need to see it! Read the full article

[biologydictionary]

Blood-Snow! Is Earth Bleeding?!

Some new observations from a research outpost in Antarctica are freaking some people out. “The Earth is Bleeding,” the internet says. While this is simply the byproduct effect of a species of algae, the fact that the phenomenon is related to climate change, and looks like blood, is really the perfect symbol. See for yourself:

"Blood" or "Watermelon" Snow, caused by a species of algae. But, to explain why blood snow is the perfect symbol of climate change, we have to understand a couple of biological concepts: Algal Blooms and Extremophiles.

Algal Blooms

Algae is a single-celled organism that is essentially constantly reproducing in the right conditions. Most of the time, in both freshwater and marine environments, nutrients are relatively sparse, sunlight is somewhat blocked, and other conditions keep algae at relatively low levels. However, there are many human activities that can inadvertently remove one or more of these barriers, causing a massive increase in algae reproduction. For instance, many deadly algal blooms occur as rivers empty into the ocean. The rivers, loaded with washed-off nutrients from farms spanning the river’s length, spill these concentrated nutrients right into the ocean. The effects can harmful and damaging to wildlife, humans, and entire marine ecosystems. Some of the largest algal blooms actually cause “dead-zones” below their surface. As the algae grow thick, the lower layer begins to die. Bacteria, eager to feed on the massive bounty of dying algae, quickly consume all the oxygen in the water and killing many organisms. Other algal blooms actually release toxic chemicals as they die off, poisoning the water for any that enter. The effects are so drastic that even adult whales can be killed.

A whale that has died due to toxins in an algal bloom. But, to understand this recent blood-colored algal bloom on the snow, we can look at one more biological concept: Extremophiles.

Extremophiles

Extremophiles are any organisms that live in what most other creatures would consider a “hostile” environment. In other words, extremophiles can survive in places that destroy other forms of life. In fact, there are many different types of extremophile: Acidophile - acid lovers Alkaliphile - “All About that Base” Halophiles - live in extremely salty places Radiophile - organisms that just LOVE toxic radiation Anaerobe - oxygen is for wimps Osmophile - too much sugar? Never a problem. While the list goes on and on, the blood algae are actually just a form of green algae that is also an extremophile. A “cryophile”, to be more precise. These algae can live in much colder temperatures than a typically algal cell, thanks to mutations that give it an extra cell wall and allow it to melt surrounding ice into fresh, clean water! This brings us back to blood algae as a symbol of climate change.

Is Earth bleeding? Maybe…

While this is not actual blood and has been observed several times, these giant red algal blooms seem to be happening more often. The barrier holding these algae back is simply the lack of water. So, once a little melting starts to happen these algae can really start to take off and melt much more ice. Since ice reflects sunlight, and water does not, the water begins to heat up and melt even more ice. Therefore, the more frequent these algal blooms become, the faster the effects of climate change will be seen. While these blooms are not known to be harmful, other algal blooms also caused by global warming and pollution could easily poison our water supply and contribute to the destruction of entire ecosystems. So, in a way, the Earth is bleeding and we should pay attention. Read the full article

[biologydictionary]

The Moth that uses Stealth-Mode to avoid Bats

When I was a kid, I thought moths were by far the dumbest insect on the planet. They always pretend that you can’t see them, they flutter in your face at the most inopportune times, and I have seen many moths fly right into an open flame. Dumb! But, the more I learned about biology, the more respect I have gained for moths. Not only do moths have a very interesting life cycle, but moths have also developed a number of defense mechanisms to avoid their main predator - Bats! While it has long been established that some moths have evolved sensory organs to hear the ultrasonic squeal of an approaching bat, scientists were confused about how moths without these organs avoided bats. By all accounts, moths without an ultrasonic hearing organ should be extinct!

This moth uses "stealth-scales" to avoid detection by bats. Finally, researchers have uncovered an important defense mechanism these moths use to avoid bats. In a recently published article, researchers have identified a second strategy that moths use to avoid bats, even if they don’t have ultrasonic ears. These moths use a super high-tech type of scale that absorbs ultrasonic frequencies like the sound insulation in a recording studio, essentially making these moths invisible to a bat’s ultrasonic sonar! To see why this is such a cool biology story, we have to look at a couple of different biological concepts: Defensive Adaptations and Predator-Prey Coevolution.

Defensive Adaptations

The scales these moths produce are a perfect lesson in defensive adaptations. While other types of moths have been evolving ultrasonic-hearing organs, these moths never inherited the mutations and genetic changes necessary to develop these defenses. But, that doesn’t mean these moths were doing nothing. Evolution is a process that occurs as the variation in a population is systematically tested. In moths, the test is simple: did the moth get to reproduce before it was eaten by a bat? Variations that do not help moths survive and reproduce are lost, while any variations present in the next generation can be considered “beneficial”. Many species of moth have gained variations that make them sensitive to the ultrasonic frequencies bats emit. This strategy has been well-documented, and researchers have even shown that when these moths sense an ultrasonic frequency, they stop flapping and begin a wild and random freefall to the ground. This helps them avoid the bat, and hopefully survive to reproduce. But, this new study shows that moths have evolved another defensive adaptation: “stealth-mode”. Instead of listening for the ultrasonic frequencies, these moths simply ensure that the signal never makes it back to the bat. The scales that they have evolved over time ensure that the signal is absorbed, rather than reflected. To the bat, this makes them effectively invisible!

These graphs show how different moths and butterflies absorb ultrasonic frequencies. As you can see in the graphic above, researchers found that at ultra-high frequencies bats use for sonar, the scales on these moths block nearly 25% of the returning signal. The two species on the left show a much lower target strength at a number of ultrasonic frequencies. Butterflies (on the right) do not have these scales, and they are much easier for bats to detect because the returning ultrasonic signal is so much stronger. This can confuse a bat chasing a moth, making it think that the signal is only a small insect or some small particle. This lowers the chance that the bat will recognize the moth as food. Thus, the survival rate of these moths increases. Evolution!

Coevolution between Predator and Prey

That brings us to our second important biological concept displayed by this system: Predator-prey coevolution. Coevolution is a process through which two or more species actively affect one another’s evolutionary trajectory. In simple terms, bats and moths are evolving together based on the adaptations each group evolves! Long before the first bats, insects likely had total dominance of the skies. Ultrasonic hearing or stealthy scales were not necessary, because there were no predators chasing them in the skies. Then, birds and bats evolved. These creatures could pursue insects in the skies. That’s when the “arms race” began. Bats, apparently in an effort to not compete with birds, evolved to become nocturnal. But, this brought up several issues. First and foremost, bats could no longer see where they were flying or what they were chasing. So, they started listening. Over the course of millions of years, bats evolved the ability to navigate using ultrasonic sonar. The bats send out a “click” and listen for the sound waves to bounce off of solid objects. In this case, insects. At first, the moths likely lost the battle. Without any defenses against this ultrasonic adaptation, the moths were eaten up. But, a few novel variants made it through the carnage. Moths evolved things like ultrasonic hearing and the newly discovered “stealth-scales”, that gave them a leg up in the war. These back-and-forth adaptations are a perfect example of predator-prey coevolution, which happens between predator and prey species in all ecosystems around the globe. But, it doesn’t stop here. Moths and bats will both continue evolving traits to fight the war. Who knows? Someday we may have bats that can kill moths with their ultrasonic clicks and moths with massive defensive scales to absorb the blows! Read the full article

[biologydictionary]

The Curious Case of the 46,000-year-old Bird

Just this week, scientists published an article in the journal Communications Biology. In this article, scientists document a nearly-perfect, intact specimen of a bird that died nearly 46,000 years ago!

A 46,000-year-old horned lark, preserved in permafrost While this might seem like a peculiar find, at best, it is actually an amazing discovery that sheds like on the history of the world! Scientists found this bird in the icy permafrost tundra in Siberia. The scientists, who were looking for frozen Mammoths in the permafrost, stumbled across the little frozen bird like a chicken finger that had fallen loose from the bag and was now permanently affixed to your freezer in a block of ice. While it may seem silly to document every dead bird that you find, this bird is special for a number of reasons. Not only does this small bird give us an idea of what the world looked like 46,000 years ago, but it also tells us a lot about the evolution of birds.

The World - 46,000 years ago

Imagine wearing a blindfold while you explore the forest and try to document its inhabitants. Without being able to clearly see the relationships between plants and animals, you are limited only to what you can feel, smell, and hear. You might start by picking up a leaf, and carefully tracing its shape. Then, you might feel around for plants around you, to see if any of them have leaves that match. The process is slow, frustrating, and rigorously intellectual. That’s essentially what archaeology is… a blind man exploring individual clues to illuminate the dark past. But, a big find like this can really start to put things into perspective. Like the blind man feeling animals in the forest, every new specimen leads to a better picture of the Earth’s history. To date when the bird died, scientists use methods of radiocarbon dating. This method, which measures levels of decaying radioactive materials within the bird’s cells, can estimate dates with very high precision. The presence of the bird suggests that the environment 46,000 years ago likely had a number of small plants that could produce seeds and fruit to sustain the bird. According to the article, scientists have also documented a large variety of plant pollens which support the idea of a cold, but a relatively diverse ecosystem.

Bird Evolution

Thanks to technological advancements in genetics, the bird can tell us a lot more than that. The bird was so well preserved that scientists were actually able to analyze its DNA. Scientists measured the bird’s mitochondrial DNA (mtDNA), which is only passed down from a mother’s egg cell. Therefore, mtDNA is an extremely valuable tool for documenting and tracing evolutionary lines. Amazingly, the frozen bird researchers found still had plenty of mtDNA to work with. When scientists analyzed the mtDNA from this particular dead bird, they found that the bird was actually related to 2 subspecies of the horned lark.

A modern horned lark This tells us that the frozen, mummified corpse was actually once part of a species of birds that have evolved and changed over time. As a new ice age crept in, some of the dead bird’s descendants migrated to warmer climates, while others succeeded in the cold, desolate tundra. Today, these two subspecies of horned lark rarely interbreed and are on their way to becoming separate species. While the process of speciation can occur very quickly, this amazingly preserved bird shows that speciation can also be a long, drawn-out process. It also suggests that while climate change will be potentially detrimental for many species, other species will develop adaptations to cope with the changes. Read the full article