EVOLUTION OF PROTEINS

EVOLUTION OF PROTEINS

What are proteins?

Proteins are polymers or combinations of various amino acids called peptides when they are bound in a chain.  A tri-peptide is composed of three amino acid residues, polypeptides of multiple ones; proteins have residues numbering in the hundreds and more.  Each amino acid incorporates a nitrogen atom in its structure at the site where it can be combined with the acid-like part of another amino acid, leaving similar junction sites on the resulting molecule so longer chains can be produced.  Further linkages via side chains can yield a great variety of shapes.

Why are proteins important?

They are the key to much of the structure and function of an organism.  Many of them are common to other distantly related species.  Some are unique to a species and even individuals or a subgroup of a species.

The proteins of our body have great diversity based on variations in the sequence and the resultant structure.  Enzymes are proteins useful in aiding chemical processes of the body.  Insulin is a protein type hormone.  Enzymes and hormones vary greatly in size but are typically much smaller than proteins used for structural purposes.  Both enzymes and hormones typically have their activity based on a peculiar aspect of their structure, often just a small portion of the molecule – the active site.

Hormones cause cells or organs, in various specific locations away from the sites of hormone production, to do their jobs.  Enzymes typically enable a chemical reaction to occur with minimal energy expenditure and can do so repeatedly.  Cooking deactivates enzymes and prevents decomposition until other organisms digest or invade the cooked food.

 Myosin and actin are two major proteins of muscle and each has a filament type structure. Large bundles of myosin slide past smaller bundles of actin and cause muscles to shorten and do their work.  Opposing muscles contract to cause the extension of an opposing relaxing muscle by force applied through the mechanics of the skeleton or tissue fluidity.

What evolutionary affects did the nitrogen atom of amino acids have?

When an amino acid or peptide is broken down the nitrogen atom can be released as an ammonium molecule, a toxic substance if concentrations build up in the body.  Most carbohydrates and lipids do not contain nitrogen so their residue, after use for energy, is carbon dioxide and water.  So is much of the protein but the ammonia cannot be passed into the air from fluid in the lungs very effectively.  Aquatic animals were able to accomplish much of the early evolution of life without needing special organs to dispose of nitrogenous waste.  The ammonia could diffuse from the body surface or gills into water where it would be useful for plants.

As organisms got larger those that could package ammonia into less toxic forms had an advantage.  Urea and uric acid are two of the substances that were selected for most successful animals.  Urea is soluble in water but non-toxic; it is the major compound containing nitrogen that is excreted by the mammalian kidney.  Uric acid is toxic but not very soluble and it is the main product produced by degradation of adenine and guanine from the nucleic acids, DNA  and RNA.  Biochemical processes in animals are varied in their potential to make various conversions of nitrogenous wastes.  Along the way, kidneys became more and more important for regulating levels of nitrogenous wastes in the blood as well as salt and water balance while retaining nutrients.

Uric acid made it possible for shelled eggs of animals to evolve for life on land.  It could accumulate in the egg without poisoning the embryo.  That made it possible for reptiles to lay their shelled eggs on land.  Birds continued the egg-laying process, as did early mammals (the platypus and echidna still do).  Eventually placental mammals developed and transferred nitrogenous wastes from the fetus to the mother for elimination by her kidneys. 

Why didn’t birds go that route?  Probably it has weight reducing value for flight.  It’s so important that only one ovary develops in a female bird, probably enabling larger eggs to be laid that can develop to greater maturity.  You can probably think of the survival advantage a mammal has from being able to takes its internal young with it and not be bound to a nest location and its hazards.

Proteins and the pharmaceutical industry

Hormone and enzyme activity must be well regulated by the body for health.  Too much or too little function can be detrimental to health.  Some classes of drugs are designed to have function like those items in the body.  They can supplement the body’s product or interfere with its function as needed to get the correct balance.  The critical aspect is getting an active site incorporated in a non-toxic molecule that can go to the needed area.  Alternatively, a toxic molecule designed for attraction to a cancer cell or overactive gland might be helpful.

Trial and error methods are being replaced by analysis of molecular structure for duplication of active sites in a synthetic substitute.  The active site in some cases is not dependent upon the chemical nature as much as the physical shape of the portion of the molecule.  Other parts of the molecule may affect some part of the process so clinical trials are needed to verify safety and effectiveness.

Unfortunately all possible interactions, with systems of the body at all stages of function and development, breakdown products and their role in the environment, and other possible hazards cannot be foreseen.  But we hope care in the process can minimize the hazards.

The computerized process of designing molecules based on fit with some portion of hormones, enzymes, cell membrane receptors or other entities is a likely source of valuable products.  But individuals and/or conventional research teams cannot be replaced as easily for less conventional and serendipitous discovery.

Joseph G. Engemann                April 30, 2014

EVOLUTION AND FATS

Carbohydrates versus fats

Both are utilized by the major mechanisms of storage and use of energy by animals.  For transport to and from locations of intake, storage, and use, glucose is the main blood sugar; fatty acids and triglycerides are the fats that are typically the most abundant forms in the blood.  The liver can convert glucose to fatty acids and fatty acids to glucose.

Storage of carbohydrates in the liver in the form of glycogen makes it easy for the liver to produce glucose needed by the liver or other organs.  Storage of glucose in fat cells involves its conversion to fatty acids before storage as fat.  Storage, release, and use have hormonal mechanisms regulating the processes.  Because fats are relatively insoluble in water but very soluble in other fats, oils, and waxes, they can be stored in large quantities in fat cells without adversely affecting the metabolism of those cells.

Energy content of fats versus carbohydrates

The efficiency of storage would seem to favor fats for energy storage even though liver glycogen can be more easily a source of glucose in the blood stream.  Fats store twice the energy per unit of weight than do carbohydrates.  Thus they have evolved as the energy store that enables many organisms to make long distance migrations or go for long periods without feeding.  Some birds lose most of their fat and over half of their body weight during annual migrations.  Fats need conversion to glucose in the liver or elsewhere to be used in the brain and energy production throughout the cells of the body.

Lipid is the generic term for most substances that dissolve or mix easily with other lipids and/or fat solvents.  Lipids include fats, oils, waxes, fatty acids, triglycerides and some other compounds such as steroids.  Whereas carbohydrates have the bulk of the carbon atoms of the molecule each associated with two hydrogen atoms and one oxygen atom, the chain of most lipid carbon atoms have no oxygen associated.  Most of the energy derived by the metabolic burning of the compounds comes from oxidation of the hydrogen atoms.  But half of the carbohydrate hydrogen atoms are already with oxygen atoms so the ratio of two hydrogen atoms to one oxygen atom is the same as in water and thus the origin of the name carbohydrate.

Uses of fats by organisms

The membranes within cells are readily formed from microscopic globules of certain lipids.  The myelin sheath insulating fibers within nerves of the central nervous system presumably functions to prevent short circuits between closely packed fibers as well as making the polarization of the fiber easier after depolarization during impulse transmission.  Fats in the diet are thought to be useful for efficient uptake of fat-soluble vitamins.  Fats secreted by sebaceous glands are useful lubricants for skin to keep it moist and pliable.  Fat can be stored at many locations in the body, but that stored under or in lower layer of the skin is especially valuable as insulation for animals living in cold habitats.

Fats having carbon chains having two adjacent carbons each lacking a hydrogen atom but sharing a second bond with each other are said to be unsaturated.  Unsaturated fats are liquid at lower temperatures than are saturated fats with the same number of carbon atoms.  We appear to be dependent on our food for necessary unsaturated fats.  Lipids with associated phosphate groups are called phospholipids and some seem to have an important role in brain function.

Steroid hormones are lipids with peculiar ring structures similar to the cholesterol molecule.  Small variations of atom clusters attached in one or more places around the rings can make big differences in their role in regulating body processes.  They are only one of the classes of hormones important in regulating life processes.

Evolution and lipids

The characteristic structure of hormones can lead to recognition of those that are the same or only have slight variation in various groups of animals.  The molting hormone of insects is recognizable as a steroid hormone.  Although we don’t have a hormone exactly like the insect’s ecdysone, it is part of an endocrine complex that seems unlikely to exist without having had a common origin from an earlier ancestor.  It is only one of many clues of chordate origin from ancient annelid ancestors (the most recent common ancestor of us and the insects).

The early evolution preceding living organisms may have been partially dependent on the insolubility of lipids in water, but lipid ability to form minute droplets (emulsify), as well as the potential of some long chain lipids to automatically form membranes in water.  Coating various mineral particles and being pulverized in countless tidal pools around the world provided much experimentation.  Along with ultraviolet light facilitating chance reactions of various concentrations of solutes produced by evaporation at low tide it was a suitable place to get some of the basics done for life to occur.  I think that might be how God did it.

Joseph G. Engemann      April 27, 2014

EVOLUTION OF CARBOHYDRATES

EVOLUTION OF AMAZING CARBOHYDRATES

The Stuff of Life

Plants and animals utilize a variety of basic materials to make the specialized parts that are so different in some ways.  Carbohydrates, proteins, and fats make up most of the volume of organic molecules and structures in the watery bath inside and/or outside the membrane bounded cells of living organisms.  Minerals make up a major part of vertebrate skeletal structures and of shells of some invertebrates.  Very important in proper functioning, and often controlling aspects of development and function, are vitamins, hormones, minerals, and trace elements in very small amounts. 

The hereditary material has a central role in perhaps most aspects of life, but little will be said about it in today’s blog.  DNA, RNA, and enzymes and the feedback mechanisms used are modified along with evolution of the things they control.

Glucose in plants versus animals

Glucose has an important role in utilization of stored energy in plants and animals.  But only a small amount can be tolerated in the cells of plants or animals.  Animals and plants can both burn it up as they metabolize it to produce energy by the same chemical pathways.  But too much in the cell would result in the cell bursting from water absorption that occurs by its diffusion into the cell from the watery bath around it.  Cells that survived are those that evolved to convert excess glucose into other compounds, especially large polymers such as cellulose in plants and glycogen in animals.

Plants can also store large amounts of glucose as starch as well.  Both cellulose and starch molecules are so large that only a few molecules can store hundreds of glucose molecules.  The generic name for such a large compound molecule is polymer.  Plants make glucose in abundance by the process of photosynthesis.  Glucose polymerized into cellulose makes a useful structural material, typically as the major part of the cell walls of plants. 

Cellulose processing was lost in the early cells that gave rise to the animal kingdom.  But animals developed a modified form of storage called glycogen that functions, as starch may do in plants at night, to quickly replace glucose when it becomes depleted in the cell from activity.

Glucose is a six carbon sugar.  Disaccharides are twelve carbon sugars such as sucrose, maltose and lactose; they are formed from particular combinations of two monosaccharides, such as glucose and fructose.  A five carbon sugar is part of the linking mechanism, for the chains forming DNA and RNA, along with one of the four purines and/or pyrimidines (adenine, cytosine, guanine, and thymine).  Each link of the chain with one of the four purines or pyrimidines uses three links at a time to code the hereditary processes of life.

A hypothesis about a balanced diet

We know that insulin helps the body in regulating blood glucose by somehow helping balance the role of storage and utilization between blood sugar and storage or release from fats and other stores.  Plants do not have insulin to my knowledge, but many of the chemical processes involved in storage and release of glucose may be similar. Varied grains, fruits, and vegetables in the diet are likely to provide some necessary substances involved in the process that are not fully known.  They and the fiber associated also provide a valuable role in maintaining the proper gut flora and fauna needed for healthy functioning of the lower digestive tract.

The first organic molecules

Organic molecules are commonly thought of as originating in living organisms.  But a few simple ones can form when lightning passes through a gaseous atmosphere containing water vapor, carbon dioxide, methane, and nitrogen.  Similar simple compounds can form in sea water exposed to red hot lava.  Both may have been important in contributing to the dissolved nutrients of seawater in early seas when the first life evolved.

Among those compounds formed in such circumstances are glucose, glycine, and adenine.  We have already discussed some of the role of glucose above.  Glycine and adenine are among simple amino acids utilized to make polymers, called proteins.  Additionally, adenine has an important role basic in ATP (adenosine tri-phosphate) for energy transfer processes in cellular metabolism.

The big picture

The above is just a rudimentary look at a portion of the processes and materials of life.  How they interact here is probably identical to how they have acted (and are or will act) in other comparable planets scattered throughout the cosmos.  Natural selection would probably produce great similarity of results through these remarkable chance directed processes that could only be controlled by an infinitely intelligent and powerful being.  It should be truly humbling to see that such a being has promised so much to us through his Son two thousand years ago.

Joseph G. Engemann      April 25, 2014

GOD

God: Science and the Media

THE MEDIA

Was Jesus Married?

Yesterday, a major network newscaster provided one of those provocative snippets of “news” with a (snide? whimsical? embarrassed?) grin without much further comment.  It had to do with a fragment of ancient text from biblical times which associated Jesus with a term for wife.  The brief associated comments made in the newscast lead one to think it implied Jesus was or might have been married.

No!

There is little reason to think Jesus was married in the sense of having a wife or being a spouse.  But it would not make much difference if he had been anymore than the fact that at least some of the original apostles were married.  But (1) such a major fact would have been very likely to be passed on down through tradition if it were true.  And (2) the terms used for spouse and marriage are and have long been used for the association of Jesus with his church.  Even today Roman Catholic nuns typically wear a wedding ring at, and perhaps after, receiving their final vows in which they are considered “married to Christ” in a spiritual sense. So (3), the fragmentary new evidence has no compelling basis for the suggestion passed on in a newscast.

Science

Science and its methods have much to reveal about God’s creation, but little if anything to reveal about God.  Because the world and all that is in it are a product of God’s creative genius and grandeur, scientists are more likely to find the truths science is capable of finding by proper respect and love for the creator of the world and all that is in it.  What we see as chance and evil are likely misunderstood products of other natural aspects of creation such as evolution and free will that can be found to be positive aspects in some way conforming to God’s plan or direction beyond our present understanding.

The positive aspect of regressive evolutionary events

One hint of this is the profound effect of extinctions and regressive aspects of evolution that were part of the path leading to human beings.  The loss of many annelid features leading to the pogonophoran intermediates giving rise to the most successful animal phylum has been described in several previous posts (the first on 05/031/2013 shows the evidence of error in current theories), concepts that are not yet clearly understood by my peers.  Evidence was partially shown by annelid theory of chordate origin which was not was not properly reinstated in scientific credibility when the evidence used to reject it was shown to be invalid. (See also the last five posts of June 2013)

God

God works in mysterious ways beyond our present comprehension.  So are God’s attributes beyond our comprehension.  Why and how this imperfect and error prone individual could lead a life that discovers the aspect of evolution noted in the previous paragraph could only be possible with God’s grace. That is quite amazing, but even more so, are the accomplishments of the also ordinary lives of many others I know.

Joseph G. Engemann     April 12, 2014

EVOLUTION AND MARRIAGE

THE NATURAL STATE

Opposition to same sex marriage seems a natural position when biology is considered.  Male to female unions is a fact of evolution of sex in humans, the pinnacle of social species.  It is not denial of a right any more than denying that the man is the mother and the woman is the father in a heterosexual marriage.  But there are rights that all should have, and they should not be denied those rights because they hold views other than the views of the majority or the powerful.

CIVIL UNIONS

Parental rights and contractual rights are among those rights.  Family rights do not end if one spouse dies.  Civil unions should be available to provide such rights without specification of sexual relationships.  The obligations that go with family responsibilities should be part of the package.  Care of minor children should be part of the responsibility of any becoming part of a civil union.

ALL IMPERFECT BUT ALL HAVE RIGHTS

No one born in the last two thousand years is perfect.  Yet Jesus tells us that God loves each of us and that we should do likewise.  Whether one’s sexuality departs from the norm because of a genetic factor or a social imprinting inflicted on them early in development is immaterial to the rights of the individual.

WHAT’S NATURAL?

The nuclear family seems to be an ideal that society should encourage without unduly restricting the behavior of those not conforming to that norm.  Failures of responsible behavior in nuclear families do not justify stopping social endorsement of traditional families. Clearly some great individuals have come from non-traditional families.  Some people smoke without getting lung cancer, but it still is socially warranted to discourage smoking.

SEEK SENSIBLE LAWS

Society is justified in prohibiting public displays of both heterosexual and homosexual behavior.  Likewise inflicting such behavior on minors as well as non-consenting adults is properly restricted.  Christian societies seem to be making great progress is establishing freedom and equality for all as we emerge from our puritanical past.  Whether the past demise of societies from social excesses since the decline of Sodom and Gomorrah is fact or story does not seem essential to knowing how to make our society the best possible.

NATURAL CONSEQUENCES

Sexually transmitted diseases have been with us before AIDS seemed to target homosexual behavior in males early in its establishment in this country.  It is amazing that STD’s are not more prevalent with the emphasis the advertising and entertainment industries put on sexual behavioral freedom.  It is extremely difficult to see how a democratic society can reach a fair agreement on a position somewhere between the extremes of Puritanism and Sexual Libertarianism.

SEEKING A SOLUTION

Same sex marriage is an oxymoron by whatever name you call it.  The proper rights its advocates are seeking can best be legally accommodated by a contractual arrangement called a civil union.  Contesting the validity of marriage as exclusively a female-male union defies history, religious tradition, and social norms.  Civil unions could also be useful for others united for practical reason apart from sexual considerations.

HOW HAVE THEY SOLVED THE PROBLEM ON OTHER PLANETS?

To me, Gay Marriage also defies the process of evolution.  I fully expect the process of evolution occurred in much the same way on millions of other planets in the universe.  In the hereafter I expect to meet others from those planets created by the same God through the process of evolution and having many attributes in common with us.  Perhaps some have different numbers of digits and other minor differences.  I don’t expect the language to be the English but I already know God loves them as well as us.

I don’t expect many people will agree with me.  The somewhat intermediate position exposes me to criticism from those on both sides.

Joseph G. Engemann     April 5, 2014