The Science of it All

Basic Geology part 1

Types and Processes for Rock Formation and Weathering

Why am I doing a dissertation on geology when my area of study is microbiology and the human genome?  Good question.  My understanding is that the geologic column is the foundation, the bedrock, (pun intended) of modern day evolutionary hypothesis or neo-Darwinism or “materialistic naturalism,” all synonyms for the old fashioned and now outdated “goo-to-you” evolution taught in our schools for the past 100 years. If I can start some cracks in the concept of the geologic column, it just might fracture completely (pun again).  Besides, it helps reinforce my concepts that the fossil record is woefully inadequate to explain anything, the geologic column is grossly distorted to match the scientist’s preconceived notions, and the Biblical concept of plate tectonics explains far more than any of the current theories do.

I have some experience in geology.  I lived in Phoenix most of my live and loved to get out into the desert and up into the mountains and the Mogollon Rim.  From Payson it looks like this:

From the edge of the rim, looking out it looks like this:

Javelina hunting in the Superstition Mountains, deer hunting in the Bradshaw Mountains and hiking the White Mountains was a wonderful way to see a variety of landscapes and marvelous geologic strata-not that I was fully aware of what that was at the time. Time marches on and I eventually moved to Texas, where the landfill for big Spring is as big as Scenic Mountain (which Payson has rocks as big as it is).

I worked for Pioneer Petroleum, in Midland, Texas, as computer support for their 3-D imagining department.  From reading in the images from the field, to watching them be transformed into 3-D images of the various strata of rocks underground and pools of oil in between the layers, it was very interesting work.  I also had the opportunity to watch as they removed core samples from a drilling site going down 2 miles.

We measured the distance of each stratum and drilled boreholes every meter into it.  We turned the borings over to the lab to be chemically analyzed for the type of rock, 14C levels, etc.  Therefore, I am not without some experience in the area, more than the average person is, but far less than someone with a degree in the field is.  With that background information, let us continue on our exploration.

The modern field of geology traces its roots back primarily to Charles Lyell, who developed the theory of uniformitarian geology[i].  This theory directly contrasted the theories of catastrophism and supernatural occurrences.  Uniformitarianism is the idea that by using observations of current natural processes, we can predict how processes occurred in the past.  In order to do this, we must accept that changes in nature occurring millions of years ago are similar to the changes that occur today.  First you have to believe in the long age theory AND believe that the environmental conditions today was the same as millions of years ago.  This is a problem for me as most evolutionary geologists and other related sciences believed that the early earth history was very traumatic and full of catastrophes- volcanoes, meteorites, and ice ages – in other words constantly changing.  Let us see if we can unfold the riddle of what the earth actually tells us.

Modern geological theory is a modification of Lyell’s uniformitarian views and recognizes Lyell was partly wrong.  The term “uniformitarianism,” as used by Lyell, actually includes four different concepts.  These four aspects of uniformitarianism with an evaluation of each are summarized in the following table:

Table 1. There are four separate concepts in Lyell’s uniformitarianism[ii]

  • Uniformity of law: This is a part of science in general, and not unique to geology.  It is still accepted that natural law is indeed uniform.  Water never flowed uphill in the past.  (If you are a Christian, it is interpreted as the Creator making a uniform and consistent world of scientific laws).
  • Uniformity of geological processes: The present is the key to the past.  The application of this means we do not invent unique processes if modern processes can explain the observations.  However, this is only partly valid; it is now known that the geological past was somewhat different from what we observe today.
  • Uniformity of rates of processes: Geological processes have always been slow and gradual.  There have not been any catastrophic geological events. This is known to be false but is still figured in their calculations.
  • Uniformity of conditions: Conditions on earth have always been the same, cycling endlessly with no direction.  This is not true and hard to support. Conditions in the Cambrian period, for example, were quite different from conditions today.  For example, our existing continents were largely covered with shallow seas during the Cambrian.  In addition, the fossils in different parts of the geological column are significantly different.

Different geological processes produce different types of rocks.  Simple to understand that.  Each rock type is composed of a particular combination of minerals, such as quartz, calcite, or feldspar.  Table 1 presents the three major categories into which rocks are classified.  The descriptive information is not specific to any one theory (MYA or short-age), but is part of the foundation for any geological theory.

Table 2. Types of rocks

Igneous rocks Forms as molten magma cools to form rock.

Examples: granite and basalt (volcanic lava).  A mass of granitic rock forms some mountains and underlies each continent.

Fossil Content: uncommon in igneous rocks, since hot magma would normally destroy any organisms.  Exceptions occur when lava or volcanic ash surround an organism and preserve it.

 

Sedimentary rocks It is a four-step process in making sedimentary rock that are erosion, transport, deposition, and cementation or compaction into solid rock.

Representative types of sedimentary rocks are classified by the size of the grains or particles that compose them: shale and siltstone— very small grains; sandstone— larger, sand-sized particles; conglomerate— a mixture of fine particles (sand or mud) and larger rounded pebbles (rounded by transport in flowing water); breccia— mixture containing angular (not rounded by water transport) pebbles or rocks; limestone— principally calcium carbonate, in the form of the mineral calcite (CaCO3) precipitated out of ocean water or alkaline rivers, streams, or lakes. Some limestones are an accumulation of carbonate shells or skeletons of organisms such as corals or mollusks.

Fossil Content: animals or plants are often buried in the sedimentary layers, and the majority of fossils are found in sedimentary rocks. Even volcanic ash, which has an igneous origin, often is deposited as sedimentary layers. These layers of ash are effective agents for preserving fossils.

 

Metamorphic rocks Form when rocks are subjected to sufficient heat and/ or pressure (perhaps by burial under additional rocks) and chemical changes to alter them into a different type of rock. These altered rocks are metamorphic rocks.

Fossil content: any fossils are generally destroyed in the process of metamorphism

 

 

While the processes described in Table 2 are occurring, another significant process, called weathering, is altering the rocks- a minor point often ignored by long-age evolutionists.  Ground water and weak acids seep through the rocks, gradually breaking them down by chemical action.  The minerals are changed into (1) clay; (2) dissolved chemical ions including sodium, potassium, and calcium; and (3) quartz and other sand-sized grains.  The dissolved ions and clay are carried in streams and rivers to lakes and oceans, where the clay settles to the bottom in the quiet water and the ions determine the water chemistry in these water bodies.  The sand grains may be transported by water and/ or wind and accumulate to form sandstone formations given other conditions.

The average thickness of the sediments on all the continents is approximately 1,500 meters (.9 miles), but in some places, it is much thicker.  How long does it take to deposit such sediments?  The answer depends upon the theory of geological history you subscribe too.  Many state that radiometric dating provides an accurate, straightforward answer.  Radiometric dating will be considered further in another article with other geological evidence that challenges the time scale based on radiometric dates.

In the next article, we will consider factors that can have an influence on the rate of erosional speed.

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[i] C. Lyell and G. P. Deshayes, Principles of Geology: Being an Attempt to Explain the Former Changes of the Earth’s Surface, by Reference to Causes Now in Operation, 3 vols. (London: John Murray, 1830– 1833).

[ii] S. J. Gould, “Toward the Vindication of Punctuational Change,” in Catastrophes and Earth History: The New Uniformitarianism, ed. W. A. Berggren and J. A. Van Couvering (Princeton, NJ: Princeton University Press, 1984), 9– 34.

 

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Intelligent Design, Philosophy, The Science of it All

How did life begin?

The naturalistic origin of life is also known as abiogenesis or sometimes-chemical evolution.

The origin of life is an exasperating problem for those who insist that life arose through purely natural processes.  Some evolutionists try to claim that the origin of life is not a part of evolution –it is a separate problem- once life began then it evolved.  Probably every evolutionary biology textbook has a section on the origin of life in the chapters on evolution.  The University of California, Berkeley, has the origin of life included in their ‘Evolution 101’ course, in a section titled “From Soup to Cells—the Origin of Life”.[1]  Some high-profile defenders of ‘all-things-evolutionary’, such as P.Z. Myers and Nick Matzke, agree that the origin of life is part of evolution, as does Richard Dawkins[2].

A well-known evolutionist of the past, G.A. Kerkut, did make a distinction between the General Theory of Evolution (GTE), which included the origin of life, and the Special Theory of Evolution (STE) that only dealt with the diversification of life (the supposed topic of Darwin’s 1859 book).[3]

So, what do we need to get life?  How did life begin?

Explaining the origin of life by solely physical and chemical processes is proving to be extremely difficult.

First: What is it that we have to have to produce a living cell?  Well what is a living cell?  Basically, a living cell is capable of acquiring all the resources it needs from its surroundings and reproducing itself.  We will not get into a discussion of what resources were necessary.  That is still debatable and under strong discussions in the scientific community.  We will assume that all of the necessary components (whatever they may be) were there in an available form to use.

Second: The first cell had to be free-living; that is, it could not depend on other cells for its survival because other cells did not exist.  (Some evolutionists try to state that a prokaryote cell ingested a eukaryote cell and then became a viable living cell.  However, this begs the question; they are already starting with a cell in one form or another). We have to stretch to imagination (well, maybe not) to believe that whatever process occurs, didn’t just happen in one area- maybe it happened a billion times over throughout the existing world. Too often, the Ider’s (Intelligent Designers) and creationists go with the concept that it happened once, somewhere, but it is possible that probably many different types of cells developed about the same time throughout the world and only certain ones survived.  I will not rule that out.

Third: Parasites cannot be a model for ‘first life’ because they need existing cells to survive.  This also rules out viruses and the like as the precursors to life as they must have living cells that they can parasitize to reproduce themselves.  It also brings up the question of how the parasite or virus developed.  Portions of genetic-like material may have been within the resources necessary for a cell to develop, however, the still would have needed a living cell to become activated.

Fourth:  Prions, misshaped proteins that cause disease, have nothing to do with the origin of life because they can only ‘replicate’ by causing proteins manufactured by an existing cell to become misshaped.  Fewer and fewer scientists are exploring this particular dead end street.

Right here there is a major problem for chemical soup approaches to the origin of life-The so-called primordial soup has been the laughing stock of creationists and the wastage of millions of taxpayer dollars by evolutionists in attempts to create it.  For without it, their concept fails.  Below is how they would like to imagine it having happened.

I want to play fair.  NOBODY was there to know or understand what the start of our Earth was- if you are an evolutionist.  If you are a Christian it was Adam, but the exact details of the oceans, continent, and atmospheric conditions are not written down so it is guessed by both sides.  I will stipulate, as above, that the resources for the necessary components for life were available in whatever form necessary.

This then begins to bring out several problems though.  Some of the necessary components of life, have carbonyl (>C=O) chemical groups that react destructively with amino acids, and other amino (–NH2) compounds.  Such carbonyl-containing molecules include sugars, which also form the backbone of DNA and RNA. (Sugars have linear forms that contain carbonyls—see Fig. 2 below.  The cyclic forms that occur in nucleic acids also predominate in solution form, but in equilibrium with the linear form. When something reacts strongly with the aldehyde, then more of the linear form is regenerated to replace that which is reacted, so all the sugar molecules will end up being consumed).  Living cells have ways of keeping them apart and protecting them to prevent such cross-reactions, or can even repair the damage when it occurs to the credit of the cell.  How this is accomplished in the natural resource environment we are discussing is anyone’s guess.

Cells are incredibly complex arrangements of simpler chemicals.  I am not going to cover every chemical that a first cell would need; it would take and has several books to cover the topic.  I will highlight some of the basic components that have to be present for any origin of life scenario.

a. Amino acids

Living things are loaded with proteins; linear strings of amino acids.  Enzymes are special proteins that help chemical reactions to happen (catalysts) without being consumed in the process.  For example, the enzyme amylase is secreted in our saliva and causes starch molecules from rice, bread, potatoes, etc., to break up into smaller molecules, which can be then be broken down to their constituent glucose molecules.  We cannot absorb starch, but we are able to absorb glucose and use it to power our bodies.

Some reactions necessary for life go so slowly without enzymes that they would effectively never produce enough product to be useful, even given billions of years.  In 2003, Wolfenden found another enzyme exceeded even this vast rate enhancement.  A phosphatase, which catalyzes the hydrolysis of phosphate dianions, magnified the reaction rate by 1021 times.  That is, the phosphatase allows reactions vital for cell signaling and regulation to take place in a hundredth of a second. Without the enzyme, this essential reaction would take a trillion years—almost a hundred times even the supposed evolutionary age of the universe (about 15 billion years)[4].

Other proteins form muscles, bone, skin, hair and all manner of the structural parts of cells and bodies.  Humans can produce well over 100,000 proteins (possibly millions; we really do not know how many), whereas a typical bacterium can produce one or two thousand different ones.

Figure 1. Leucine, (Chemical formula: C₆H₁₃NO₂) the most common amino acid, which is a specific arrangement of atoms of carbon (C), hydrogen (H), oxygen (O), and nitrogen (N).  It is essential in humans—meaning the body cannot synthesize it and thus must obtain from the diet.  In addition, natural selection cannot operate until there are already living organisms to pass on the information coding for the enzymes, so it cannot explain the origin of these enzymes to be used by other cells.

Actually, it should make one wonder about the faith commitment to evolution from goo to you via the zoo, in the face of such amazingly fine-tuned enzymes vital for even the simplest life!

Proteins are made up of 20 different amino acids (some microbes have an extra one or two).  Amino acids are not simple chemicals and they are not easy to make in the right way without enzymes (which are themselves composed of amino acids); see Figure 1.

The 1953 Miller–Urey experiment is still presented as having managed to make some amino acids without enzymes.  It is often portrayed as explaining ‘the origin of life’.  Although tiny amounts of some of the right amino acids were made, the conditions set up for the experiment could never have occurred on Earth; for example, any oxygen in the ‘atmosphere’ in the flask would have prevented anything from forming.  Furthermore, some of the wrong types of amino acids were produced, as well as other chemicals that would ‘cross-react’, preventing anything useful forming.

When Stanley Miller repeated the experiment in 1983 with a slightly more realistic mixture of gases, he only got trace amounts of glycine, the simplest of the 20 amino acids needed.  Crucial to the success of the experiment was Miller’s water trap in which the amino acids generated could dissolve and thus be protected from subsequent destructive contact with the spark.  However, on the hypothesized primordial Earth with no oxygen (and therefore no ozone), the products would have been exposed to destructive ultraviolet rays.

The origin of the correct mix of amino acids remains one of many unsolved problems.

Figure 2. Glucose, linear form.

b. Sugars

Some sugars can be made just from chemistry without enzymes (which remember are only made within the cells themselves).  However, mechanisms for making sugars without enzymes need an alkaline environment, which is incompatible with the needs for amino acid synthesis.

The chemical reaction proposed for the formation of sugars needs the absence of nitrogenous compounds, such as amino acids, because these react with the formaldehyde, the intermediate products, and the sugars, to produce non-biological chemicals.

Ribose, the sugar that forms the backbone of RNA, and in modified form DNA, an essential part of all living cells, is especially problematic.  It is an unstable sugar (it has a short half-life, or breaks down quickly) in the real world at near-neutral pH (neither acid nor alkaline).

c. The components of DNA and RNA

How can we get the nucleotides that are the chemical ‘letters’ of DNA and RNA without the help of enzymes from a living cell? The chemical reactions require formaldehyde (H2C=O) to react with hydrogen cyanide (HC≡N). However, formaldehyde and cyanide (especially) are deadly poisons. They would destroy critically important proteins that might have formed let alone poison the cell from inside if not neutralized correctly.

Figure 3. Cytosine, one of the simpler of the five nucleotides that make up DNA and RNA. In this form of chemical diagram, each unlabelled bend in the ring has a carbon atom at the bend.

Cytosine (Figure 3), one of the five essential nucleotide bases of DNA and RNA, is very difficult to make in any realistic pre-biotic scenario and is also very unstable. I could write an entire chapter on how difficult producing a stable version of cytosine is – maybe I will some day.  DNA and RNA also have backbones of alternating sugars and phosphate groups.  The problems with sugars have been discussed above.  Phosphates would be precipitated by the abundant calcium ions in seawater or cling strongly onto the surfaces of clay particles.  Either scenario would prevent phosphate from being used to make DNA.

d. Lipids

Lipids (‘fats’) are essential for the formation of a cell membrane that contains the cell contents, as well as for other cell functions.  The cell membrane, comprised of several different complex lipids, is an essential part of a free-living cell that can reproduce itself.  Some evolutionary theorists will claim that some lipids came together and formed a bubble that contained some other proteins and amino acids and was the start of an original cell that grew big enough to divide for the efficiency of transport of nutrients within it.  Way too many ifs, ands or buts involved in this concept.

Lipids have much higher energy density than sugars or amino acids, so their formation in any of the possible necessary resource situations is a problem for origin of life scenarios.  The reason is high energy compounds are thermodynamically much less likely to form than lower energy compounds.

The fatty acids that are the primary component of all cell membranes have been very difficult to produce, even assuming the absence of oxygen (a ‘reducing’ atmosphere).  Even if such molecules were produced, ions such as magnesium and calcium, which are themselves necessary for life and have two charges per atom (++, i.e. divalent), would combine with the fatty acids, and precipitate them, making them unavailable.  This process likewise hinders soap (essentially a fatty acid salt) from being useful for washing in hard water—the same precipitation reaction forms the ‘scum’.  Arthur V. Chadwick, Ph.D.  a Professor of Geology and Biology  states “All phenomena are essentially unique and irreproducible. It is the aim of the scientific method to seek to relate effect (observation) to cause through attempting to reproduce the effect by recreating the conditions under which it previously occurred. The more complex the phenomenon, the greater the difficulty encountered by scientists in their investigation of it. In the case of the scientific investigation of the cause of the origin of life, we have two difficulties: the conditions under which it occurred are unknown, and presumably unknowable with certainty, and the phenomenon (life) is so complex we do not even understand its essential properties.[5]

Figure 4. A potassium transport channel from Wikipedia commons.  The red and blue lines show the position of the lipid membrane and the ribbons represent the transporter, which comprises a number of proteins (different colors).  To give some idea of the complexity, each loop in each of the spirals is about four amino acids.

Some popularizes of abiogenesis like to draw diagrams showing a simple hollow sphere of lipid (a ‘vesicle’) that can form under certain conditions in a test-tube (mentioned above under Lipids).  However, such a ‘membrane’ could never lead to a living cell because the cell needs to get things through the cell membrane, in both directions.  Such transport into and out of the cell entails very complex protein-lipid complexes known as transport channels, which operate like electro-mechanical pumps.  They are specific to the various chemicals that must pass into and out of the cell.  Many of these pumps use energy compounds such as ATP to drive the movement against the natural gradient.  Even when movement is with the gradient, from high to low concentration, it is facilitated by carrier proteins.

The cell membrane also enables a cell to maintain a stable pH, necessary for enzyme activity, and favorable concentrations of various minerals (such as not too much sodium).  This requires transport channels (‘pumps’) that specifically move hydrogen ions (protons) under the control of the cell.  These pumps are highly selective and are beyond the scope of this article-source for another probably.

Transport across membranes is so important that “20–30% of all genes in most genomes encode membrane proteins”.[6]  The smallest known genome of a free-living organism that of the parasite Mycoplasma genitalium, codes for 26 transporters[7] amongst its 482 protein-coding genes.

A pure lipid membrane would not allow even the passive movement of the positively-charged ions of mineral nutrients such as calcium, potassium, magnesium, iron, manganese, etc., or the negatively-charged ions such as phosphate, sulfate, etc., into the cell, and they are all essential for life.  A pure-lipid membrane would repel such charged ions, which dissolve in water, not lipid. Indeed, a simple fat membrane would prevent the movement of water itself (try mixing a lipid like olive oil with water)!

Membrane transporters would appear to be essential for a viable living cell.

In the 1920s the idea that life began with soapy bubbles (fat globules) was popular (Oparin’s ‘coacervate’ hypothesis) but this pre-dated any knowledge of what life entailed in terms of DNA and protein synthesis, or what membranes have to do.

Figure 5. The chirality of typical amino acids. ‘R’ represents the carbon-hydrogen side-chain of the amino acid, which varies in length. R=CH3 makes alanine, for example.

e. Handedness (chirality)

Amino acids, sugars, and many other biochemical’s, being 3-dimensional, can usually be in two forms that are mirror images of one another, this is called handedness or chirality (Figure 5).

Now living things are based on biochemical’s that are pure in terms of their chirality (homochiral): left-handed amino acids and right-handed sugars. One problem though:  chemistry without enzymes (like the Miller–Urey experiment), if they can get anything to happen, produces mixtures of amino acids that are both right-and left-handed. It is likewise with the chemical synthesis of sugars (with the formate reaction, for example).[8]

Origin-of-life researchers have battled with this problem and all sorts of potential solutions have been suggested but the problem remains unsolved.  Even getting 99% purity, which would require some very artificial, unlikely mechanism for ‘nature’ to create, does not cut it.  Life needs 100% pure left-handed amino acids.  The reason for this is that placing a right-handed amino acid in a protein in place of a left-handed one results in the protein having a different 3-dimensional shape. None can be tolerated to get the type of proteins needed for life.

 

[1] http://evolution.berkeley.edu/evosite/evo101/IIE2aOriginoflife.shtml (accessed 17 October 2013).

[2] Myers, P.Z., 15 misconceptions about evolution, 20 February 2008, scienceblogs.com; Matzke, N., What critics of neo-creationists get wrong: a reply to Gordy Slack, pandasthumb.org. Dawkins tries to deal with the origin of life in his book The Greatest Show on Earth, where he claims to ‘prove evolution’. See Sarfati, J., The Greatest Hoax on Earth? ch. 13, 2010, Creation Book

[3] Kerkut, G.A., Implications of Evolution, Pergamon, Oxford, UK, p. 157, 1960 (available online at ia600409.us.archive.org/23/items/implicationsofev00kerk/implicationsofev00kerk.pdf); creation.com/evolution-definition-kerkut

[4] Lad, C., Williams, N.H. and Wolfenden, R., The rate of hydrolysis of phosphomonoester dianions and the exceptional catalytic proficiencies of protein and inositol phosphatases, Proceedings of the National Academy of Science 100(10):5607–5610, 13 May 2003.

[5] http://origins.swau.edu/papers/life/chadwick/default.html

[6] Krogh, A. et al., Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes, Journal of Molecular Biology 305(3):567–580, 2001; dx.doi.org/10.1006/jmbi.2000.4315

[7] Transporter Proteins in Mycoplasma genitalium G-37; membranetransport.org/index.html (accessed 1 Aug. 2017).

[8] The ‘right’ and ‘left’ in terms of chirality refer to the position of the amino group (NH2) as displayed on a standardized diagram (Fischer projection) of an amino acid.