The Science of it All, Intelligent Design

One last bit of reflection

One last bit of reflection

I was astonished when one of the biochemistry professors I was working with on a project to modify a human anatomy/physical therapy program donated by NASA, discussed the elegance of the automatic decision-makers working on the molecular scale to keep the various chemicals of life at the right levels in each cell!  It was a little off topic at the time but was certainly one of my interests.  I mentioned that they certainly seemed designed and he was quick to change his attitude and attributed these ingenious molecular decision-makers to unguided evolutionary processes.  His message was clear: however remarkable these molecular control systems may be, they are nothing more than natural accidents— just like everything else in biology.

I let it slide and nothing more said during the rest of the design project.  I knew— intuitively, anyway— that no string of biological accidents could possibly be so clever as to manufacture themselves or other biological parts.  At that time, I sensed the weight of “scientific authority” standing with his interpretation and against mine.  Notice, I used the word authority here instead of evidence.  He was the degreed individual; I was the understudy, hired to improve the software.  However, by this time, I had completed three semesters of college microbiology and sports biomechanics.  For all the claims that I had heard in lectures and read in textbooks about the inventive power of Darwin’s evolutionary process, I had not seen any convincing scientific basis for these claims.  No one had shown how the amazing cellular machines of life could be accidental inventions instead of deliberately designed ones.

The troubling contradiction between what the voice of scientific consensus was telling me and what the voice of my own intuition was telling me had to be resolved.  That is what I have set out to do, to resolve this apparent conflict within my understanding.  I am certain that this conflict exists in all of us to some degree.  To the extent we share the intuition that life cannot be an accident; understanding is what eliminates the contradiction.  Technical understanding can be overwhelming; I know I had to read some of the data more than once to understand it.  I will offer simplified details of the important technical information.  I will not turn this into a science lecture.  Instead, common science will be the thread that holds everything together.

The most peculiar aspect of Darwinism is not that it takes credit for things that seem too extraordinary to be explained but rather that the explanation offered seems too ordinary for the job.  As a software developer, I recognize the other concepts that continue on here.  Intuitions are interpreted differently (Intuition is the ability to acquire knowledge without proof, evidence, or conscious reasoning, or without understanding how the knowledge was acquired)

Whether the method I describe is the one that I actually use is less important than whether it justifies my conclusions. Specifically, I want to know whether the intuition that makes us all doubt Darwin’s theory is sound.  If the answer to this is yes, as I think I can confirm, then Darwin’s theory is in trouble whether or not we ever have a fully satisfactory account of how intuitions work.

I think the intuition by which we immediately perceive certain things to be the products of purposeful intent is close to the idea that some things are too good to be true.  This expression does not mean that good things cannot happen; it means certain good things cannot just happen.  They never come out of thin air.  They only happen if someone makes them happen.  Only someone who has that knowledge can accomplish tasks that we would need the knowledge to accomplish.

Whenever we think we would be unable to achieve a particularly useful result without first learning how we judge that result unattainable by accident.  The important point is that we all reach these judgments, often unanimously, and this rule fits these judgments reasonably well.  I use the term universal design intuition— or simply design intuition— to refer to the common human faculty by which we intuit design or the necessity for learning.

If no one makes breakfast, then breakfast goes unmade.  Likewise, for cleaning up after breakfast, for making the bed, and so on.  Everyday experience consistently shows us that even simple tasks like these never accomplish themselves.  Whether we taught ourselves these skills or taught by others, the point is that knowledge had to be acquired in the form of practical know how.

According to the design intuition, neither bricks nor shoes are made unless someone makes them.  As familiar as this intuition is, it turns out to have huge implications for biological origins, because the claimed exceptions are so concentrated there. And what dramatic exceptions they are!  Bricks are not made until someone makes them (or today, until someone makes the machine that makes them), but somehow much more complex things, like dragonflies and horses, were made without anyone making them, we are told.

Sensibly, we know and understand that nothing impressive ever happens by accident.  Far beyond such simple things are the pinnacles of human technology, like robots, communications satellites, and smart phones, which we know cannot appear by accident.  At the highest reaches of the complexity scale is the true masterpieces— things like hummingbirds and dolphins— all of them alive, all of them eluding our best efforts to understand them.  Some technophiles like to think that human ingenuity will one day produce their equal, and good things will surely come from rising to that challenge-obtainable or not.

Astrophysicist Neil deGrasse Tyson described this utopian view as follows in the first episode of the “Cosmos: A Spacetime Odyssey” television series:

“This adventure is made possible by generations of searchers strictly adhering to a simple set of rules: test ideas by experiment and observation; build on those ideas that pass the test; reject the ones that fail; follow the evidence wherever it leads, and question everything. Accept these terms, and the cosmos is yours.”

Somehow, with the conferring of rare honors, with the establishment of scholarship funds and the dedication of buildings that bear a person’s name, with oil portraits and marble busts and postage stamps bearing a person’s likeness, somehow the fallible aspects of humanness we most easily relate to evaporate.  This leaves us with an image of an individual that hovers midway between heaven and earth, neither divine enough to be worshiped nor human enough to be hugged.  Perhaps this tendency to idolize the legends of science is connected to a skewed view of the entire scientific enterprise.  Many of us, including myself, have bought into the idea that science, though practiced by humans, has managed to rid itself of the human flaws that leave their mark on every other human undertaking.  The purity of science is guaranteed by the rigor of “the scientific method,” we think.

if ideas could be tested with a meter, the way batteries and fuses can, then Tyson’s simple rules would work.  But if we intend to question everything, perhaps we should begin by questioning whether the human testing of human ideas can really be so simple, considering how complicated humans are.  Nowhere are these complications more evident than in the discussion of big ideas that touch the way we live, because here we find that everyone— scientists included— have a strongly held view.  Moreover, the very biggest ideas are those that offer answers to the all-important question of how we got here.

Oddly enough, I now see how the pursuit of prestige goes a long way toward explaining how science is stuck on certain wrong ideas.  In the professional world of science, prestige is bestowed in the form of praise, and not just any praise but the rare praise of those who are themselves most highly praised.  Why would anyone assume that praiseworthy science always gets the praise it deserves?

The answer, I think, is that when we fall for the utopian view of science, truth and prestige do appear to be weighted equally.  If we assume scientists are single-mindedly driven by the quest for truth and nothing else, then we expect those scientists with the keenest perception of the truth to rise to the top.  These top-notch scientists form an elite body of experts whose consensus opinion is the surest indicator of the truth there is.  Or so we believe.  Prestige and truth then seem inseparable, as though they are just two different names for the same thing.  Moreover, we need only see that it can easily become an authoritarian science.  With the truth perceived to be so reliably in the hands of the elites, we ordinary folks need not concern ourselves with the details when the elites (the knowledgeable) are challenged.  Instead, we wait patiently for them to deliver their official response, which we assume is surely correct.

My intent in showing the less flattering side of science is not to make me look good or others look bad (many of them are highly qualified individuals), and certainly not to make science look bad.  My purpose is instead to promote a realistic view of humanity and of science as a human undertaking.  We will not really love science until we learn to love real science— not a hypothetical pursuit in a utopian world but an intrinsically human pursuit in this world, however imperfect.

If you are wondering whether it is legitimate for scientists to hope for a particular result when they set their goals, it certainly is.  It is done all the time.  The search for extraterrestrial intelligence is a well-known example.  SETI involves the work of many scientists who hope their search will one day prove successful.  They have no proof, but science never starts with proof.  Like every other worthwhile undertaking, science starts with ambition.

Many scientists devote themselves to finding cures for various diseases for which there is no proof that these long-sought cures will be found, but the goal and the ambition are there.  That is no small thing.  Scientific proof never comes without those key ingredients.  Harm comes to science, not by people hoping to find a particular result, but by people trying to suppress results that go against their hopes. When we consider who has the power to suppress unwelcome results, we see right away that the view most likely to create that suppression is the majority view of the scientific community.

If science is the application of reason and observation to discover objective truths about the physical world, then doing science requires accepting just a few things— none of them controversial.  First, we must accept that objective truths exist, as we all naturally do (I have a five part series on Objective Truth starting here: https://larryemarshall.wordpress.com/2016/06/04/objective-truth-part-one/ ). Then we must accept that some of these truths pertain to the physical world and that some of those that do can be discovered through human observation and reasoning.  Since we all engage in this discovery process from an early age, we all naturally accept these propositions.

There is nothing more.

Adding anything to this essential set of propositions causes two serious problems.  One: the resulting embellished definition of science excludes what should not be excluded, namely any work that adheres to the essential set without adhering to the embellishment.  For example, if a group of people were to insist that science can’t be done properly without accepting that life exists on other planets, then that group will refuse to consider any work done from a contrary perspective, even though this work may be perfectly legitimate science.  Second, the embellishments run the risk of pressuring scientists into accepting wrong answers by ruling the right answers “unscientific.”

The reason adherents to this version hold science to be the only legitimate source of truth are that they also hold to materialism.  This preconceived set of beliefs commits them to the idea that there is not anything that exists that is not physical stuff.  Because science is the only way to know the truth about physical stuff, this leads them to conclude that science is the only source of truth.  The materialist commitment itself is completely unnecessary to science and therefore a harmful embellishment.

According to this now-familiar view, people of faith who challenge Darwinism are really pushing religion, even if their challenge has a scientific look to it.  The real problem for science, however, is not people having agendas (as they always do) but rather the institutionalization of agendas.  This is the embellishment problem we discussed above.  Once an embellished view of science becomes established, active suppression of dissent becomes inevitable, with predictable consequences.  Everything that opposes the institutionalized agenda is labeled “anti-science” by those working to protect the agenda.

Therefore, with this background, we will begin to study rocks (not the ones in my head).  Instead, the ones that make up the world around us and which have been misdated and misanalyzed for many, many years now.

 

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Intelligent Design

Evolution= Upside Down Science

Evolution= Upside Down Science

As I have struggled to determine my thesis for my degree in Philosophy of Science, I went and reread 28 books that I had already finished and made copious notes in them.  I put Camel, Blue Cheer, Tangerine Dream and Chris De Burgh on my mp3 player and sat outside with two Yorkies (Yorkshire Terriers), and six Leghorns on an overcast day.  After about two hours of watching the clouds float by, I had my thesis: “How Abnormalities in the Long-age Geologic Column Infer a Short-age Hypothesis”.  I believe that the evidence for a short-age earth is convincing and will supplant the long established 4.5 billion years currently established.  Bear with me as I lay out the ensuing evidence in a series of articles.

I feel like I am repeating the same things that many others have, but that seems to be the process.  Nobody will deny that today’s science relies on empirical analysis— in other words, verification through repeated measurement and testing.  The “scientific method” is the basis for the common steps that biologist’s and other scientists use to gather information to solve problems.  These steps include observation, hypothesis (prediction), data collection, experimentation to test the hypothesis under controlled conditions, and conclusions.

A good question to ask, though, is what does empirical science have to do with the past and origin of life and the earth?  Empirical analysis is verification through repeated measurement and testing.  Testing conducted under controlled conditions to validate a hypothesis or perhaps even to verify a specific law of science is common.    Empirical analysis is a wonderful testing tool but its application is limited to the present— the way things are and the way they work in the present.

Science that puts men on the moon, which provides us with Wi-Fi across the nation and ever more expensive new telephones/devices, is based on scientific principles that can be tested and repeated in the present.  Theories about the origin of man, the earth, and the universe that happened in the past cannot be tested.  Therefore, they cannot rely directly on “empirical analysis.”  Howsoever, observation and empirical analysis are often used to indirectly evaluate the ‘slow and gradual’ old age assumptions of evolutionary doctrine.  It is most important to realize that secular scientists assume evolution and old age as their foundation or basis for reconstruction or interpretation— they assume that evolution and an old earth are true.

An individual geologic fact is accepted or rejected as valid only if it fits the old earth, evolutionary model.  This is a very important concept to understand.  The presumption of evolution “as fact” exists in many sciences including biology, geology, astronomy, paleontology, and anthropology.  The primary difference between Intelligent Design, scientific creation, creationism, and evolution is not about the data but rather, the “interpretation” of data— for example, interpretation of observed geological landforms, the fossil record, and radioisotopes.  The question I will examine in this series of articles is, “Is evolution true or is it a great deception?”

The whole process of dating the earth (specifically its’ rocks) begins with the presumption of evolution and an old earth.  Scientists analyze the data, retain, and incorporate it consistent with evolution— and all contrary evidence and data are rejected or ignored.  At this point, certain individuals would say “There is no evidence that is contrary,” How wrong they are- the vast amount of data is ignored and brushed aside in this “scientific process”.  Contrary evidence to evolution is viewed as an anomaly or simply wrong.  An individual fact is accepted or rejected as valid only if it fits the evolutionary model.

“If evolution was merely a scientific theory that was open to evaluation based on the evidence, then its evidentiary failings would be freely acknowledged and additional theories could be considered as they are warranted. But far from being a free marketplace of ideas where scientists consider themselves at liberty to pursue the evidence where it leads, the modern scientific establishment has bound itself to a single system of interpretation, with myriad variations but one bottom line: evolution is a fact, and alternatives must be rejected out of hand.”  “Evolution’s evangelists” (May 2008). Acts & Facts, 37 (5), Dallas, TX: Institute for Creation Research, 10. Copyright © 2008

Secular scientists maintain that evolution is a ‘science’ and creation is a ‘religion’.  Evolution is not testable using empirical analysis and, therefore, does not meet the definition of ‘science.’, Besides that, evolution does not meet the definition of theory, as in “evolutionary theory.” A theory is an explanation of a set of related observations based on hypotheses and verified by independent researchers— but the fact is, evolution (genuine gain in genetic information or net increase in complexity) has never been observed in fossils or living populations.  In fact, evolution is not even worthy of the term hypothesis which is an educated guess based upon observation.  At best, evolution is an unsubstantiated hypothesis.

The bottom line is that evolution has never been observed or proven by empirical science— it is just assumed true.  I emphasize that evolution is not science… it is a philosophical worldview, nothing more.  Therefore, what motivates scientists to maintain a tight grip on “supernatural” or the concept of God or creation is considered to be outside the realm of real science.

Theories of how the universe, the earth, and man originated may come and go, but the belief that it happened by chance is an “unshakeable faith” for many today. Evolution has never been observed within fossils or living populations, there are no transitional types, and there are no known biological processes for evolution. Evolution has never been observed within fossils or living populations, there are no transitional types, and there are no known biological processes for evolution. Divine Creation is inconceivable to many scientists because the science community is largely atheistic.

Evolutionists claim that evolution is a scientific fact, but they almost always lose scientific debates with creationist scientists.  Accordingly, most evolutionists now decline opportunities for scientific debates, preferring instead to make unilateral attacks on creationists.  The fact is that evolutionists believe in evolution because they want to.  It is their desire at all costs to explain the origin of everything without a Creator.  Evolutionism is thus intrinsically an atheistic religion.  Some may prefer to call it humanism, and “new age” evolutionists place it in the context of some form of pantheism, but they all amount to the same thing.  Whether atheism or humanism (or even pantheism), the purpose is to eliminate a personal God from any active role in the origin of the universe and all its components, including man.

Life is here on earth, so secular scientists feel they must explain life “naturalistically”— consequently, they believe that evolutionary doctrine and ignoring data contrary to evolution is legitimate.  To avoid having to recognize God, “professing to be wise, they became fools.”  (Romans 1: 22, NAS)  But there is an even more ominous reason for belief in evolutionary doctrine.  It is tied to the ancient (spiritual) rebellion of men against their Creator as foretold in Genesis 11: 4 and found throughout biblical history.  It refers to the fact that humanity, ever since the rebellion of the first man, Adam, has had an inherited tendency to oppose the Creator’s rule or sovereignty over their lives (Romans 1: 18-32).

While neither the creation model nor the evolutionary model can be proven or disproven, these two views can be compared to see which one fits the data better.  When compared, the young earth model (creation and a worldwide flood) fits the data perfectly while the old earth model (evolution with ‘slow and gradual’ geologic events) has continual flaws— it is essentially upside down science.

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Intelligent Design, The Science of it All

Disrupting Long Held Beliefs

Disrupting Long Held Beliefs

You have been taught that the earth is 4-5 billion years old and the universe about 13.5 billion years old for how many years?  If you are a Christian, it has to have caused some difficulties for you in your journey when the Bible teaches that the earth is only 6,000 to 10,000 years old.  Reconciling the differences has been a problem and has split religious individuals in half with some believing the Bible is inerrant and others trying to make the Bible fit into a MYA (Million Years Age) philosophy.

First, I need to do a brief introduction to the science of geology for my readers so we can at least talk about the subject on a similar level.  I will describe conventional geology theory, with essentially modern geological processes functioning for hundreds of millions of years, and short-age geology, with geological processes functioning for only thousands of years. One might say two very different points of views.

The geological processes to be described will include types of rocks and how they form, the depositional environments in which sedimentary rocks accumulate and how to recognize these environments, how mountains and landscape develop, and erosion processes that shape the land.  Glaciation, the stratigraphic sequence of rock layers, and the fossils they contain and how they were preserved will also be discussed.

This is not the best comparison chart I could have found.  It will do for now, I hope to find a better one later, Even if I have to make it myself.  The important thing is to remember that thee millions of years on the life are condensed in thousands of years during and after the flood on the right side.  We will refer to the names of various periods on the left.

I will introduce two differing theories that attempt to account for the origin of the Cambrian explosion to the recent geological column and its fossils.  Conventional geology estimated to be 541 million years of time and short-age geology is just a few thousand years.  Both of theories must account for a number of geological features and processes.  These are the formation of rocks and minerals, accumulation of sedimentary deposits in various ancient environments, formation of mountains, and erosion of the sediments to form our modern landforms, glaciations on mountains and over continents, and the origin of the fossils in the fossil record.

In evaluating data and interpretations in geology/ paleontology, it will often be difficult to apply the concept of inference-to-the-best-explanation because we are dealing with events that happened long times ago and not directly observed.  If we do not have adequate modern analogues for comparison with the rocks (and we have never observed a global geological catastrophe), we will be somewhat hampered in reaching a confident interpretation of the data.

The most direct source of evidence of the history of ancient life comes from the fossil record.  It poses difficulties for both interventionism and macroevolution.  The vertical stratigraphic sequence of fossils from one-celled prokaryotic (cells with no nucleus) organisms in the Precambrian to eukaryotes (cells with a nucleus), invertebrates, fish, amphibians, reptiles, mammals, birds, and, finally, humans and the associated questions of geologic time with its support from radiometric dating are the real challenges that face interventionists who accept a literal biblical creation.  The following material introduces the basic concepts of geology with both conventional and short-age interpretations of the concepts.

Geological processes, generally like those observable today, operating over a time period of several billion years produced earth’s geological features.

LOOKING NORTH ACROSS THE CANYON AT THE NORTH RIM, GRAND CANYON NATIONAL PARK.

“Life” (cells that are alive,t hey have movement, take in nourishment, excrete by-products) have been on the earth during much of Earth’s history according to F. M. Gradstein and others in their book  “The Geologic Time Scale” (Boston: Elsevier, 2012).  The Phanerozoic (Cambrian to recent) rocks formed during the last 541 million years, and the fossil record is a record of the evolution and extinction of life forms through this time period.  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.

Modern geological theory is a modification of Lyell’s uniformitarian views and recognizes that 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 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.  (Interpreted as the Creator making a uniform and consistent world of scientific laws if you are a Christian).
  • 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 if the geological past was very 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, 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.

The four points in the above table is the basic concept that any theory of geology must satisfy.  So also, should the concept of short-age geology. It’s basic tenets are as follows.  The Phanerozoic (denoting the eon covering the whole of time since the beginning of the Cambrian period, and comprising the Paleozoic, Mesozoic, and Cenozoic eras) record consisted of just a few thousand years.  The major taxonomic (the science of defining groups of biological organisms on the basis of shared characteristics) groups of animals and plants arose at the beginning of that time through independent origins, by creation in other words.  Much of the fossil record consists of remains of these organisms that ended up buried in a sequence resulting from the order of events before, during, and after a worldwide geological catastrophe rather than from an evolutionary sequence.

After the catastrophe, geological processes gradually slowed to the rates observable today and significant fossil deposits formed because of the progressively less catastrophic events during this time.  A significant part of the Cenozoic fossil record, probably formed after the global catastrophe, which would include evolutionary sequences of organisms within the individual created groups.

 

Whether the basic structure of the earth and the lower portions of the geological column (e.g., the Precambrian) had a recent origin or formed over billions of years is a separate question beyond the scope of our discussion.  Other authors have covered it very well.  We will discuss short-age geology as it pertains only to the Phanerozoic part of the geological column.

The short-age geologist proposes that, at some time in the past, a disturbance in the earth’s crust temporarily disrupted the normal relationships between land and water bodies, initiating a period of rapid geologic activity on a global scale.  This period of rapid erosion and sedimentation produced a significant but unknown portion of the geological column.  The geological and geophysical processes that occurred during that event have determined the characteristics of the rocks formed at that time and the distribution of various fossils in the rocks.  They influenced the distribution and character of radioactive elements in the minerals used in radiometric dating.

A short-age geology theory expressed in this form is a simple descriptive statement.  It says nothing about the un-testable question of whether God was involved in initiating this geologic event.  No supernatural powers, no magic or mythical events.  It will satisfy the four requirements in Table 1.  It does not attempt to explain any process or event that may have operated outside the known laws of geology, chemistry, or physics.  This particular descriptive theory can be used as a basis for defining specific hypotheses concerning the sedimentary processes and the amount of time involved in depositing individual formations or in shaping the earth’s landforms.

These hypotheses can be tested in the same way that any geologist tests hypotheses.  Two geologists could be doing research on the same rock formation. One geologist might believe that the formation took a long time— thousands or millions of years— to be deposited.  The other geologist would believe the formation was deposited considerably quicker.  They will probably ask different questions, but they both look for the same general types of data as they study the rocks.  Each must analyze their own data, as well as other published data, and interpret the meaning of all the data. When they disagree, each geologist analyzes the other’s work and reevaluates their own work and tries to determine what additional data would be needed to clarify the issue.  If each is doing good work, the findings will be published in a scientific journal so others can benefit from it.

In time, as more data accumulates it will point to rapid deposition, very slow deposition, or something in between.  If we evaluate the data fairly, eventually it should imply which theory is truer, unless our inability to go back in time and directly observe what happened, limits the data too much.  All geologists will use the same observational and experimental procedures in their research.  One primary difference in the research approach of short-age geologists and other geologists is what they predict the eventual outcome will be: The short-age geologist is confident that when “the data is all in,” they will indicate that much of the geologic column was deposited in a short time.  A conventional geologist is more likely to have confidence that the data eventually will indicate that the entire geologic column was deposited very slowly or in rapid spurts with long periods of time between.

Many would say the data already is conclusive and has disproved the short-age theory.  However, the short-age geologist notes with interest the definite trend toward catastrophism in geology that began a few decades ago.  Some of the pertinent articles are listed below:

  • V. Ager, The Nature of the Stratigraphical Record, 2nd ed. (New York: John Wiley and Sons, 1981)
  • A. Berggren and J. A. Van Couvering, eds., Catastrophes and Earth History: The New Uniformitarianism (Princeton, NJ: Princeton University Press, 1984)
  • Albritton, Catastrophic Episodes in Earth History (New York: Chapman & Hall, 1989); R. J. Huggett, Catastrophism: Systems of Earth History (New York: Edward Arnold, 1990)
  • Koeberl and K. G. MacLeod, Catastrophic Events and Mass Extinctions: Impacts and Beyond (Boulder, CO: Geological Society of America, 2002).

Nevertheless, a number of lines of evidence challenge the short-age theory. Discrepancies between a theory and the available data can arise in at least two different ways: either (1) the theory is wrong or (2) important discoveries are waiting for diligent researchers who use their theory to guide their research. Interventionists/ short-age geologists recognize that if their theory is true, significant phenomena have yet to be discovered.  Does interventionism stifle research, as some have suggested? If interventionism is understood correctly and if its predictions of new phenomena waiting to be discovered are taken seriously, it can be a stimulus for vigorous new approaches to research.  I will now review the basic concepts of physical and historical geology and make initial comparisons of how these two theories deal with this evidence.

First up: Rock Types and Processes for Their Formation and Weathering

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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.

Intelligent Design, The Science of it All

Something New to Contemplate

Something New to Contemplate

It is only recently that some defenders of evolution have tried to divorce the origin of life from consideration.  It is probably because the hope of finding an answer is rapidly fading, as one scientific discovery after another of sophisticated machinery in even the simplest living cells makes the problem of a naturalistic origin ever more difficult.  Popular articles on origin-of-life research have often portrayed the field as constantly advancing and quickly converging on a purely Materialistic Naturalism explanation for the origin of the first autonomous cell.  This creates an important proposition that atheists must believe.  That is life came from non-living chemicals, a process called chemical evolution or abiogenesis (Abiogenesis, biopoiesis, or informally, the origin of life, is the natural process by which life arises from non-living matter, such as simple organic compounds.)  Every so often, the lame stream media headlines trumpet the latest and greatest solution, even though specialists in the area know that they are not even close to solving this problem.  Moreover, they never ask, why is this theory replacing the other theory that we highlighted and headlined a year or so ago.

Common arguments about the origin of life have traditionally focused on the unlikelihood of life forming by chance.  I myself have promoted this concept and of course have had others say, “It just had to happen once” as naive as that statement is.  Perhaps most famously, physicist Fred Hoyle calculated the probability of a cell coalescing to be roughly 1 part in 10 to the power of 40,000.  He compared this probability to the chances of a tornado plowing through a junkyard and assembling a jet airplane.  Now, I am not happy with that analogy because it takes us away from the concept of a cell that we should be dealing with.  So let us go with the smallest human protein which is made up of 44 amino acids (Human protein Q6YH21, a collagen-like molecule associated with acetylcholinesterase in skeletal muscle, has a variant gene NM_080542, which encodes for the shortest protein in the human body).  If we have 20 of each of these 44 amino acids floating in a solution it would be similar to these 880 amino acids suspended in Lake Erie (to want to make it turbulent).  Well, not quite, we need to shorten it by about 2 square miles.  Lake Erie is 116 cubic miles in volume, so that comes out to 1.277 x 10^24 gallons or 1,277,295,890,000,000,000,000,000 gallons.  So cut out 6 cubic miles and redo the math.  In addition, we would want these amino acids to randomly form together so the lake has a lot of waves and currents and tides.  The interesting thing is we are assuming that the necessary molecules have already formed into the amino acids and that the protein molecule will form randomly and properly and be folded correctly into this protein.  This event happens hundreds of thousands of times every minute within each cell of your body.

It is possible, we might get a protein to form, but it is highly improbable.  Plain and simple. So you understand the difference between possibility and probability now?

 

Closely linked to  the concept of probability is that of entropy, since probability is proportional to the number of configurations (N) in which some state could occur, and entropy is proportional to the log of N.  As an example, the number of ways water molecules can arrange themselves in the solid state is much smaller than the number ways in the liquid or gas states, so ice is the state with the lowest entropy.  Due to this connection, the probability argument is restated that nature tends to move from states of lower entropy to higher entropy, which simply means that nature moves towards states that are highly probable.  This tendency is known as the second law of thermodynamics.

Analogously, some systems do, in fact, naturally move from states of higher entropy to those of lower entropy (i.e., seemingly low probability) if the lower-entropy states are highly biased to occur.  Such a bias is created by a second driving tendency.  Namely, nature tends to move from states of higher energy to those of lower energy.  For instance, rocks roll downhill, since lower altitude corresponds to lower gravitational energy.  Likewise, molecules of water attract each other, so ice is a lower energy state than water or gas as a result of more hydrogen bonds forming on average between neighboring molecules. At low enough temperatures, this attraction overcomes the tendency to move toward higher entropy resulting in water freezing.  We will come back to the  water later.

Jeremy England, a physicist from MIT had a brainstorm of an idea that life is very good at increasing the entropy of its surroundings: life absorbs energy and dissipates it as heat, and this by definition increases the surroundings’ entropy. In addition, of course, if something can self-replicate, then it will generate more energy dissipaters.

However, even in these cases of locally decreasing entropy, the second law of thermodynamics is not violated, for the changes are always exothermic — heat is released. The heat leaving the local system (e.g., a cup of freezing water) and entering the surrounding environment increases the latter’s entropy by an amount greater than the entropy decrease of the local system. Therefore, the total entropy of the universe increases. The problem for all theories of origin of life now becomes quite evident. The simplest functional cell compared to its most basic building blocks has both lower entropy and higher energy.

Natural systems never both decrease in entropy and increase in energy at the same time.  Therefore, the origin of life through purely natural processes would seem as implausible as water on a hot summer day spontaneously freezing or a river flowing unaided uphill for thousands of miles.  Physicists and chemists (in order to try to explain what they cannot calculate) often combine entropy and energy (or enthalpy) together into what is called the free energy of a system. The change of free energy is always negative for spontaneous changes (e.g., wood burning or ice melting in summer), and it directly relates to the total increase in entropy of the universe.  The challenge for the origin of life is then explaining how billions of atoms could spontaneously come together into a state of significantly higher free energy.

Various calculations have been done, all using different variables and the probability has always been essentially zero.  At face value, this thermodynamic analysis for the origin of life would seem to negate any possible materialistic solution to the problem.  Theorists have long recognized one remaining loophole (but remember, these are theorists- a person concerned with the theoretical aspects of a subject).

Most calculations have assumed that the system was in a state near equilibrium.  However, many argue that the origin of life took place in a system strongly driven away from equilibrium.  This would be a pond subjected to intense sunlight or the bottom of the ocean near a hydrothermal vent flooding with its surroundings superheated water and high-energy chemicals.  These settings are commonly referred to as non-equilibrium dissipative systems.  Their common characteristic is that classical thermodynamics breaks down, so the previous analyses do not completely hold.  Instead, principles of non-equilibrium thermodynamics must be applied, which are far more complex and less well understood.  Moreover, the energy from these outside sources is hoped to enable the free-energy barrier to be overcome.  Therefore, scientists are relying on less than scientific methods to prove their points.

However, such appeals to non-equilibrium systems do little to solve the basic thermodynamic problems.  First, no system could be maintained far from equilibrium for more than a limited amount of time. Any progress made toward forming a cell would be lost as the system reverted toward equilibrium (lower free energy) and thus away from any state approaching life.

This has been extensively promoted as a ‘groundbreaking idea’ about why we have life.  Despite the hype, nothing is being offered to explain how life could have evolved from lifeless chemicals; still a massive unsolved hurdle.

The input of raw solar, thermal or other forms of energy actually increase the entropy of the system, thus moving it in the wrong direction.  For instance, the ultraviolet light from the sun or heat from hydrothermal vents would be more likely to break apart  complex chemical structures than form them.

In non-equilibrium systems the differences in temperature, concentrations, and other variables act as thermodynamic forces which drive heat transfer, diffusion, and other thermodynamic flows. These flows create microscopic sources of entropy production, again moving the system away from any reduced-entropy state associated with life. In short, the processes occurring in non-equilibrium systems, as in their near-equilibrium counterparts, generally do the opposite of what is actually needed.

Intelligent Design, Philosophy

The enigma of purpose

The enigma of purpose

If you subscribe to news feeds, read the newspaper, or watch TV, you certainly believe that we humans have been behaving badly. In recent years, we humans have variously blamed other (it is always others) humans for causing: global cooling, global warming, famines, floods, mass extinctions, plagues, deforestation, landslides, earthquakes, and so much more. All of the problems (real or imagined) on planet Earth are apparently our fault, and it’s only supposed to get worse. Naturalist and evolutionist Sir David Attenborough summed up this thinking well: “Humans are a plague on earth,”  he wrote in an article  in the  telegraph.co.uk, 22 January 2013 But this raises a very interesting question: if naturalistic evolution is true, why does it matter that we’re a “plague on earth”?

The idiocy of these media reports (and there are plenty of articles on different websites that criticize them).  Instead, I want to point out the obvious disconnect between the headlines and the evolutionary beliefs subscribed to by many of these same media outlets, their correspondents, and the environmentalists they quote.

If (and it is a big IF) evolution is true and man is nothing more than a highly-evolved primate, the result of random mutations and natural selection over millions of years, then we humans are just another part of nature.  Anything we do is simply nature in action.  If a species becomes extinct because of human intervention, it is just natural selection.  If the burning of fossil fuels causes a runaway greenhouse effect that cooks the planet, it will be a natural occurrence.  If the world is one day obliterated by a nuclear holocaust, it certainly won’t be an unnatural event.  And why not?  In the atheistic, evolutionary worldview, everything is natural.  If atheistic evolution is true, the word ‘unnatural’ can have no meaning!

However, this is not the reality we seem to experience.  We mourn the loss of biodiversity, agonize over the size of our carbon footprint, protest the proliferation of nuclear weapons, and we are rightly horrified by acts of cruelty to animals.  I’m not saying that all humans behave like this, but since many of us do, all of us can.  For some reason, we humans are held to a higher moral standard than the rest of nature.

Evolutionists have to believe humankind has evolved to a point where we can understand the natural process that has made us what we are but, at the same time, the logical ramifications of that same natural process do not bind us.

Ask an environmentalist why they do what they do and they will likely tell you they want to ‘leave the planet in better shape than they found it,’ or something similarly noble.  In his closing remarks for the 2000 BBC Natural History Unit documentary State of the Planet, Attenborough says;  “Surely we have a responsibility to leave for future generations a planet that is healthy, inhabitable by all species.” (State of the Planet, BBC Natural History Unit, Part 3, 2000)

Apparently, our mission, should we decide to accept it, is to purposefully plan for the future of planet Earth.  These are admirable intentions!  However, they are not what we would expect given evolution.  As Richard Dawkins makes clear in his book The Blind Watchmaker:

“Natural selection, the blind unconscious automatic process, which Darwin discovered and which we now know is the explanation for the existence and apparently purposeful form of all life has no purpose in mind.  It has no mind, no mind’s eye. It does not plan for the future. It has no vision, no foresight, no sight at all [emphasis added].”  (Dawkins, R., The Blind Watchmaker, W.W. Norton & Company, New York, USA, 1986)

But somehow this blind, purposeless, natural process has managed to produce human beings that have foresight and can purposely plan for the future. Sir David exhorts us to use this foresight to manipulate the natural order so that we can achieve his purposes. In doing so we are often purposefully engaging in behaviour that, whether we realise it or not (and most do not), is exactly the opposite of what we would expect if evolution were true.

Environmentalists work tirelessly to save animals from extinction, even animals such as lions and tigers that potentially compete for food with us.  Animals, which given half a chance, would not hesitate to drive us to extinction.  This is opposite the basic evolutionary narrative where survival of the fittest is supposedly a main driver of behavior.  Apparently, Tennyson’s “Nature, red in tooth and claw” does not apply if the tooth is brushed twice daily and the claw occasionally painted.

Nevertheless, it is in our behavior toward ourselves and our fellow humans that the evolutionary disconnect is both most obvious and, at the same time, most studiously ignored.  We care for our sick, allowing potentially genetically inferior individuals to survive (using up valuable resources) and reproduce (reducing population fitness).  We medically intervene to enable infertile couples to reproduce and pass on their (likely inferior) genes.  At the same time, seemingly, healthy individuals will use contraception to limit their offspring and many will even undergo medical procedures to abort the offspring they have already conceived.

We actively choose lifestyles that limit our likelihood of procreation (celibacy, same-sex relationships, or just choosing never to have children). We encourage our young to delay sexual activity.  We even legislate with the intention of limiting sexual partners (anti-polygamy laws and marriage itself).  What is interesting is those who would advocate for multiple partners will often point to examples in nature to support their belief that monogamy is unnatural.  On the surface, this might seem reasonable, until you realize that in nature the result of multiple partners is more offspring, whereas in humans, more offspring is usually the last thing the practitioners want.

We engage in warfare with the intent of annihilating those who disagree with us while at the same time enacting rules to ensure that this happens humanely.  When we capture an enemy, our focus must immediately change from trying to kill them to treating them with dignity, knowing full well that they would probably not hesitate to kill us given the opportunity to escape.  We often adhere to these rules despite knowing that our enemy likely will not.

So many of our intentions, good and bad, seem anti-evolutionary in their execution.

Evolutionists have devised explanations for this behavior.  But the necessarily contradictory nature of these explanations only serves to reinforce the absurdity of evolution as a scientifically plausible reason for our purposive behavior. As respected chemist and member of the US National Academy of Sciences, Philip Skell pointed out:

“Natural selection makes humans self-centered and aggressive—except when it makes them altruistic and peaceable. Or natural selection produces virile men who eagerly spread their seed—except when it prefers men who are faithful protectors and providers. When an explanation is so supple that it can explain any behavior, it is difficult to test it experimentally, much less use it as a catalyst for scientific discovery.”  (Philip Skell, ‘Why Do We Invoke Darwin? Evolutionary theory contributes little to experimental biology’, The Scientist 19(16):10, 29 August 2005.)

Our best intentions are a natural outworking of the fact that man was created in the image of God and given dominion over His creation (Genesis 1:26–30). Our worst intentions are a direct result of Adams rebellion (Genesis 3:14–19). The evolutionary worldview fails to make sense of so many of our intentions because, as the Bible clearly teaches, we are not the result of evolution.

Next time you read or hear of something mankind has supposedly done to jeopardize the future health of our planet, remember that these reports are (in most cases) unwittingly reinforcing the biblical account of Creation and the Fall.

Education vs Common Core, Intelligent Design, Philosophy

I think therefore I believe I might just be what it is I think

“Cogito ergo sum”  is a Latin philosophical proposition by René Descartes usually translated into English as “I think, therefore I am”.  The phrase originally appeared in French as “je pense, donc je suis” in his Discourse on the Method, so as to reach a wider audience than Latin would have allowed.  Many of my generation and younger (I don’t know or want to know the current “hip” description for them- “hippie” was mine I have no idea who “millennial’s,” “X-Generation,” “baby boomers”-Hippies may overlap them) have used that phrase as a reason to deny the existence of a “God”.

They use this phrase, and many more taken out of context of the original writers overall thesis, and use it as the basis of what they wish to believe.  All the science fiction movies and novels have added greatly to the depth of their beliefs so that it is virtually unshakeable.  I like the ones who have used the “Star Wars” “May the force be with you” to generate a level of consciousness that we must all strive to obtain.  So let us explain how incredible wrong they are about René Descartes and his belief about God and why they say it is not so- those few who are capable of debating in intelligent fashion.

René Descartes (1596–1650) is widely regarded as the father of modern philosophy. His noteworthy contributions extend to mathematics and physics.  This entry focuses on his philosophical contributions in the theory of knowledge. Specifically, the focus is on the epistemological project of Descartes’ famous work, Meditations on First Philosophy.  Upon its completion, the work was circulated to other philosophers for their comments and criticisms. Descartes responded with detailed replies that provide a rich source of further information about the original work.  He indeed published the first edition (1641) of the Meditations together with six sets of objections and replies, adding a seventh set with the second edition (1642).

Most individuals ignore the rest of his entire work and concentrate on just that phrase in order to justify their beliefs. However, that is unfair, as that one statement is directly in opposition to his final thoughts and conclusions.  So it behooves me to go through his Meditations and set everyone straight.

Famously, Descartes defines knowledge in terms of doubt. While distinguishing rigorous knowledge (scientia) and lesser grades of conviction (persuasio), Descartes writes:

I distinguish the two as follows: there is conviction when there remains some reason which might lead us to doubt, but knowledge is conviction based on a reason so strong that it can never be shaken by any stronger reason. (1640 letter to Regius, AT 3:65)

 

This passage (and others) clarify that Descartes understands doubt as the contrast of certainty.  As my certainty increases, my doubt decreases; conversely, as my doubt increases, my certainty decreases.  The requirement that knowledge is to be based in complete, or perfect certainty, amounts to requiring a complete absence of doubt — an indubitability, or inability to undermine one’s conviction.

In his First meditation he lays out his thesis to the esteemed Dean and Faculty of the Theological Center in Paris: “I have always considered that the two questions respecting God and the Soul were the chief of those that ought to be demonstrated by philosophical rather than theological argument. For although it is quite enough for us faithful ones to accept by means of faith the fact that the human soul does not perish with the body, and that God exists, it certainly does not seem possible ever to persuade infidels of any religion, indeed, we may almost say, of any moral virtue, unless, to begin with, we prove these two facts by means of the natural reason.  And inasmuch as often in this life greater rewards are offered for vice than for virtue, few people would prefer the right to the useful, were they restrained neither by the fear of God nor the expectation of another life; and although it is absolutely true that we must believe that there is a God, because we are so taught in the Holy Scriptures, and, on the other hand, that we must believe the Holy Scriptures because they come from God (the reason of this is, that, faith being a gift of God, He who gives the grace to cause us to believe other things can likewise give it to cause us to believe that He exists), we nevertheless could not place this argument before infidels, who might accuse us of reasoning in a circle.“

Descartes states that he has put off examining the foundations upon which he has built all his false beliefs. But he must now do so, in order to establish firm and lasting truths in the sciences. Examining each of his opinions for falsehood would be tedious; rather, Descartes says that if he can simply show that there is cause for doubt for an opinion, then he can throw that opinion out.  So he states”

“In the first Meditation I set forth the reasons for which we may, generally speaking, doubt about all things and especially about material things, at least so long as we have no other foundations for the sciences than those which we have hitherto possessed. But although the utility of a Doubt which is so general does not at first appear, it is at the same time very great, inasmuch as it delivers us from every kind of prejudice, and sets out for us a very simple way by which the mind may detach itself from the senses; and finally it makes it impossible for us ever to doubt those things which we have once discovered to be true.”

The senses seem like a good place to start, since they often mislead us. But would it not be insane to reject also such deliverances as that we have hands, eyes, etc.? Probably. We have no clear criterion for distinguishing between our waking and sleeping lives. But whatever we dream, Descartes suggests that the constituting elements of them, i.e., ‘simples’, must surely have a basis in reality. The idea is that ‘simples’ are that out of which we form complex ideas (e.g., of a unicorn). So if we find the simplest elements in nature, we will have found the most universal, which then must be true.  The mathematical and physical sciences, then, which don’t depend on composites, might be considered to be indubitable. Can 1 + 2 not be 3? People often make mistakes in the above disciplines. So we can both doubt that God is benevolent and the capacity of our reason to deliver true judgments. Thus, Descartes resolves to throw out all his previous beliefs, and assume that God is maliciously bent on deceiving him. His famous saying is in this Meditation, but I will deal with it later.

He writes on to the Professors:

“In the second Meditation, mind, which making use of the liberty which pertains to it, takes for granted that all those things of whose existence it has the least doubt, are non-existent, recognizes that it is however absolutely impossible that it does not itself exist. This point is likewise of the greatest moment, inasmuch as by this means a distinction is easily drawn between the things which pertain to mind—that is to say to the intellectual nature—and those which pertain to body.”

He asks what is there concerning which he can have not the slightest occasion for doubt? It is that he exists.  This follows, he argues, from the fact that even if he denies that he has a body, or that the world exists, or that he is not being deceived by a malicious God, there is still an object of those denials: himself.  While he can suppose his body to not belong to him, he can’t suppose thinking to not belong to him.  Thus, he knows only that he is a Thinking thing –one who “doubts, understands, affirms, denies, wills, refuses, and that also imagines and senses.”

Continuing to write:

“In the third Meditation it seems to me that I have explained at sufficient length the principal argument of which I make use in order to prove the existence of God. But no ne the less, because I did not wish in that place to make use of any comparisons derived from corporeal things, so as to withdraw as much as I could the minds of readers from the senses, there may perhaps have remained many obscurities which, however, will, I hope, be entirely removed by the Replies which I have made to the Objections which have been set before me. “

Descartes notes that his being certain of his being a thinking thing, which is a “first instance of knowledge,” reveals what is needed for him to be certain of anything: a clear and distinct perception of what is affirmed. But if it could be that something so clear and distinct could be false, he would not be certain of the thing’s truth. Thus, everything he perceives clearly and distinctly is true.

“In the fourth Meditation it is shown that all these things which we very clearly and distinctly perceive are true, and at the same time it is explained in what the nature of error or falsity consists. This must of necessity be known both for the confirmation of the preceding truths and for the better comprehension of those that follow.” 

Descartes now moves to deduce other truths from those that he has established: that God exists, and that Descartes depends on him for his existence at all moments.  From the previous Meditation, God can never deceive Descartes.  He says that while deception may seem like “an indication of cleverness or power, the will to deceive undoubtedly attests to maliciousness or weakness.  Accordingly, deception is incompatible with God.  Descartes wonders then, if God won’t deceive, why he has endowed us with judgments that seem given to frequent error.

Why, then, does error come about?  Descartes offers that it is because though our intellect is finite, our will is infinite. Errors in judgment are caused by indifference of the will, which occurs when the will affirms or denies despite there being no (good) reason to do either.  A will that is properly inclined by a clear and distinct perception on the part of reason prevents error in judgment.  In concluding, Descartes argues that God does not owe us, who have not merited anything, an infinite intellect, which, besides, is not proper to us.  In addition, though God concurs in our actions, he has responsibility only for the good in our actions; the bad are a result of negation.  We are responsible for our sins, because we can choose to abstain from willing/judging things that we do not understand, and only will/judge things that we perceive clearly and distinctly.

“In the fifth Meditation corporeal nature generally is explained, and in addition to this the existence of God is demonstrated by a new proof in which there may possibly be certain difficulties also, but the solution of these will be seen in the Replies to the Objections. And further I show in what sense it is true to say that the certainty of geometrical demonstrations is itself dependent on the knowledge of God.”

Now Descartes seeks to return to the subject of whether material things exist, which was pushed aside in the first Meditation. A natural starting point is the ideas that we have of objects. He says that he has 4 distinct ideas of extension, which he is able to enumerate parts in and to which he is able to ascribe such properties as size, shape, motion, etc. there are no external objects, he is able to think of triangles at will, and upon their essences, which are not fabricated. He can demonstrate their properties in his mind. He can use the truths of geometry, arithmetic on these objects and find the sine and cosine and they would be correct.  If it follows from the fact that whatever he perceives clearly and distinctly to belong to an idea of something he brings forth, that it belongs to that thing, then it follows that God exists.

As long as Descartes remembers that he clearly and distinctly perceived once that there is a God, who doesn’t deceive, no counterargument can be given that puts doubt on any of his clear and distinct beliefs. But this still leaves out the existence of material objects. Do we perceive them clearly and distinctly, apart from their ideas?

Finally in the Sixth I distinguish the action of the understanding from that of the imagination; the marks by which this distinction is made are described . I here show that the mind of man is really distinct from the body, and at the same time that the two are so closely joined together that they form, so to speak, a single thing.

As long as he remembers that he clearly and distinctly perceived once that there is a God, who doesn’t deceive, no counterargument can be given that puts doubt on any of his clear and distinct beliefs. But this still leaves out the existence of material objects. Do we perceive them clearly and distinctly, apart from their ideas?

Descartes begins his project of determining whether we can know that external objects exist by distinguishing between the imagination and intellect. Imagination is a faculty that we use for picturing what we’re thinking about..  We can think of the earth by imagining in our mind.  But the conceive of the earth as an eight sided octagon takes a bit more understanding of a complex combination of ideas. Thus, Descartes argues, imagination is not essential to our mind. Understanding is. He conjectures that perhaps the imaginative faculty belongs to something distinct from his mind, a body maybe.

Various themes about innate truths are introduced in the Fifth Meditation. Among them concerns the effects of repeated meditation: truths initially noticed only by means of inference might eventually come to be apprehended self-evidently. In the build-up to the passage claiming that the Evil Genius Doubt is finally and fully overcome, Descartes has his mediator say:

“But as regards God, if I were not overwhelmed by preconceived opinions, and if the images of things perceived by the senses did not besiege my thought on every side, I would certainly acknowledge him sooner and more easily than anything else. For what is more self-evident [ex se est apertius] than the fact that the supreme being exists, or that God, to whose essence alone existence belongs, exists?

Although it needed close attention for me to perceive this, I am now just as certain of it as I am of everything else which appears most certain. And what is more, I see that the certainty of all other things depends on this, so that without it nothing can ever be perfectly known”. (Med. 5, AT 7:69)

First, he sensed that he had hands, feet, etc.  Further, he judged what was beneficial and what was harmful, what opportune, what inopportune, by means of his sensation of pleasure and pain.  He also sensed colors, odors, etc., on whose basis he distinguished, say, sky from seas.  Ideas bombarded him constantly, in other words.  Why then did he think there were external bodies?  Because, the ideas they presented were more vivid, more explicit than he could muster through meditation, nor could he not sense them when they were present, or imagine them when they were not.  With regard to his having a body, he sensed, by nature’s teaching, which his body was his, since his will to eat, e.g., was always connected to hunger in his stomach.  In addition, his moods shifted in accordance with the particularity of his sensations.

Because God is not a deceiver, what nature teaches us is probably true.  So, our bodies are tightly joined with our minds, so much so that they constitute one thing. Nature also teaches us that there are other bodies around us.  Descartes clarifies that by “nature” he means only what pertains to our composite minds and bodies, and so what we are allowed to infer on the basis of sense appearance

The full statement that the progressives steal part of is: “What of thinking?  I find here that thought is an attribute that belongs to me; it alone cannot be separated from me. I am, I exist, that is certain.  But how often?  Just when I think; for it might possibly be the case if I ceased entirely to think, that I should likewise cease altogether to exist. I do not now admit anything which is not necessarily true: to speak accurately I am not more than a thing which thinks, that is to say a mind or a soul, or an understanding, or a reason, which are terms whose significance was formerly unknown to me. I am, however, a real thing and really exist; but what thing? I have answered: a thing which thinks.”

When I try to doubt my own existence, I immediately apprehend that I must exist in order to be attempting the doubt.  Similarly (on this interpretation), when I try to doubt God’s existence, or omnipotence, or benevolence — or any other attribute contained in the very conception of an all-perfect being — I immediately apprehend, as Descartes writes, that any such skeptical conception of God “implies a conceptual contradiction — that is, it cannot be conceived” (1643 letter to Voetius, AT 8b:60).

If our schools had only taught critical thinking in high school classes, we might have an entirely different world out thinking of thinking rational beings.  Instead we have a group that when told that Rhett Butler said “Frankly, Ma’am. I don’t give a damn” they now know all about Gone With The Wind and the Civil War.

Didja Know, Intelligent Design

Grand Canyon Research

Grand Canyon: legal battleground?

The Blue Angel Trail along the Grand Canyon

Two days ago Dr. Andrew A. Snelling, of Answers in Genesis USA, sued the U.S. Interior Department. He accuses them, and more particularly the National Park Service, of abridging his Constitutional rights. Specifically, he sought to study key features of the Grand Canyon. And the Park Service will not let him. The case arises from a plain case of scientific obscurantism. But this time the evolutionists, not any creationists, are obscuring the facts.

The complaint

Snelling’s lawyers, Michael Kitchen of Margrave Celmins PC and Gary McCaleb of Alliance Defending Freedom, filed the complaint. ADF released this statement the same day (9 May 2017). Sarah Kramer of ADF also left this blog entry describing the case. One day later, Bob Unruh of WorldNetDaily left this account. In it he asked whether the “grand illusion” concerning the Grand Canyon would soon lose its credence.

Only by reading the complaint can one grasp the legal and moral issues at stake. In it, Dr. Snelling’s lawyers give the details.

In November of 2013, Dr. Snelling applied for permission to study folding sedimentary structures, from the Paleozoic group of strata. He sought to collect up to sixty half-pound samples from four places in the Grand Canyon. Dr. Snelling had already reserved several Colorado River rafting trips between April and July 2014 to collect the samples.

Everything went fine, until Ronda Newton, the Research Permitting Coordinator, asked for two peer reviews of his research proposal. Dr. Snelling had applied for and gotten permits for earlier research in the Grand Canyon. She asked for these in February of 2014. No one had ever asked for peer reviews of his proposals before. Still, he found three scientists willing to review his proposal.

So then Ms. Newton sent the application materials to two evolutionists. That act started all the trouble.

Two ringers and an empty suit

Karl Karlstrom, PhD, is a professor of Earth and Planetary Sciences at the University of New Mexico. In January of 2014 he had published, in the journal Nature, his own article on the Grand Canyon. In it he said the Grand Canyon formed five to six million years ago, when several older structures linked up. Thus he himself broke with convention, which says the Grand Canyon formed 70 million years ago.

One would suppose Dr. Karlstrom would gladly take an interest in a proposal that the Grand Canyon was younger still. Not so. The science did not seem to pose a problem. But Dr. Snelling’s religious views did. So also did the views of the three earlier peer reviewers. Then Dr. Karlstrom suggested to let Dr. Snelling take his samples somewhere else—without saying where else.

Dr. Huntoon gives the game away

Ms. Newman could and should have asked Dr. Karlstrom to clarify the “somewhere else.” She did not. Instead she sent the application to another professor, Peter Huntoon, PhD, of the University of Wyoming. Dr. Huntoon at least had studied those same Paleozoic folds that Dr. Snelling wanted to sample.

Whereas Dr. Karlstrom had made an effort to sound reasonable, Dr. Huntoon did not. He couldn’t get past the creation advocacy angle. He wrote:

[It] is not a question of fairness to all points of view, but rather adherence to your narrowly defined institution mandate predicated in part on the fact that ours is a secular society as per our constitution.

In other words, the National Park Service should never approve any research that questions the secular model of Earth origins. That statement alone shows that science, and especially origins science, are not value-free. Anyone who still thinks so, should ask Dr. Huntoon. Then he specifically suggested the Park Service should deny permits to people representing interests he deemed inappropriate. If his earlier statement did not make his bias abundantly clear, this did.

Any truly objective official should have thrown out Dr. Huntoon’s report on its face. No scientist ever speaks of another as “representing inappropriate interests.” Unless said scientist is an origins scientist, or a dedicated global-warming alarmist. Then he or she does it all the time. Dr. Huntoon set the prize example. And Ms. Newton? She accepted that report, because it told her what she wanted to hear. For good measure, Dr. Huntoon told Ms. Newton more of the same in an e-mail. “Reviewing is fine,” said he, “just not processing the dead-end creationist material.”

The empty suit

Ms. Newton then sought an opinion from Dr. Ron Blakely of North Arizona University. And he said only that “it is difficult to review such an outlandish proposal.” What was so outlandish? What did he find outlandish? Dr. Blakely never said.

The Park Service denies the permit

On 4 March 2014, the Park Service denied the permit. Martha Hahn, Chief of the Science and Resource Management Research Office, wrote the denial. She said only,

it has been determined that equivalent examples of soft-sediment folds can be found outside of Grand Canyon National Park.

Where outside the Grand Canyon? Dr. Snelling asked Mss. Newman and Hahn again and again where to find those “equivalent examples.” And they did not even bother to return his telephone calls. Nor could they, in all honesty, have told him anything different from what he had already found out. To wit: he couldn’t find any “equivalent examples” anywhere except in the Grand Canyon.

Ms. Hahn wanted to make sure Dr. Snelling would not take his samples anyway. So she warned him the Park Service would never let him do research in any National Park if he did. Not only that, but Ms. Newton suggested that Ms. Hahn alert two other persons to watch out for Dr. Snelling or other “folks like this” on the Colorado River.

Dr. Snelling re-files

So Dr. Snelling missed his opportunity. But, trying to be reasonable, he re-filed on 8 February 2016. This time he proposed to collect only forty samples. He also answered every concern Dr. Karlstrom and others had raised. (Remember: at least Dr. Karlstrom did address the science to some extent.)

Again the Park Service delayed the application. This time they demanded more details on the site locations. Dr. Snelling did specify his sampling locations with margins of 100 feet. Other researchers should specify sampling sites with such precision.

Dr. Snelling waited to hear back from the Park Service. And waited. And waited.

Curiously, he did get a permit, but not to take the samples. Instead he must make a dry run to take pictures and get on-site GPS coordinates for every sample site. The Park Service sent the permit on 25 April 2016, but dated it 15 July 2016. The Park Service has never before demanded that any researcher do that kind of dry-run recon. Even the research guidelines for the Grand Canyon do not demand anything remotely like this. Naturally, Dr. Snelling refused. And on 5 July 2016, Ms. Newman (see above) sent an e-mail refusing any sampling permit.

Refusal to answer

Finally, on 22 December 2016, Dr. Snelling called his lawyers. They wrote straight to Christine Lehnertz, the Superintendent of Grand Canyon National Park. In their letter they set forth the legal issues the delay raised. Alliance Defending Freedom have done this before, in three other cases that involve the Grand Canyon.

Believe it or not, Ms. Lehnertz did not answer the letter or even say whether she got it. Dr. Snelling’s lawyers sent another letter on 31 January 2017, with the same lack of result. On 31 March 2017, Representative Trent Franks (R-Ariz.) wrote to Ms. Lehnertz, asking her to grant the permit. She ignored the congressman also.

The issues go beyond the Grand Canyon

Most of these acts took place during the Obama administration. All that has happened during the Trump administration, is refusal to answer letters. Still, the complaint cites Donald Trump’s specific Executive Order on religious freedom.

Dr. Snelling alleges five causes of action:

  1. Abridgment of his freedom of speech, by denying a permit for scientific investigation on obviously specious grounds. The actual grounds amount to viewpoint discrimination. To prove this, Dr. Snelling has the correspondence of Drs. Karlstrom, Blakely, and especially Huntoon.
  2. Interference with the free exercise of his religion, by the same act and on the same grounds.
  3. Denying him due process of law.
  4. Denying him the equal protection of the law.
  5. Breaking the Religious Freedom Restoration Act.

Scientific process issues

The scientific issues should concern any intellectually honest scientist. Evolutionists always call what they are doing “science,” and what creation advocates do, “pseudoscience.” They point to “statements of faith” like that from Answers in Genesis, while denying they subscribe to any similar statements. Yet three scientists have criticized Dr. Snelling on the grounds of his religious faith. Of the three, only Dr. Karlstrom raised any scientific concerns anyone might call legitimate. (Dr. Snelling answers those concerns.) The other two have disgraced themselves, their discipline, and the entire community of scientists.

Dr. Huntoon has given the worst offense. How dare he deem any avenue of scientific inquiry “inappropriate”? What does he fear? Could he fear that Dr. Snelling might develop evidence challenging the moral foundations of “our…secular society”?

But Dr. Huntoon actually gives a typical offense against religious and academic freedom. He illustrates the intellectual corruption of origins science today. His type of “investigator” doesn’t want to investigate, but to shut down any investigation of the fundamental question of origins. That question is: did the universe, this earth, and life come to exist over billions of years, or mere thousands? Maybe this explains why no one ever accepted the Walter T. Brown Written Debate Challenge.

Worse even than Dr. Huntoon’s attitude, is that of Mss. Newman, Hahn, and Lehnertz. In no other context, and under no other circumstances, would anyone in their positions accept the kind of petty, puerile, and spiteful objections Dr. Huntoon raised. They would mention him, if at all, only to condemn him. Instead Ms. Newman sought him out for the exact kind of opinion he gave. Her colleagues went along with this. That such persons remain in government employ, should concern anyone who cares about freedom of religion or scientific inquiry.

Evillution, Intelligent Design

Richard Dawkins Greatest Hoax in Science

This will be the first article detailing many of the “popular” so-called Atheists currently writing and confusing individuals today.  I promise not to be fair- it is only right to point out stupidity when one steps into and cannot get it off your shoes easily.

Clinton Richard Dawkins is probably the most famous evolutionist, anti-creationist and atheist today, and a staunch admirer of Charles Robert Darwin (1809–1882) the beginner of the muddling mess of science today.  His father  was an agricultural civil servant in the British Colonial Service in Nyasaland (now Malawi). His father was called up into the King’s African Rifles during World War II and returned to England in 1949, when Dawkins was eight.  This background may have had an influence on his further development.  Living in a dusty, sparse area with less than perfect sanitation and then being transported into the luxury of a 100 acre farm in England.

He gained his degree in Zoology at the Balliol College, Oxford, in 1962.   he was tutored by Nikolaas Tinbergen (1907–1988), who shared the 1973 Nobel Prize in Physiology or Medicine for his discoveries about instinct, learning and choice in animals.  Dawkins continued to study under Tinbergen, at the University of Oxford, receiving his M.A. and Ph.D. degrees in 1966.

Dawkins then took a position of assistant professor of zoology at the University of California, Berkeley, which in late 60’s was a hotbed of radicalism, I know, I spent some time rioting there.  He returned to Oxford as a lecturer in 1970 and he researched animal decision-making.  Since the 1970s, he has concentrated on improving his writing skills for popular audiences, for which he is far more famous than for his scientific research on animal behavior.

Dawkins’ first book, The Selfish Gene (1976), advocated a gene-centered view of evolution.  In other words, life first began from a ‘replicator’ that could make approximate copies of itself, which would therefore predominate in some kind of primordial soup that no one has been able to duplicate.  Those copies that could make internal biological machines to help them copy better and then would reproduce more.  Dawkins claims that these replicators are our genes, and our bodies are just ‘gigantic lumbering robots’ which are their ‘survival machines’.  This book also independently introduced the idea of the ‘meme’, a set of ideas that is replicated in other minds. (This has had an explosion with the advent of Facebook).

Dawkins regards his second book, The Extended Phenotype (1982), as his most important contribution to evolutionary biology.  This was kind of sequel and defense of The Selfish Gene; whereas in his first book, Dawkins argues that the organism is the gene’s survival machine, in his second he extends the genes’ influence to the environment modified by the organism’s behavior.  If this behavior helps the organism’s survival, then the genes ‘for’ that behavior will reproduce best.  His examples include beaver dams and termite mounds, as well as animal behavior that benefits a parasite afflicting it, hence the genes of that parasite. He also forgot one of his beloved Darwinian concepts, that the environment could have an effect on the organism to change the gene.  How he could forget that is anybody’s guess.  Mine is the advance on the book.

In 1986, Dawkins wrote The Blind Watchmaker, an attack on the argument that design in the living world demonstrates an intelligent Designer.  Instead, apparent design is the result of evolution by natural selection.  He regards that as a vital argument for his own Atheistic faith:

“An Atheist  before Darwin could have said, following Hume: ‘I have no explanation for complex biological design. All I know is that God isn’t a good explanation, so we must wait and hope that somebody comes up with a better one.’ I can’t help feeling that such a position, though logically sound, would have left one feeling pretty unsatisfied, and that although atheism might have been logically tenable before Darwin, Darwin made it possible to be an intellectually fulfilled atheist.” (BW, p.6)

Dawkins participated in the Huxley Memorial Debate at the Oxford Union one of very few.  He was opposing the proposition, “That the doctrine of creation is more valid than the theory of evolution.”  With him was the leading English evolutionist John Maynard Smith (1920–2004), and they were opposed by two biblical creationist scientists: triple doctorate organic chemist and pharmacologist A. E. Wilder-Smith (1915–1995) and Edgar Andrews (1932– ), then Professor of Materials at the University of London.

The audience of Oxford students voted and it  was a modest win for the evolution side, 198–115. Yet Dawkins was not happy—in his closing comments, he had “implored” the audience (his word) not to give a single vote to the creationist side, since every such vote “would be a blot on the escutcheon of the ancient University of Oxford[i].”  Ironically, it would be a return to Oxford’s roots, since it was founded by creationists.  After that, he is on record refusing to debate any biblical creationist. Somewhat like a baby throwing a hissy fit.

In 1995, he was appointed the Simonyi Professor for the Public Understanding of Science at Oxford. This was an endowment by leading Microsoft software designer and billionaire Charles Simonyi (b. Simonyi Károly, 1948) explicitly done just for Dawkins. The endowment stated, “The aim of the Professorship is “to communicate science to the public without, in doing so, losing those elements of scholarship which constitute the essence of true understanding.”  It was established with the express intention that the holder “be expected to make important contributions to the public understanding of some scientific field.”  Whether Dawkins lived up to that lofty goal is debatable.

One report said: “Evolution’s first great advocate, 1860s biologist Thomas Henry Huxley, earned the nickname ‘Darwin’s bulldog’ from his fellow Victorians. I n our own less decorous day, Dawkins deserves an even stronger epithet: ‘Darwin’s Rottweiler, perhaps,’ Simonyi suggests[ii].”  Dawkins retired from this post in September 2008.  You will be unable to find any example from this period were Dawkins aided the public understanding of any real science such as physics or chemistry, or even of the history or philosophy of science. However, during this professorship, Dawkins wrote seven books on evolution/atheism.  It is not surprising that British author Paul Johnson called it “Oxford’s first Chair of Atheism.[iii]

One of them, Climbing Mount Improbable (1996), Dawkins’ admits is one of his own favorites and is aimed to defend slow and gradual evolution. The title is a parable: many structures in living organisms are so complex that there is a vanishingly small probability of producing them in a single step—this corresponds to leaping the high Mt Improbable in a single step.  However, Dawkins says, this mountain has a gently upward-sloping terrain on the other side, where a climber can ascend gradually, constantly progressing to the top.  This corresponds to the neo-Darwinian mechanism of evolution—mutations + natural selection.  Mutations produce gradual improvements, and natural selection means that organisms which have them are slightly more likely to leave offspring provided they are in the right spot at the right time and are compatible to intertwine their chromosomes through what every process is available.  So a later generation of organisms is slightly more complex, or higher up the slope of Mt Improbable.

In his largest book, The Ancestor’s Tale: A Pilgrimage to the Dawn of Evolution (2004, 688 pages hardcover), Dawkins aimed to illustrate the history of life on Earth.  This was a series of 40 tales, from the point of view of man’s alleged evolutionary precursors[iv], and the name is a play on the Middle English classic The Canterbury Tales by Geoffrey Chaucer (c. 1343–1400). This has made him probably the best known exponent of evolution in the world.

Richard Dawkins not only regards Darwinism as compatible with atheism, but that atheism is a logical outcome of evolutionary belief- which I tend to agree with.  He has long promoted atheism both individually and as part of Atheistic organizations.  Dawkins is an Honorary Associate of the National Secular Society, a vice-president of the British Humanist Association (since 1996), a Distinguished Supporter of the Humanist Society of Scotland, a Humanist Laureate of the International Academy of Humanism, and a fellow of the Committee for Skeptical Inquiry. In 2003, he signed Humanism and Its Aspirations, published by the American Humanist Association.

In his 1991 essay “Viruses of the Mind”, Dawkins singled out theistic religion as one of the most pernicious of these viruses, that is, he regards theism as a kind of disease or pathology, and parents who teach it to their children are, in Dawkins’ view, supposedly practicing mental child abuse  But the sorts of criteria Dawkins applies have led critics to wonder whether Dawkins’ own strident atheism itself could be a mental pathology—or ‘atheopathy’- A neologism, coined by Jonathan Sarfati, which combines the word “atheist” and the suffix “-path” (“one afflicted by a specified disorder”) to create a word meaning something like “one afflicted by atheism.

Dawkins criticized those who resorted to prayers after 9/11.  Somehow he overlooked the record-breaking tens of millions killed by Atheistic regimes last century.  This was thoroughly documented by Rudolph Rummel (1932– ), Professor Emeritus of Political Science at the University of Hawaii, who coined the term democide for murder by government (I have written about it at: https://iamnotanatheist.wordpress.com/2017/03/28/religious-wars-vs-democide/ )

This antitheism continued in the presentation of a Channel 4 program in the UK, called The Root of All Evil?  (2006). The title was Channel 4’s choice, not Dawkins’, but he argued that humanity would be better off without belief in God.  In this program, Dawkins interviewed a number of Christian leaders, and visited several holy sites and communities of major religions.  However, some critics attacked the program for not having informed Christian responses.  For example, Dawkins’ fellow Oxford PhD, Alister McGrath (1953– ), Professor of Historical Theology (with a PhD in molecular biophysics), claimed that after his responses Dawkins seemed uncomfortable, so he was not surprised that his own contribution to the show remained on the cutting room floor[v].

Dawkins’ defense of atheism produced his best-seller to date, The God Delusion (2006), with 1.5 million copies sold.  Many high-profile Atheists praised it, and naturally Christians criticized it.  For example, Philip Bell, M.Sc. and former cancer researcher, published a detailed review[vi], and there are other books responding to it[vii]. However, leading logician and Christian philosopher Alvin Plantinga (1932– ), currently “John A. O’Brien Professor of Philosophy at the University of Notre Dame”, was not impressed with Dawkins’ excursions outside biology into philosophy, claiming that they could be called sophomoric were it not a grave insult to most sophomores[viii].  Now, I am not sure about you, but since it is my money, before I buy a book I read as many reviews, both positive and negative that I can before buying it. Stupidly, I bought this one and was not disappointed.

Prof. McGrath himself responded to the book (co-authored with his wife)[ix]. This also revealed that Dawkins’ support among Atheists was not universal—famous evolutionary philosopher Michael Ruse writes in the blurb, “The God Delusion makes me embarrassed to be an Atheist, and the McGraths show why.”  Ruse also said that the “new Atheists” led by Dawkins are “a b****y disaster”[x], and said the following about the book:

“Question: What do you think of The God Delusion by Richard Dawkins? Your approach is a lot milder? (The book lays open on his bed in the hotel room in Amsterdam where Ruse is interviewed.)

“Answer: I am just as critical of this book as of the work of Intelligent Design authors like Michael Behe, despite the fact that I, as an agnostic, am closer to Dawkins, and am 99% in agreement with his conclusions. But this book is stupid, politically disastrous and bad academics.  If someone spoke about biology and evolution as he does on theology, Dawkins would react without mercy.

“A good academic will inform himself in depth in a subject he is writing about. Dawkins did not. He is neither a philosopher nor a theologian. I am not a biologist myself, but at least I study the subject in depth before I write about it. And that arrogance and that pedantic attitude of his. …

“Dawkins’ book confirms my analysis of evolution as pseudo-religion.  His secular humanism has quasi-religious characteristics.[xi]

Another Atheist , Terry Eagleton, Professor of Cultural Theory at the National University of Ireland, Galway, began his review of The God Delusion with these words:

“Imagine someone holding forth on biology whose only knowledge of the subject is the Book of British Birds, and you have a rough idea of what it feels like to read Richard Dawkins on theology[xii].”

Eagleton continues:

“… does he imagine like a bumptious young barrister that you can defeat the opposition while being complacently ignorant of its toughest case? Dawkins, it appears, has sometimes been told by theologians that he sets up straw men only to bowl them over, a charge he rebuts in this book; but if The God Delusion is anything to go by, they are absolutely right.12

Dawkins publicly debated his book with John Carson Lennox, Professor of Mathematics at Oxford.  Lennox is also a Christian apologist and Intelligent Design supporter, and teacher of Science and Religion at Oxford, and the author of several books on the relations of science with religion and ethics.  This debate did not cover evolution, but the wider Christianity vs atheism topics covered in The God Delusio[xiii]n. Dawkins seemed quite red-faced and uncomfortable during the debate.

However, Dawkins refuses to debate best-selling author Dinesh D’Souza, author of What’s So Great about Christianity[xiv] among others, even though D’Souza is a theistic evolutionist not a creationist[xv]. Yet many of Dawkins’ fellow ‘new Atheists’ such as Christopher Hitchens and Daniel Dennett have been willing. In an open letter, D’Souza contrasted Dawkins’ eagerness to entrap non-scientist Christians on his TV shows with a refusal to debate a strong opponent on level terms:

“To be honest, I find your behavior extremely bizarre.  You go halfway around the world to chase down televangelists to outsmart them in an interview format that you control, but given several opportunities to engage the issues you profess to care about in a true spirit of open debate and inquiry, you duck and dodge and run away. …

“If you are so confident that your position is right, and that belief in God is an obvious delusion, surely you should be willing to vindicate that position not only against Bible-toting pastors but also against a fellow scholar and informed critic like me!

“If not, you are nothing but a showman who takes on unprepared and unsuspecting opponents when you yourself control the editing, but when a strong opponent shows up you manufacture reasons to avoid him.[xvi]

Now for a little rehash of what has been covered so far.  We will go into his next book on another post.  It is the information age- little information at a time. Dawkins started off as a “real scientist” and then moved on the showbiz aspect of popularity.  If even his own “kind” (Atheists) have harsh words for him you can image what others believe.

——————————

[i] Cooper, G. and Humber, P., Fraudulent report at AAAS and the 1986 Oxford University debate, http://www.samizdat.qc.ca/cosmos/origines/debate_gc.htm.

[ii] Downey, R., in Eastsideweek, 11 December 1996.

[iii] Johnson, P., If there is no God, what is the Oxford atheist scared of? Spectator, p. 19, 16 March 1996.

[iv] See review by Weinberger, Lael, Long tails, tall tales, J. Creation 22(1):37–40, 2008; creation.com/ancestors-tale.

[v] McGrath, A., “Do stop behaving as if you are God, Professor Dawkins”, Mail Online, 9 February 2007.

[vi] See Bell, P., Atheist with a Mission: Critique of The God Delusion by Richard Dawkins, J. Creation 21(2):28–34, 2007; creation.com/delusion.

[vii] Slane, R., The God Reality: A critique of Richard Dawkins’ The God Delusion, Day One, UK.

[viii] Plantinga, A., The Dawkins Confusion: Naturalism ad absurdum, Christianity Today (Books and Culture), March/April 2007; http://www.christianitytoday.com/bc.

[ix] McGrath, Alister and McGrath, Joanna Collicutt, The Dawkins Delusion? Atheist fundamentalism and the denial of the divine, SPCK, UK, 2007.

[x] Kumar, J., http://talk.thinkingmatters.org.nz/, 19 August 2009

[xi] Ruse, Michael, interview with De Volkskrant (Netherlands), p. 7, 7 April 2007, (translated by Frans Gunnink).

[xii] Eagleton,T., Lunging, flailing, mispunching, London Review of Books 28(20), 19 October, 2006, last accessed 25 January, 2007; http://www.lrb.co.uk.

[xiii] See The God Delusion Debate (DVD), available from CMI.

[xiv] Regnery, Washington DC, 2007.

[xv] See review by Cosner, L., Mostly masterful defence of Christianity; pity it’s slack on creation, J. Creation 22(2):32–35, 2008; creation.com/souza.

[xvi] D’Souza, cited in: The rout of the New Atheists, http://voxday.blogspot.com, 21 July 2008..

Intelligent Design

Is anything possible?

It is obvious from my discussions with those on Facebook and in other environments, that there is an incredible lack of understanding about the difference between what is possible and what is probable.  Along with it goes the concept of impossible and highly improbable.  As much as I would like to place the blame on the school system (which has a lot to do with) one has to look elsewhere for the complete story.

Our society has gotten on the supercilious concept that anything is possible.  We encourage the concept that nothing is impossible.  We can achieve anything we set our mind to (not withstand environmentally, political, monetary, geographical or educational pitfalls), Girls can grow up to become astronauts like Sally Ride and possibly die alongside men in an ignoble death.  Women can break the ‘glass ceiling’ and become President- if they do not burnout on lies first. Men can join a boy-band with virtually no skills and become rich and famous- and then act like a fool behind his bodyguards.  In other words, we sincerely believe that for anybody ANYTHING is possible.

However, there is such a thing as reality (reality is the state of things as they actually exist, rather than as they may appear or might be imagined.)

If Stephen Hawking were to believe that it possible for him to drive a stock car at Daytona on race day we would have a problem.  However, even with an incredible amount of reengineering of the controls and safety equipment, it is HIGHLY IMPROBABLE that Mr. Hawking will be able to no matter how much he feels it should be possible.

Bruce Jenner (AKA Caitlyn Jenner) believes it is possible to be a women.  Sorry sir, not going to happen.  Every cell in his/hers/its body contains an XY chromosome.  In addition, that means you are a male, no matter how much hormone treatment and surgery you have had performed on you.

It might help if we define some of the terms we will be using:

Reality: the world or the state of things as they actually exist, as opposed to an idealistic or notional idea of them:

Probable and possible are two commonly used words in the English language. Even though these words do not share the same roots, they convey an idea very slightly different from each other.  Therefore, as always with such things, there is confusion regarding the meaning and the usage of the words.

Oxford Advanced Learner’s dictionary defines ‘probable’ as “likely to happen, to exist or to be true”, while ‘possible’ is defined as “that might exist or happen but is not certain to”

Probable implies that there is a very high chance or likelihood that a certain event might occur.  On the other hand, possible means that the subject [whatever the word possible is describing about] might happen or might not happen, but there is no certainty of the outcome.

The most common use of possibility and probability is in flipping coins and rolling die.  It is simple when you do it once.  If you do it many times you can get into all sorts of trouble when you try to “play the odds.”

We have taken a circuitous route to get to the point of this post.  A recent Facebook post I had mention that extreme improbability of chemicals in the ‘pre-biotic soup’ to chemical combine with the other chemicals and then to form together to create a building block of what would become life. Because of this discussion one of the poster provided this answer:

“Realistically, this is the problem of an infinite number of monkeys typing away randomly at an infinite number of keyboards and given an infinite amount of time, one of them will produce Shakespeare. The problem with all that is when the first monkey writes the first sonnet, then you no longer have an infinite number, it has then become finite. And the predicted result has occurred. Just because you calculate the odds against a random set of complex proteins forming as being too great to ever happen only means that when it did, the experiment was over. Life formed. The monkey wrote ‘To be or not to be. — ‘The measure of time is impossible for humans on this scale.”

One overriding mistake by this learned individual: Modern cosmogony (the branch of science that deals with the origin of the universe, especially the solar system)  accepts finitism, in the form of the Big Bang, rather than Steady State theory which allows for an infinite universe, but on physical rather than philosophical grounds.

I figure a lot of it may be that we do not normally imagine things so huge, that often it is beyond our ability to even fantasize even if we think we have and can.  I even did a visual image of the amount of debt that Obama added to our total debt.   Those graphics are at: https://larrythecontrarian.wordpress.com/2015/03/07/our-national-debt-graphically/

However, let us go further and respond to the obvious misunderstandings inherent in the response and produce some actual visually understandable images.  I mean when one says a billion, billion, billion, billion to 1 possibility what does that really mean.

Within any given alphabet of x possible characters (where each character has an equal chance of occurring), the probability of any one of the characters occurring is 1 chance in x. For instance, if a monkey could bang randomly on a simplified typewriter possessing only keys for the 26 English letters, and assuming he was a perfectly random little monkey, there would be 1 chance in 26 that he would hit any particular letter at any particular moment.

The ‘famous’ atheist Richard Dawkins wrote “I don’t know who first pointed out that, given enough time, a monkey bashing away at random on a typewriter could produce all the works of Shakespeare[1].”  The idea originated with French mathematician Émile Borel, who pointed out in 1913 how unlikely it would be that a million monkeys typing ten hours a day would produce exactly all the books in the world’s libraries. Borel used this to illustrate the extreme unlikelihood of certain events, but Darwinists such as Dawkins now use the image of typing monkeys to illustrate the opposite: the likelihood that random processes can produce information.  According to the “infinite monkey theorem,” an infinite number of typing monkeys (or a finite number of monkeys typing for an infinite time) will eventually produce the works of William Shakespeare[2].

In theory, an infinite number of monkeys with an infinite amount of time would write the works of Shakespeare—mixed in with an infinite amount of utter nonsense.  But the real world isn’t infinite. On July 1, 2003, a Monkey Shakespeare Simulator was posted on the Internet.  The simulator does not use real monkeys, of course; it is a computerized random letter generator in which each “monkey” type’s one letter per second and the number of monkeys is continually increasing.  The simulator compares its output with the works of Shakespeare and reports matches—though it waits for such matches to appear on their own instead of selecting for a target sequence, as Dawkins’s did in a simplified program he wrote. After a year and a half, the longest match produced by the Monkey Shakespeare Simulator was twenty-four letters from a line in The Second Part of King Henry IV, which took the equivalent of 2,738 trillion trillion trillion monkey-years to produce. (A year later, the record had been extended to over thirty letters, which took trillions and trillions more monkey-years to produce[3].)

The poster believes that along about say 1,502 trillion, trillion 768 billion, 532 million, 456 thousand two hundred and one time a monkey actually typed something worthy of Shakespeare and the rest since then has been useless typing.

If you want to believe that, then please get in touch with me, I have some sea front property in Yuma, AZ I would like to sell.

I believe I have shown that not only is it IMPOSSIBLE for the monkeys to type anything remotely similar to a Shakespeare sonnet, it is also completely IMPROBABLE.  However, one can always hope that anything is possible..

Or let us take another approach: This has a somewhat comical appeal to me, is that of a blind monkey typing. Suppose that, instead of 26 letters plus spaces and punctuation in our English alphabet, there are only 20 possible choices for the monkey for each keystroke. We’ll use 20 because that’s the number of different kinds of amino acids our cells link together to make proteins (for now, we’ll ignore substitutions of amino acids; the math is so overpowering it works either way, and some proteins allow little or no substitution). We can compare the odds of a monkey accidentally typing a specified sequence of letters with the odds of the accidental formation of a specified sequence of amino acids.

Here’s a line from Shakespeare: “What fools these mortals be.[4]”  It has a total of 27 letters/ spaces. How likely is it that a monkey will accidentally type this exact sequence?  Again, we assume the monkey has a choice of exactly 20 letters/ spaces for each keystroke and is equally likely to type, completely at random, any particular letter/ space in any position. Of course, our blind monkey could get lucky and type this exact sequence the very first time.  But what are the odds?

Because there are 27 letters/ spaces, the number of possible sequences of this length is 2027, or about 1035. The number of seconds in the history of the universe, since the big bang, is about 4 × 1017.  So, even if we have a billion (109) quick-typing monkeys, who type the entire 27 characters every single second since the beginning of the universe (obviously this is fanciful, the monkeys couldn’t have existed at the beginning of the universe, but we are just trying to get a sense of the magnitude of the problem), we “only” get a total of 4 × 1026 sequences, and the chance that any of these monkeys ever typed “what fools these mortals be” is about 1 in 250 million (because 1035 is about 250 million times bigger than 4 × 1026).

So the odds of accidentally forming a precise sequence of 27 amino acids are laughingly small. Let’s now expand our imaginations to assume that every star in the universe has a planet with 1 billion monkeys typing. If we use a large estimate for the number of stars in the universe, we can expect that one of these monkeys will type “what fools these mortals be” within about 10 seconds[5].

But that’s just the beginning of complexity. Now let’s estimate the odds of accidentally creating a specified string of 75 amino acids. There are 75 letter/ spaces in “What a piece of work is a man how noble in reason how infinite in faculties.” There are a total of 2075 or about 4 × 1097 amino acid sequences of this length. Suppose, instead of a mere billion monkeys, each star in the universe has a planet with a billion billion billion billion monkeys, or 1036 monkeys, and each monkey can type even this 75 letters/ spaces sequence in just 1 second, to keep it simple[6]. OK, maybe too much math, definitely too many monkeys, but the likelihood of any of these blind monkeys ever typing our specified sequence in a time equal to the history of the universe is less than 1 in 1019, or less than one part in ten billion billion. So the odds of forming a single, relatively short specified protein with 75 amino acids by accident are vanishingly small, regardless of how many stars with Earthlike planets may exist. We are beyond laughingly small to pretty darn ridiculous.

Don’t tell me amino acids can be created by accident. Don’t tell me about “billions and billions” of years for life to arise. Don’t tell me about “countless” stars and planets in the universe. It all doesn’t matter. Using simple concepts of number— exponents— one can expose as false claims that life arose by accident.

Case made.  And then you have to worry about the possibility of amino acids gathering together into polypeptides and then proteins.  A simple quick view of that is at http://www.bing.com/videos/search?q=amino+acids+linked+together&&view=detail&mid=DD31E1EE7A5798B02B01DD31E1EE7A5798B02B01&FORM=VRDGAR

I promised to give you counterarguments, and here is one from Richard Dawkins and Stephen Jay Gould, among others. They say it is “false” that Darwin’s theory rests on chance alone; they say it works by “cumulative selection.” Say you start with a piece of gibberish and you want to transform it into meaningful text— you want to transform gibberish into “what fools these mortals be.” You give the gibberish a spin— you randomly change letters, or mutate the DNA code in the world of life— and some of the resulting English letters/ DNA letters may be correct. Not many, but perhaps one or maybe more. You hold on to any that are correct. You give the remaining English letters/ DNA letters a second spin/ mutation, and perhaps you get another one or more that are correct, and now you hold on to those also. You keep doing this. This process will converge in a reasonable period of time to yield the English phrase, or the DNA code, you are looking for. Dawkins and many others, with umpteen degrees and peer-reviewed articles to their credit, claim this “cumulative selection” drives Darwinian evolution. To which I meekly respond, in the words of the great John McEnroe: “YOU CANNOT BE SERIOUS!” How does the gene know what it is looking for? How does it “cumulatively select” good letters and keep mutating only the bad letters? You get a designed product, and we’re not supposed to notice the wizard behind the curtain running the show? You sneak intelligence in the back door but still claim the process is “natural”? So to Dawkins and many others, “cumulative selection” works like this. You have an ordinary gene (let’s call him “Joe”) just sitting there, hiding out in the DNA, minding his own business.  Not a lot happens in the genome. Sure there’s replication, but the error rate on that is only one letter in a billion.  But one day there is a mistake, and a DNA letter is changed by accident.  Joe says, “Hey, that feels good, I might be able to use that someday” and decides to hang onto that change for future generations.  It’s a slow process, but Joe is patient. Sure enough, just 125,314 generations later, somehow, inexplicably, a string of DNA letters from Joe’s buddy Hal gets inserted by accident when Joe is being replicated, and Joe says, “You know, that feels good too. I’ve got a hunch I might be able to use those extra letters someday, particular if another 27 changes are made in just the right spots in my DNA code.”  Well what do you know, but it all works out perfect for Joe in just 72,437,197 more generations.

http://www.bing.com/videos/search?q=amino+acids+linked+together&&view=detail&mid=A558CA27923DC3BC2FD0A558CA27923DC3BC2FD0&rvsmid=DD31E1EE7A5798B02B01DD31E1EE7A5798B02B01&fsscr=-1485&FORM=VDQVAP

Reality is a far cry from possibility.

 

[1] Richard Dawkins, The Blind Watchmaker: Why the Evidence of Evolution Reveals a Universe Without Design (New York: W. W. Norton, 1986), 47–49.

[2] “Infinite Monkey Theorem,” Answers.com. Available online (April 2006) at: http://www.answers.com/topic/infinite-monkey-theorem.

[3] The Monkey Shakespeare Simulator http://user.tninet.se/~ecf599g/aardasnails/java/Monkey/webpages/index.html.

[4] The quote is attributed to Roman philosopher Seneca the Younger.

[5] Some current estimates are about 1023 stars in the universe, but let’s say 1025 to be generous. So this calculation assumes 1034 imaginary monkeys typing!

[6] Now, over the life of the universe, all of these monkeys can be expected to type about 4 × 1078 sequences. For this calculation we multiply 4 × 1017 (the number of seconds since the big bang) times 1025 (number of stars) times 1036 (number of monkeys on each star), to get 4 × 1078 sequences.

Intelligent Design

Why ID part 4

Why ID part 4

chromosomes

The difference between LIVING and non-living is DNA and all of its many components.  We will try to give a brief, but detailed study of this particular chemical and try to understand what the DNA enigma is.  How DNA was discovered has been the subject of many fascinating books- I suggest the first 5 chapters of “Signature in the Cell” by Stephen Meyers for a good history.

DNA is made up of 4 distinct chemicals (adenine [A], thymine [T], cytosine [C] and guanine [G] that provide the information of life (not really, as in all things there are exceptions to the rule sometimes, thymine [T]is replaced with uracil [U]).

  1. Notice they form two groups: 1) pyrimidines: a nitrogenous base with a six-sided ring structure; a biologically significant derivative of pyrimidine, especially the bases cytosine, thymine, and uracil found in RNA and DNA  and 2) purines: a nitrogen-containing substance derived from uric acid that is the precursor of several biologically important compounds; a derivative of purine, especially either of the bases adenine and guanine, which are found in RNA and DNA.  Bio-chemists knew that the same amount of  Thymine and Adenine as well as the same amount of Cytosine and Guanine  existed in each chromosome.

purines-pyrimidines

We knew that there is a structural asymmetry in the construction of the backbone of the DNA molecule. The phosphate groups attach to a different carbon molecule on one side of the ribose sugar than they do on the other.  On one side of the ring structure of the sugar, the phosphate attaches to what is called its 5′ carbon (five prime carbon); on the other, the phosphate attaches to what is called its 3′ carbon.  It was known by chemists for a long time but nobody had the insight to understand the nature of the double helix.  Everyone was trying to make the two backbone run parallel to each other.

This did not work- all kinds of odd ball models were being developed and published and then rejected by bio-chemists.  Then along came the contrarians Watson and Crick.  Crick realized that the pattern she was describing— called a “monoclinic C2 symmetry” pattern— was indicative of an anti-parallel double helix structure. Instead of the two strands running from 5′ to 3′ in the same direction, Crick realized that Franklin’s data indicated that one helix was running up in the 5′ to 3′ direction and the other strand was running down in the 5′ to 3′ direction the other way.  Watson as he was building the model realized that they were two separate strands entwined around each other.

The following: https://www.youtube.com/watch?v=yqESR7E4b_8  is a great description of how DNA and RNA work.  It goes into developing hemoglobin and then sickle cell anemia, but up until that, it is great.  It is from www.wehi.edu.au , Walter and Eliza Hall Institute for Medical Research.

The Watson-Crick model clearly indicated that DNA had an impressive chemical and structural complexity.  It was a very long molecule composed on the outside by a regular arrangement of sugar and phosphate molecules.  On the inside, it could contain an almost infinite variety of different arrangements of the four bases.  This produced an impressive potential for variability and complexity of sequence as required by any potential carrier of hereditary information.  Most biologists thought life consisted solely of matter and energy.  However, after Watson and Crick, biologists came to recognize the importance of a third fundamental entity in living things: information.  At some point in the history of the universe, biological information came into existence.  Nevertheless, how?

Theories that claim to explain the origin of the first life must answer this question.  How could disparate chemicals bond together in such a manner as to pass on information to a receptor that could read it?  How did the receptor develop?  What we are talking about here is ‘biological/chemical information’ and the beginning of LIFE itself.

What is ‘biological information’?   Both philosophers and biologists have contributed to an ongoing foundational discussion of the status of this mode of description in biology.  It is generally agreed that the sense of information isolated by Claude Shannon and used in mathematical information theory is legitimate, useful, and relevant in many parts of biology. In this sense, anything is a source of information if it has a range of possible states, and one variable carries information about another to the extent that their states are physically correlated.  We will cover Shannon’s law in more detail later.

bioinformation-flow

Details about this image will become available as we continue on the path of the mystery of the mystery.  In Darwin’s time few, if any, biologists talked about biological or genetic information (that information just was not known at the time), but today they routinely refer to DNA, RNA, mRNA, tRNA and proteins as carriers or repositories of information.  Biologists will tell us that DNA stores and transmits “genetic information (without really knowing what ‘that’ is), that it expresses a “genetic message (they can see what that is),” that it stores “assembly instructions (they can see what is created) ,” a “genetic blueprint,” or “digital code.”  Biology has entered its own information age, and scientists seeking to explain the origin of life have taken note.  Life does not consist of just matter and energy, but also information.  According to evolutionists, matter and energy were around long before life, so this third aspect of living systems has now taken center stage.  At some point in the history of the universe, biological information came into existence.  But how?  Theories that claim to explain the origin of the first life must answer this question.  However, what exactly is information?  What is biological information?  Beginning in the late 1940s, mathematicians and computer scientists began to define, study, measure, and quantify information.  However, they made distinctions between several distinct types or conceptions of information.  What kind of information does DNA have?  What kind of information must origin-of-life researchers “explain the origin of”?  It is important to answer these questions because DNA contains a particular kind of information, one that only deepens the mystery surrounding its origin.

How do you define information?  Is it just a piece of knowledge?  Is it something that communicates something?  See Shannon’s Information theory (https://larryemarshall.wordpress.com/2016/12/26/shannons-theory-of-information/)

If you did not read the above link, good luck on understanding the following. We left that document with the question: So what kind of information does DNA possess, Shannon information or some other?

We need to look at what molecular biologists have discovered since 1953 about the role of DNA within the miniature world of the cell.  In the wake of Watson and Crick’s seminal 1953 paper, scientists soon realized that DNA could store an immense amount of information.  The chemistry of the molecule allows any one of the four (or five if discussing RNA) bases to attach to any of the sugar molecules in the backbone.  This allows the kind of almost incalculable variable sequencing that any carrier of genetic information would need to have.  In addition, the weak hydrogen bonds that hold the two anti-parallel strands together suggest a way the molecule might allow itself to be unzipped.  This allows the exposed sequence of bases to be duplicated in a unique and fascinating manner.  It would seem that DNA was ideal for storing information-rich sequences of chemical (alphabetic) characters.

However, how DNA expressed this information and how it could possibly be using that information remained uncertain.  These answers would come due to new developments in the field of protein chemistry.  Scientists today know that protein molecules perform virtually all of the critical functions in the cell.  Proteins build cellular machines and structures, they carry and deliver cellular materials, and they catalyze chemical reactions that the cell needs to stay alive.  Proteins also process the genetic information.

To accomplish this critical work, a typical cell uses thousands of different kinds of proteins; each with a distinctive shape related to its function.  It is kind of like Microsoft Office.®  Access, Excel, PowerPoint, Outlook, Word- all completely different programs, different sizes, different functions, however, they can interact with each other, pass data to and from each other and many other functions that assist you in maintaining top functionality while working on your computer.

By the 1890s, various biochemists had begun to recognize how proteins were central to the maintenance of life in the cells.  The biochemists knew proteins were heavy (“ high molecular weight”) molecules that were involved in many of the chemical reactions going on inside cells.  Chemists were also able to determine that proteins were made of smaller molecules called amino acids during the first half of the twentieth century.  Many scientists, for awhile,  thought that proteins were so important that they (the proteins), rather than DNA molecules, were the repositories of genetic information.

Until the 1950s, scientists repeatedly underestimated the complexity of proteins. William Astbury[1] was an outstanding scientist who had studied physics at Cambridge during and after World War I.  He then worked with William Bragg[2], the pioneering X-ray crystallographer whose son Lawrence later supervised Watson and Crick.  Astbury was convinced that proteins held the key to understanding life.  He thought they should exhibit a simple, regular structure that could be described by a mathematical equation or some general law.

He was used to studying highly regular and orderly structures as a crystallographer. Salt crystals, the first structures determined using X-ray techniques, have a highly repetitive or regular structure of sodium and chlorine atoms arranged in a three-dimensional grid, a pattern in which one type of atom always has six of the other types surrounding it.

salt-crystals-macro-photography-36648325

Astbury was convinced that proteins— the secret of life—life— should exhibit a similar regularity.  During the 1930s he made a discovery that seemed to confirm his expectation.  Astbury used X rays to determine the molecular structure of a fibrous protein called keratin, the key structural protein in hair and skin.[3]  Astbury discovered that keratin exhibits a simple, repetitive molecular structure, with the same pattern of amino acids repeating over and over again— just like the repeating chemical elements in a crystal (or the repeating pattern of bases that P. A. Levene[4] had mistakenly proposed as a structure for DNA).  Astbury concluded (unfortunately) that all proteins, including the mysterious globular proteins so important to life, would exhibit the same basic pattern he discovered in keratin.  Many of Astbury’s contemporaries shared the same view.  In 1937, for example, two leading American biochemists, Max Bergmann[5] and Carl Niemann[6], of the Rockefeller Institute, argued that the amino acids in all proteins occurred in regular, mathematically expressible proportions.[7]  It took 25 years before this mistaken thought process was understood and corrected.

About the same time that Watson and Crick were trying to solve the structure of DNA (the late 1950’s), another Cambridge scientist made a discovery that would challenge Astbury’s view of proteins.  While working just a couple miles from Watson and Crick at famous Laboratory for Molecular Biology (or LMB), biochemist Fred Sanger[8] determined the structure of the protein molecule insulin.  Sanger’s discovery would later earn him the first of two Nobel prizes in chemistry. Sanger showed that insulin consisted of irregular sequences of various amino acids, rather like a string of differently colored beads arranged with no discernible or repeating pattern[9].

insulinstructure

The above was the part of chemistry class (both high school and college) that I hated the most-drawing stupid diagrams.  To me as long as you knew the formula (C257H383N65O77S6), what the heck difference did it make if you knew the diagram?  But some of those old fuddy-duddy’s insisted on you drawing it out exactly like what they had in the book, but it really did not matter when they found out the actual protein looked like below.  All that time, energy, arguments and grade points wasted.

insulinmokecule

Subsequent work on other proteins would show the same thing: the sequencing of amino acids is usually highly irregular and defies description by any general rule.[10]

Many biologists at the time still expected proteins, considered by many the fundamental unit of life, to exhibit regularity, if not in the arrangement of their amino acids, then at least in their overall three-dimensional shapes or structures  would end up exhibiting some sort of geometric regularity. Some imagined that insulin and hemoglobin proteins, for example, would look like “bundles of parallel rods[11].”  As Johns Hopkins biophysicist George Rose recounts, “Protein structure was a scientific terra incognita[12].  With scant evidence to go on, biologists pictured proteins vaguely as featureless ellipsoids: spheres, cigars, Kaiser rolls[13].”

frenchbread

Then came the publication of a paper by John Kendrew who studied chemistry at Cambridge and graduated in 1939.  After doing research on radar technology during the war, he took up the study of molecular biology at the Medical Research Council Laboratory in Cambridge in 1946.  There Kendrew began to work closely with Max Perutz, the Austrian crystallographer who, along with Lawrence Bragg, had officially supervised Watson and Crick.  In 1958, Kendrew made his own contribution to the molecular biological revolution when he published a paper on the three-dimensional structure of the protein myoglobin[14].

myoglobin

Kendrew’s work revealed an extraordinarily complex and irregular three-dimensional shape, a twisting, turning, tangled chain of amino acids. Whereas protein scientists had anticipated that proteins would manifest the kind of regular order present in crystals, they found instead a complex three-dimensional structure.

In the Nature paper, he wrote, “Perhaps the most remarkable features of the molecule are its complexity and its lack of symmetry.  The arrangement seems to be almost totally lacking in the kind of regularities which one instinctively anticipates, and it is more complicated than has been predicted by any theory of protein structure[15].”

Biochemists recognized that proteins exhibited another rather remarkable property.  In addition to their complex shapes and irregular arrangements of amino acids, proteins also exhibit ‘specificity’.  By specificity, biologists mean that a molecule has some features that have to be what they are, within very fine tolerances, for the molecule to perform an important function in that cell. Any deviation will cause that protein to fail to perform is function.

Proteins show specificity in two ways.  First, proteins display a specificity of shape.  The strangely irregular shapes of proteins that Kendrew and others discovered are essential to the function of the proteins.  In particular, the three-dimensional shape of a protein gives it a close association with other equally specified and complex molecules or with simpler substrates.  This enables it to catalyze specific chemical reactions or to build specific structures within the cell.  In other words, the proteins all fit together in a certain way, which allows the chemical relationship to proceed.

4protiens

Because of its three-dimensional specificity, one protein usually cannot substitute for another.  A topoisomerase[16] can no more perform the job of a polymerase[17] than Excel can format a letter better than Word.

Enzymes are proteins that catalyze specific chemical reactions.  The simplified figure below shows an enzyme called a beta-galactosidase and a two-part sugar molecule (a disaccharide) called lactose.  The enzyme’s shape and dimensions must exactly conform to the shape and dimensions of the disaccharide molecule, so that the lactose molecule can nestle into the pockets of the enzyme.  Once it does, a chemically active part of the enzyme, called an active site, starts a chemical reaction.   The reaction breaks the chemical bonds holding the two parts of the sugar together and liberates two individual molecules of glucose, both of which the cell can use easily.

These two molecules can then be used in further reactions necessary in maintaining the life and health of the cell.

lactose-to-gucose

Consider how another example of the specific shape of proteins allows them to perform specific functions.  The eukaryotic cell has an uncanny way of storing the information in DNA in a highly compact way (Eukaryotes are cells that contain a nucleus and other membrane-bound organelles; prokaryotic cells lack these features.)

types-of-cells

Strands of DNA are wrapped around spool-like structures called nucleosomes.  The nucleosomes are made of proteins called histones.  It is the specific shape of the histone proteins that enables them to do their job.

Histones 3 and 4, for example, fold into well-defined three-dimensional shapes with a precise distribution of positive electrical charges around their exteriors.  This precise shape and charge distribution enables DNA strands to coil efficiently around the nucleosome spools and store an immense amount of information in a very small space[18].  Due to the nucleosome spooling, the information storage density of DNA is many times that of our most advanced silicon chips[19] [20].

histone-3h-and-54

In the case of nucleosomes,  there is an uncanny distribution of positively charged regions on the surface of the histone proteins that exactly matches the negatively charged regions of the double-stranded DNA that coils around it[21].

crochetnucleosome

Proteins have a second type of specificity— one that will explain the first. Proteins do not just display a specificity of shape; they also display a specificity of arrangement.  Whereas proteins are built from rather simple amino-acid “building blocks,” their various functions crucially depend on the specific arrangement of those building blocks.  The specific sequence of amino acids in a chain and the resulting chemical interactions between amino acids largely determine the specific three-dimensional structure that the chain will adopt when completed. Those structures or shapes determine what function, if any, the amino acid chain can perform in the cell— whether as an enzyme, structural component, or a machine for processing information[22]. Below is a simplified picture of how that might work.

lock-and-key-enzyme

Next up the I will try to tie this all together with the importance  of the Sequence Hypothesis, the ‘genetic code’ and the “Shannon Information Plus”.  After that the “Origin Of”.


[1] An English physicist and molecular biologist who made pioneering X-ray diffraction studies of biological molecules.

[2] A British physicist and X-ray crystallographer, discoverer (1912) of Bragg’s law of X-ray diffraction, which is basic for the determination of crystal structure

[3] Astbury and Street, “X-Ray Studies of the Structure of Hair, Wool and Related Fibres”; Judson, The Eighth Day of Creation, 61– 62; Olby, The Path to the Double Helix, 63.

[4] An American biochemist who studied the structure and function of nucleic acids. He characterized the different forms of nucleic acid, DNA from RNA, and found that DNA contained adenine, guanine, thymine, cytosine, deoxyribose, and a phosphate group. He specialized in decoding protein and peptide structures.

[5] He developed the Bergmann-Zervas carbobenzoxy method for the synthesis of polypeptides.

[6] an American biochemist who worked extensively on the chemistry and structure of proteins,

[7] Bergmann and Niemann, “Newer Aspects of Protein Chemistry.”

[8] In 1958, he was awarded a Nobel Prize in chemistry “for his work on the structure of proteins, especially that of insulin”.

[9] According to Judson: “The man who released the present-day understanding of molecular specificity in living processes was Frederick Sanger. His determination, beginning in the mid-forties, of the amino-acid sequences of bovine insulin proved that they have no general periodicities. His methods and this surprising result had many consequences, of course: the most general and profound was that proteins are entirely and uniquely specified” (The Eighth Day of Creation, 88– 89, 585). See Sanger and Thompson, “The Amino Acid Sequence in the Glycyl Chain of Insulin.”

[10]Judson, The Eighth Day of Creation, 581– 85.

[11] Olby, The Path to the Double Helix, 265.

[12] a term used in cartography for regions that have not been mapped or documented.

[13] Rose, “No Assembly Required,” 36, 28.

[14] is an iron- and oxygen-binding protein found in the muscle tissue in almost all mammals. It is related to hemoglobin, which is the iron- and oxygen-binding protein in blood, specifically in the red blood cells.

[15] Kendrew, et al., “A Three-Dimensional Model of the Myoglobin Molecule,” 662– 66.

[16] enzymes that regulate the overwinding or underwinding of DNA. The winding problem of DNA arises due to the intertwined nature of its double-helical structure.

[17] an enzyme that synthesizes long chains or polymers of nucleic acids. DNA polymerase and RNA polymerase are used to assemble DNA and RNA molecules

[18] Lodish, et al., Molecular Cell Biology, 321– 23.

[19] Gitt, In the Beginning Was Information, 192– 93.

[20] A bioengineer and geneticist at Harvard’s Wyss Institute have successfully stored 5.5 petabits of data — around 700 terabytes — in a single gram of DNA, smashing the previous DNA data density record by a thousand times. https://www.extremetech.com/extreme/134672-harvard-cracks-dna-storage-crams-700-terabytes-of-data-into-a-single-gram

[21] Lodish, et al., Molecular Cell Biology, 322.

[22] Alberts, et al., Molecular Biology of the Cell, 111– 12, 127– 31.