Tag Archives: biology

The Origin of Life: An Inside Story – 2016 Lectures (with Dr. James Tour)

For the preaching of the cross is to them that perish foolishness; but unto us which are saved it is the power of God. For it is written, I will destroy the wisdom of the wise, and will bring to nothing the understanding of the prudent. Where is the wise? where is the scribe? where is the disputer of this world? hath not God made foolish the wisdom of this world? For after that in the wisdom of God the world by wisdom knew not God, it pleased God by the foolishness of preaching to save them that believe. For the Jews require a sign, and the Greeks seek after wisdom: But we preach Christ crucified, unto the Jews a stumblingblock, and unto the Greeks foolishness; But unto them which are called, both Jews and Greeks, Christ the power of God, and the wisdom of God. Because the foolishness of God is wiser than men; and the weakness of God is stronger than men. For ye see your calling, brethren, how that not many wise men after the flesh, not many mighty, not many noble, are called: But God hath chosen the foolish things of the world to confound the wise; and God hath chosen the weak things of the world to confound the things which are mighty; And base things of the world, and things which are despised, hath God chosen, yea, and things which are not, to bring to nought things that are: That no flesh should glory in his presence.

1 Corinthians 1:18-29

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The Optimal Design of the Genetic Code

genetics 2

Were there no example in the world of contrivance except that of the eye, it would be alone sufficient to support the conclusion which we draw from it, as to the necessity of an intelligent Creator.

William Paley, Natural Theology

In his classic work, Natural TheologyWilliam Paley surveyed a range of biological systems, highlighting their similarities to human-made designs. Paley noticed that human designs typically consist of various components that interact in a precise way to accomplish a purpose. According to Paley, human designs are contrivances—things produced with skill and cleverness—and they come about via the work of human agents. They come about by the work of intelligent designers. And because biological systems are contrivances, they, too, must come about via the work of a Creator.

For Paley, the pervasiveness of biological contrivances made the case for a Creator compelling. But he was especially struck by the vertebrate eye. For Paley, if the only example of a biological contrivance available to us was the eye, its sophisticated design and elegant complexity alone justify the “necessity of an intelligent creator” to explain its origin.

As a biochemist, I am impressed with the elegant designs of biochemical systems. The sophistication and ingenuity of these designs convinced me as a graduate student that life must stem from the work of a Mind. In my book The Cell’s Design, I follow in Paley’s footsteps by highlighting the eerie similarity between human designs and biochemical systems—a similarity I describe as an intelligent design pattern. Because biochemical systems conform to the intelligent design pattern, they must be the work of a Creator.

As with Paley, I view the pervasiveness of the intelligent design pattern in biochemical systems as critical to making the case for a Creator. Yet, in particular, I am struck by the design of a single biochemical system: namely, the genetic code. On the basis of the structure of the genetic code alone, I think one is justified to conclude that life stems from the work of a Divine Mind. The latest work by a team of German biochemists on the genetic code’s design convinces me all the more that the genetic code is the product of a Creator’s handiwork.1

To understand the significance of this study and the code’s elegant design, a short primer on molecular biology is in order. (For those who have a background in biology, just skip ahead to The Optimal Genetic Code.)

Proteins

The “workhorse” molecules of life, proteins take part in essentially every cellular and extracellular structure and activity. Proteins are chain-like molecules folded into precise three-dimensional structures. Often, the protein’s three-dimensional architecture determines the way it interacts with other proteins to form a functional complex.

Proteins form when the cellular machinery links together (in a head-to-tail fashion) smaller subunit molecules called amino acids. To a first approximation, the cell employs 20 different amino acids to make proteins. The amino acids that make up proteins possess a variety of chemical and physical properties.

Each specific amino acid sequence imparts the protein with a unique chemical and physical profile along the length of its chain. The chemical and physical profile determines how the protein folds and, therefore, its function. Because structure determines the function of a protein, the amino acid sequence is key to dictating the type of work a protein performs for the cell.

DNA

The cell’s machinery uses the information harbored in the DNA molecule to make proteins. Like these biomolecules, DNA consists of chain-like structures known as polynucleotides. Two polynucleotide chains align in an antiparallel fashion to form a DNA molecule. (The two strands are arranged parallel to one another with the starting point of one strand located next to the ending point of the other strand, and vice versa.) The paired polynucleotide chains twist around each other to form the well-known DNA double helix. The cell’s machinery forms polynucleotide chains by linking together four different subunit molecules called nucleotides. The four nucleotides used to build DNA chains are adenosine, guanosine, cytidine, and thymidine, familiarly known as A, G, C, and T, respectively.

As noted, DNA stores the information necessary to make all the proteins used by the cell. The sequence of nucleotides in the DNA strands specifies the sequence of amino acids in protein chains. Scientists refer to the amino-acid-coding nucleotide sequence that is used to construct proteins along the DNA strand as a gene.

The Genetic Code

A one-to-one relationship cannot exist between the 4 different nucleotides of DNA and the 20 different amino acids used to assemble polypeptides. The cell addresses this mismatch by using a code comprised of groupings of three nucleotides to specify the 20 different amino acids.

The cell uses a set of rules to relate these nucleotide triplet sequences to the 20 amino acids making up proteins. Molecular biologists refer to this set of rules as the genetic code. The nucleotide triplets, or “codons” as they are called, represent the fundamental communication units of the genetic code, which is essentially universal among all living organisms.

Sixty-four codons make up the genetic code. Because the code only needs to encode 20 amino acids, some of the codons are redundant. That is, different codons code for the same amino acid. In fact, up to six different codons specify some amino acids. Others are specified by only one codon.

Interestingly, some codons, called stop codons or nonsense codons, code no amino acids. (For example, the codon UGA is a stop codon.) These codons always occur at the end of the gene, informing the cell where the protein chain ends.

Some coding triplets, called start codons, play a dual role in the genetic code. These codons not only encode amino acids, but also “tell” the cell where a protein chain begins. For example, the codon GUG encodes the amino acid valine and also specifies the starting point of the proteins.

The Optimal Genetic Code

Based on visual inspection of the genetic code, biochemists had long suspected that the coding assignments weren’t haphazard—a frozen accident. Instead it looked to them like a rationale undergirds the genetic code’s architecture. This intuition was confirmed in the early 1990s. As I describe in The Cell’s Design, at that time, scientists from the University of Bath (UK) and from Princeton University quantified the error-minimization capacity of the genetic code. Their initial work indicated that the naturally occurring genetic code withstands the potentially harmful effects of substitution mutations better than all but 0.02 percent (1 out of 5,000) of randomly generated genetic codes with codon assignments different from the universal genetic code.2

Subsequent analysis performed later that decade incorporated additional factors. For example, some types of substitution mutations (called transitions) occur more frequently in nature than others (called transversions). As a case in point, an A-to-G substitution occurs more frequently than does either an A-to-C or an A-to-T mutation. When researchers included this factor into their analysis, they discovered that the naturally occurring genetic code performed better than one million randomly generated genetic codes. In a separate study, they also found that the genetic code in nature resides near the global optimum for all possible genetic codes with respect to its error-minimization capacity.3

It could be argued that the genetic code’s error-minimization properties are more dramatic than these results indicate. When researchers calculated the error-minimization capacity of one million randomly generated genetic codes, they discovered that the error-minimization values formed a distribution where the naturally occurring genetic code’s capacity occurred outside the distribution. Researchers estimate the existence of 1018 (a quintillion) possible genetic codes possessing the same type and degree of redundancy as the universal genetic code. Nearly all of these codes fall within the error-minimization distribution. This finding means that of 1018 possible genetic codes, only a few have an error-minimization capacity that approaches the code found universally in nature.

Frameshift Mutations

Recently, researchers from Germany wondered if this same type of optimization applies to frameshift mutations. Biochemists have discovered that these mutations are much more devastating than substitution mutations. Frameshift mutations result when nucleotides are inserted into or deleted from the DNA sequence of the gene. If the number of inserted/deleted nucleotides is not divisible by three, the added or deleted nucleotides cause a shift in the gene’s reading frame—altering the codon groupings. Frameshift mutations change all the original codons to new codons at the site of the insertion/deletion and onward to the end of the gene.

The Genetic Code Is Optimized to Withstand Frameshift Mutations

Like the researchers from the University of Bath, the German team generated 1 million random genetic codes with the same type and degree of redundancy as the genetic code found in nature. They discovered that the code found in nature is better optimized to withstand errors that result from frameshift mutations (involving either the insertion or deletion of 1 or 2 nucleotides) than most of the random genetic codes they tested.

The Genetic Code Is Optimized to Harbor Multiple Overlapping Codes

The optimization doesn’t end there. In addition to the genetic code, genes harbor other overlapping codes that independently direct the binding of histone proteins and transcription factors to DNA and dictate processes like messenger RNA folding and splicing. In 2007, researchers from Israel discovered that the genetic code is also optimized to harbor overlapping codes.4

The Genetic Code and the Case for a Creator

In The Cell’s Design, I point out that common experience teaches us that codes come from minds. By analogy, the mere existence of the genetic code suggests that biochemical systems come from a Mind. This conclusion gains considerable support based on the exquisite optimization of the genetic code to withstand errors that arise from both substitution and frameshift mutations, along with its optimal capacity to harbor multiple overlapping codes.

The triple optimization of the genetic code arises from its redundancy and the specific codon assignments. Over 1018 possible genetic codes exist and any one of them could have been “selected” for the code in nature. Yet, the “chosen” code displays extreme optimization—a hallmark feature of designed systems. As the evidence continues to mount, it becomes more and more evident that the genetic code displays an eerie perfection.5

An elegant contrivance such as the genetic code—which resides at the heart of biochemical systems and defines the information content in the cell—is truly one in a million when it comes to reasons to believe.

Original article: The Optimal Design of the Genetic Code

Seaside & Disease

Men and women are different.

They think differently, emote differently, solve problems differently, seek different social goals, and contribute different biology to sexual reproduction.

Yes, they are the same species, but they are radically different. Same chemistry, just in different order and proportion.

Anyone who does not know this, including Ph.D. professors, commentators, social justice warriors, Marxists, or anyone else, is too ignorant to be in any meaningful discussion.

Let’s be blunt: these are stupid people who believe stupid things.

They cannot even grasp the obvious, if for no other reason than they foolishly commingle biology with, well, anything they wrongly believe justifies their fake outrage.

Such foolishness belongs to the past — leave it there. The Far Left distinguishes itself by clawing things apart. In our time, they are trying to rip “sex” and “gender” and “gender identity” apart. It is a false uncoupling meant to obfuscate legitimate neuroses, which proves how much they really care about personality disorders.

Consider this:

The words “seaside” and “disease” have the exact same number of letters, same number of vowels, same number of consonants, same number of syllables, they are both nouns, the roots from which they are derived are both over 500 years old, they both have two S’s and two E’s, and they are both written in the English language.

But they mean totally different things.

 

COULD LIFE HAVE EMERGED SPONTANEOUSLY ON THE EARLY EARTH?

Last time we saw how the progress of science in the last 30 years has proved that the environment of the early Earth would not have allowed the emergence of the basic building blocks of life. This time, let’s allow the atheist to assume the building blocks were created by the noodly appendage of the Flying Spaghetti Monster, (peas be upon him), and see whether it’s possible for the blocks to chain themselves together to make a living cell withinin a reasonable amount of time (400 million years, say).

For this post, I will be referencing an article by Stephen C. Meyer, which he published in the Catholic journal “First Things”. I chose this article deliberately because it was written at the level of an ordinary layman, so we could all understand everything well enough to feel confident explaining it to our neighbors. All unattributed quotes are from this article.

The combatants

The contest over origins features two opposing points of view:

  • A Creator and Designer is responsible for the origin of life
  • Matter, chance and long periods of time are sufficient to explain the origin of life

What’s at stake?

Atheistic Cornell University professor Will Provine explains what logically follows from naturalistic evolution:

There are no gods, no purposes, and no goal-directed forces of any kind. There is no life after death. When I die, I am absolutely certain that I am going to be dead. That’s the end of me. There is no ultimate foundation for ethics, no ultimate meaning in life, and no free will for humans, either. What an unintelligible idea.

So, the stakes are high.

Why doubt the apparent design in nature?

There are two main reasons why atheists doubt the appearance of design in nature:

Minimal life functionality requires information

In order for a living organism to support life, it must be able to perform minimal functions:

  • store information
  • transmit information
  • edit information
  • use that information to regulate metabolic processes

There must be sufficient information inside the cells of that organism to support those functions. How does this information exist in the cell, and where did it come from?

Atheism is a pre-scientific worldview

Meyer describes the primitive superstitions of tribes of atheists living in primitive, pre-scientific cultures:

…in the 1870s and 1880s scientists assumed that devising an explanation for the origin of life would be fairly easy….they assumed that life was essentially a rather simple substance called protoplasm that could be easily constructed by combining and recombining simple chemicals such as carbon dioxide, oxygen, and nitrogen. …just as salt could be produced spontaneously by adding sodium to chloride, so… could a living cell be produced by adding together several chemical constituents and then allowing spontaneous chemical reactions to produce the simple protoplasmic substance that they assumed to be the essence of life.

Atheists believe in all kinds of primitive pre-scientific myths, like the eternal universe, etc., which the progress of science has falsified. Can the progress of science falsify the atheistic superstitions about the origin of life?

The Oparin-Haldane hypothesis

Atheists began to panic in the early 20th century as discoveries began to pile up confirming the that the entire physical universe, and time itself, was created by a supernatural force that existed transcendentally, independent of matter, energy, space and time. (See here for a listing of 6 of these discoveries from the progress of science). Atheists decided that they’d better get involved in this “science” thing that the Christians had started.

Meyer reports on one of their first groundless speculations:

During the 1920s and 1930s a more sophisticated version of this so–called “chemical evolutionary theory” was proposed by a Russian biochemist named Alexander I. Oparin…. Oparin, like his nineteenth–century predecessors, suggested that life could have first evolved as the result of a series of chemical reactions.

It was hoped that that the Flying Spaghetti Monster would appear to his true believers and ground this blind speculation, allowing atheists to continue in their flight from rationality and moral obligations.

The Miller-Urey experiment

Pre-biotic synthesis (see below) produces amino acids, which are the first step in explaining the origin of the simplest life, on atheism:

As we saw last time, the Miller-Urey experiments that were designed to produce the building blocks of life (amino acids) were horribly flawed and did not reflect the conditions that would have existed on the early Earth.

I’ll summarize the problems with the experiment:

  • the gasses were used in the experiment were not those present on the early Earth
  • molecular oxygen was excluded from the experiment
  • Harmful UV radiation was filtered out by the experimenter intervention
  • interfering cross-reactions were prevented by experimenter intervention

Other problems:

  • extinction events, such as meteorite impacts, were excluded not considered
  • the chirality problem (left-handed amino acids, right-handed sugars) was not considered
  • the problem of getting all peptide bonds was not considered

This experiment, though flawed, still exists in biology textbooks today, along side faked photographs of peppered moths and doctored drawings of embryos. All must praise the Flying Spaghetti Monster, and at taxpayer expense!

The problem of biological information

To create life, you need to sequence amino acids into proteins, and sequence the nucleotides on DNA strands.

Meyer explains:

To form a protein, amino acids must link together to form a chain. Yet amino acids form functioning proteins only when they adopt very specific sequential arrangements, rather like properly sequenced letters in an English sentence. Thus, amino acids alone do not make proteins, any more than letters alone make words, sentences, or poetry. In both cases, the sequencing of the constituent parts determines the function (or lack of function) of the whole.

…As it turns out, specific regions of the DNA molecule called coding regions have the same property of “sequence specificity” or “specified complexity” that characterizes written codes, linguistic texts, and protein molecules. Just as the letters in the alphabet of a written language may convey a particular message depending on their arrangement, so too do the sequences of nucleotide bases (the A’s, T’s, G’s, and C’s) inscribed along the spine of a DNA molecule convey a precise set of instructions for building proteins within the cell. The nucleotide bases in DNA function in precisely the same way as symbols in a machine code. In each case, the arrangement of the characters determines the function of the sequence as a whole…. In the case of DNA, the complex but precise sequencing of the four nucleotide bases (A, T, G, and C) stores and transmits the information necessary to build proteins.

…As Bernd–Olaf Kuppers recently stated, “The problem of the origin of life is clearly basically equivalent to the problem of the origin of biological information.”

How do atheists account for this biological information?

Atheistic superstitions about the biological information

Le’s take a look at the atheist’s faith-based explanations of the origin of life: chance, law and self-organization.

For the first one, let’s calculate the odds of building a protein composed of a functional chain of 100 amino acids, by chance. (Think of a meaningful English sentence built with 100 scrabble letters, held together with glue)

1. Chance:

  • Bonding: You need 99 peptide bonds between the 100 amino acids. The odds of getting a peptide bond is 50%. The probability of building a chain of one hundred amino acids in which all linkages involve peptide bonds is roughly (1/2)99or 1 chance in 1030.
  • Chirality: You need 100 left-handed amino acids. The odds of getting a left-handed amino acid is 50%. The probability of attaining at random only L–amino acids in a hypothetical peptide chain one hundred amino acids long is (1/2)100 or again roughly 1 chance in 1030.
  • Sequence: You need to choose the correct amino acid for each of the 100 links. The odds of getting the right one are 1 in 20. Even if you allow for some variation, the odds of getting a functional sequence is (1/20)100 or 1 in 1065.

The final probability of getting a functional protein composed of 100 amino acids is 1 in 10125. Even if you fill the universe with pre-biotic soup, and react amino acids at Planck time (very fast!) for 14 billion years, you are probably not going to get even 1 such protein. And you need at least 100 of them for minimal life functions, plus DNA and RNA.

Research performed by Doug Axe at Cambridge University, and published in the peer-reviewed Journal of Molecular Biology, has shown that the number of functional amino acid sequences is tiny:

Doug Axe’s research likewise studies genes that it turns out show great evidence of design. Axe studied the sensitivities of protein function to mutations. In these “mutational sensitivity” tests, Dr. Axe mutated certain amino acids in various proteins, or studied the differences between similar proteins, to see how mutations or changes affected their ability to function properly. He found that protein function was highly sensitive to mutation, and that proteins are not very tolerant to changes in their amino acid sequences. In other words, when you mutate, tweak, or change these proteins slightly, they stopped working. In one of his papers, he thus concludes that “functional folds require highly extraordinary sequences,” and that functional protein folds “may be as low as 1 in 1077.”

The problem of forming DNA by sequencing nucleotides faces similar difficulties. And remember, mutation and selection cannot explain the origin of the first sequence, because mutation and selection require replication, which does not exist until that first living cell is already in place.

2. Law:

The idea here is that components, such as nucleotides, might have special bonding affinities that might cause them to bond together spontaneously into functional sequences. Like if certain SCRABBLE tiles had an affinity for certain other tiles that caused them to bond together whenever they met.

Meyer writes:

Consider what would happen if the individual nucleotide “letters” in a DNA molecule did interact by chemical necessity with each other. Every time adenine (A) occurred in a growing genetic sequence, it would likely drag thymine (T) along with it. Every time cytosine (C) appeared, guanine (G) would follow. As a result, the DNA message text would be peppered with repeating sequences of A’s followed by T’s and C’s followed by G’s.

3. Self-organization:

The idea here is that some spontaneous order might arise due to some physical force, just like rocks sort themselves by size in a rock agitator because of gravity.

Meyer writes:

…just as magnetic letters can be combined and recombined in any way to form various sequences on a metal surface, so too can each of the four bases A, T, G, and C attach to any site on the DNA backbone with equal facility, making all sequences equally probable (or improbable). The same type of chemical bond occurs between the bases and the backbone regardless of which base attaches. All four bases are acceptable; none is preferred. In other words, differential bonding affinities do not account for the sequencing of the bases. Because these same facts hold for RNA molecules, researchers who speculate that life began in an “RNA world” have also failed to solve the sequencing problem…

Understanding what creates information

The bottom line is that in order for software code, or even English letters, to be functional, it needs to defy ordering mechanisms. Biological sequences are functional for the same reason that software code or English text is functional – because some intelligent agent chose an irregular sequence of characters in order to achieve a specific purpose. Look at the letters in this post – they are not ORDERED by physical laws. They are SELECTED by an intelligent agent.

Meyer writes:

To see the distinction between order and information, compare the sequence “ABABABABAB ABAB” to the sequence “Time and tide wait for no man.” The first sequence is repetitive and ordered, but not complex or informative.

What causes specified, complex sequences?

…the information contained in an English sentence or computer software does not derive from the chemistry of the ink or the physics of magnetism, but from a source extrinsic to physics and chemistry altogether. Indeed, in both cases, the message transcends the properties of the medium… Our experience with information–intensive systems (especially codes and languages) indicates that such systems always come from an intelligent source…

And this is what everybody means by “intelligent design”. This design inference came from the progress of science. The more we discovered about the cell, the more nature pointed towards a creative, designing intelligence. The only option left to atheists now is blind faith that the Flying Spaghetti Monster will swoop in and undo the progress of science over the last 100 years. Good luck with that, atheists!

Further study

One of my favorite resources on the origin of life is this interview from the University of California with former atheist and origin of life researcher Dean Kenyon. Kenyon, a professor of Biology at San Francisco State University, wrote the textbook on “chemical evolution”, which is the view that chemicals can arrange themselves in order to create the first living cell, without intervention.

This interview from the University of California with another origin of life researcher, Charles Thaxton, is also one of my favorites.

Original article: Could Life Have Originated Spontaneously on the Early Earth?

Harvard Talk: Postmodernism & the Mask of Compassion

The interview is brilliant and inspiring.

I have become a fast enthusiast of legitimate psychologists like Dr. Jordan B. Peterson who, armed with their decades of clinical experience, are standing up to the Far Left neo-Marxist berserkers and their craven, nihilistic policies and political stake-planting.

The mere fact men like Dr. Peterson have risked censorship and possible expulsion, up to and even being charged with a hate crime, merely for reminding people of the extant science behind biology, sex, gender and identity is chilling, and quickly reminds one of the darkest hours of the 20th century when the same nihilistic nonsense slaughtered 100+ million men, women, and children in Russia, Romania, China, Hungary, Germany, Cuba…

That the Far Left can so hypocritically deny their own roots proves the powerful hold the Father of Lies has over them.

Hugh Ross and Fazale Rana – Who was Adam?

Almost seven full hours of wonderfully detailed discussions on the biological, genetic, anatomical and paleo-anthropological development of modern man.