Tag Archives: biology

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?

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Undeniable: How Biology Confirms Our Intuition That Life is Designed by Douglas Axe

Undeniable 2

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.

Scientists Generate “Naïve” Pluripotent Stem Cells from Human Embryo

Researchers from the University of Cambridge have developed a new technique that allow us to derive stem cells from human embryos and reprogram them for medical use and research.

For the first time, scientists from the University of Cambridge have showed that is possible to derive naïve pluripotent stem cells from a human embryo. This is considered one of the most flexible types of stem cell, carrying the potential to develop into all types of human tissue aside from the placenta.

There are two sources of human pluripotent stem cells that are being used in medicinal or biomedical research: embryonic stem cells and induced pluripotent stem cells.

Embryonic stem cells are derived from fertilized egg cells, cells that are commonly discarded from IVF procedures. Pluripotent stem cells are skin cells that are reprogrammed to a pluripotent form. Typically these cells have already been “primed” into specific cell types, however “naïve” cells have had all instructions erased in order to make it much easier to direct them to whatever type of cell is needed.

Naïve-like human induced pluripotent stem cells had recently been created by reprogramming, however it had been unknown whether they could also be obtained directly from the human embryo.

When an egg cell is fertilized by a sperm, it begins to divide and replicate before the embryo takes shape. Around day five, the embryonic cells cluster together to form a structure called the ‘blastocyst’. This occurs before implantation into the uterus. The blastocyst comprises three cell types: cells that will develop into the placenta and allow the embryo to attach to the womb; cells that form the ‘yolk sac’ which provides nutrients to the developing fetus; and the ‘epiblast’ comprising the naïve cells that will develop into the future body.

A New Technique for Pluripotent Stem Cells

In a study published in Stem Cell Reports, a team of scientists from the Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute were able to remove cells from the blastocyst at day six, and grow them individually in culture. They separated the eggs and thus stopped the “communication” between them to prevent them being steered to a particular path of development.

The research was supported by the Medical Research Council, Biotechnology and Biological Sciences Research Council, Swiss National Science Foundation and the Wellcome Trust.

“Until now it hasn’t been possible to isolate these naïve stem cells, even though we’ve had the technology to do it in mice for thirty years – leading some people to doubt it would be possible,” explains Ge Guo, the study’s first author, “but we’ve managed to extract the cells and grow them individually in culture. Naïve stem cells have many potential applications, from regenerative medicine to modelling human disorders.”

In principle, these stem cells have no restrictions on what type of adult tissue they will develop into. Dr Jenny Nichols, joint senior author of the study, says that one of the most exciting applications of their new technique would be to study disorders that arise from cells that contain an abnormal number of chromosomes. Ordinarily, the body contains 23 pairs of identical chromosomes (22 pairs and one pair of sex chromosomes), but some children are born with additional copies, which can cause problems – for example, children with Down’s syndrome are born with three copies of chromosome 21.

“Even in many ‘normal’ early-stage embryos, we find several cells with an abnormal number of chromosomes,” explains Dr Nichols. “Because we can separate the cells and culture them individually, we could potentially generate ‘healthy’ and ‘affected’ cell lines. This would allow us to generate and compare tissues of two models, one ‘healthy’ and one that is genetically-identical other than the surplus chromosome. This could provide new insights into conditions such as Down’s syndrome.”

Original article: Scientists Generate “Naïve” Pluripotent Stem Cells from Human Embryo

MFN1 structures reveal nucleotide-triggered dimerization critical for mitochondrial fusion

Mitochondria are double-membraned organelles with variable shapes influenced by metabolic conditions, developmental stage, and environmental stimuli. Their dynamic morphology is a result of regulated and balanced fusion and fission processes. Fusion is crucial for the health and physiological functions of mitochondria, including complementation of damaged mitochondrial DNAs and the maintenance of membrane potential. Mitofusins are dynamin-related GTPases that are essential for mitochondrial fusion. They are embedded in the mitochondrial outer membrane and thought to fuse adjacent mitochondria via combined oligomerization and GTP hydrolysis. However, the molecular mechanisms of this process remain unknown. Here we present crystal structures of engineered human MFN1 containing the GTPase domain and a helical domain during different stages of GTP hydrolysis. The helical domain is composed of elements from widely dispersed sequence regions of MFN1 and resembles the ‘neck’ of the bacterial dynamin-like protein. The structures reveal unique features of its catalytic machinery and explain how GTP binding induces conformational changes to promote GTPase domain dimerization in the transition state. Disruption of GTPase domain dimerization abolishes the fusogenic activity of MFN1. Moreover, a conserved aspartate residue trigger was found to affect mitochondrial elongation in MFN1, probably through a GTP-loading-dependent domain rearrangement. Thus, we propose a mechanistic model for MFN1-mediated mitochondrial tethering, and our results shed light on the molecular basis of mitochondrial fusion and mitofusin-related human neuromuscular disorders14.

Full article: Mitochondrial Fusion

 

Fascinating article for biology fans.