Wintery Knight

…integrating Christian faith and knowledge in the public square

How likely is it for blind forces to sequence a functional protein by chance?

How likely is it that you could swish together amino acids randomly and come up with a sequence that would fold up into a functional protein?

Evolution News reports on research performed by Doug Axe at Cambridge University, and published in the peer-reviewed Journal of Molecular Biology.

Excerpt:

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.10 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 10^77.”11 The extreme unlikelihood of finding functional proteins has important implications for intelligent design.

Just so you know, those footnotes say this:

[10.] Douglas D. Axe, “Estimating the Prevalence of Protein Sequences Adopting Functional Enzyme Folds,” Journal of Molecular Biology, 1-21 (2004); Douglas D. Axe, “Extreme Functional Sensitivity to Conservative Amino Acid Changes on Enzyme Exteriors,” Journal of Molecular Biology, Vol. 301:585-595 (2000).

[11.] Douglas D. Axe, “Estimating the Prevalence of Protein Sequences Adopting Functional Enzyme Folds,” Journal of Molecular Biology, 1-21 (2004).

And remember, you need a lot more than just 1 protein in order to create even the simplest living system. Can you generate that many proteins in the short time between when the Earth cools and the first living cells appear? Even if we spot the naturalist a prebiotic soup as big as the universe, and try to make sequences as fast as possible, it’s unlikely to generate even one protein in the time before first life appears.

Here’s Doug Axe to explain his research:

If you are building a protein for the FIRST TIME, you have to get it right all at once – not by building up to it gradually using supposed Darwinian mechanisms. That’s because there is no replication before you have the first replicator. The first replicator cannot rely on explanations that require replication to already be in place.

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Study: the early Earth’s atmosphere contained oxygen

Here’s a paper published in the prestigious peer-reviewed science journal Nature, entitled “The oxidation state of Hadean magmas and implications for early Earth’s atmosphere”. This paper is significant because it undermines naturalistic scenarios for the origin of life.

Evolution News explains what the paper is about.

Excerpt:

A recent Nature publication reports a new technique for measuring the oxygen levels in Earth’s atmosphere some 4.4 billion years ago. The authors found that by studying cerium oxidation states in zircon, a compound formed from volcanic magma, they could ascertain the oxidation levels in the early earth. Their findings suggest that the early Earth’s oxygen levels were very close to current levels.

[...]Miller and Urey conducted experiments to show that under certain atmospheric conditions and with the right kind of electrical charge, several amino acids could form from inorganic compounds such as methane, ammonia, and water. Several experiments have been done using various inorganic starting materials, all yielding a few amino acids; however, one key aspect of all of these experiments was the lack of oxygen.

If the atmosphere has oxygen (or other oxidants) in it, then it is an oxidizing atmosphere. If the atmosphere lacks oxygen, then it is either inert or a reducing atmosphere. Think of a metal that has been left outside, maybe a piece of iron. That metal will eventually rust. Rusting is the result of the metal being oxidized. With organic reactions, such as the ones that produce amino acids, it is very important that no oxygen be present, or it will quench the reaction. Scientists, therefore, concluded that the early Earth must have been a reducing environment when life first formed (or the building blocks of life first formed) because that was the best environment for producing amino acids. The atmosphere eventually accumulated oxygen, but life did not form in an oxidative environment.

The problem with this hypothesis is that it is based on the assumption that organic life must have formed from inorganic materials. That is why the early Earth must have been a reducing atmosphere. Research has been accumulating for more than thirty years, however, suggesting that the early Earth likely did have oxygen present.

[...]Their findings not only showed that oxygen was present in the early Earth atmosphere, something that has been shown in other studies, but that oxygen was present as early as 4.4 billion years ago. This takes the window of time available for life to have begun, by an origin-of-life scenario like the RNA-first world, and reduces it to an incredibly short amount of time. Several factors need to coincide in order for nucleotides or amino acids to form from purely naturalistic circumstances (chance and chemistry). The specific conditions required already made purely naturalist origin-of-life scenarios highly unlikely. Drastically reducing the amount of time available, adding that to the other conditions needing to be fulfilled, makes the RNA world hypothesis or a Miller-Urey-like synthesis of amino acids simply impossible.

So here’s where we stand. If you are a materialist, then you need a reducing environment on the early Earth in order to get organic building blocks (amino acids) from inorganic materials. However, the production of these organic building blocks (amino acids) requires that the early Earth atmosphere be oxygen-free. And the problem with this new research, which confirms previous research, is that the early Earth contained huge amounts of oxygen – the same amount of oxygen as we have today. This is lethal to naturalistic scenarios for creating the building blocks of life on the Earth’s surface.

Other problems

If you would like to read a helpful overview of the problems with a naturalistic scenario for the origin of life, check out this article by Casey Luskin.

Excerpt:

The “origin of life” (OOL) is best described as the chemical and physical processes that brought into existence the first self-replicating molecule. It differs from the “evolution of life” because Darwinian evolution employs mutation and natural selection to change organisms, which requires reproduction. Since there was no reproduction before the first life, no “mutation – selection” mechanism was operating to build complexity. Hence, OOL theories cannot rely upon natural selection to increase complexity and must create the first life using only the laws of chemistry and physics.

There are so many problems with purely natural explanations for the chemical origin of life on earth that many scientists have already abandoned all hopes that life had a natural origin on earth. Skeptical scientists include Francis Crick (solved the 3-dimensional structure of DNA) and Fred Hoyle (famous British cosmologist and mathematician), who, in an attempt to retain their atheistic worldviews, then propose outrageously untestable cosmological models or easily falsifiable extra-terrestrial-origin-of-life / panspermia scenarios which still do not account for the natural origin of life. So drastic is the evidence that Scientific American editor John Horgan wrote, “[i]f I were a creationist, I would cease attacking the theory of evolution … and focus instead on the origin of life. This is by far the weakest strut of the chassis of modern biology.”3

The article goes over the standard problems with naturalistic scenarios of the origin of life: wrong atmosphere, harmful UV radiation, interfering cross-reactions, oxygen levels, meteorite impacts, chirality, etc.

Most people who are talking about intelligent design at the origin of life talk about the information problem – how do you get the amino acids to form proteins and how do you get nucleotide bases to code for amino acids? But the starting point for solving the sequencing problem is the construction of the amino acids – there has to be a plausible naturalistic scenario to form them.

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Scientists troubled by lack of simple explanation for our life-permitting moon

This entire article from Evolution News is a must-read. It talks about a recent paper by a naturalist named Robin Canup which appeared in Nature, the most prestigious peer-reviewed science journal.

So, there’s too much to quote here. I’ll grab a few snippets to give you the gist of it, then you click through and read the whole thing. 

The moon is important for the existence of a life permitting planet:

Canup knows our moon is important for life:

The Moon is more than just a familiar sight in our skies. It dictates conditions on Earth. The Moon is large enough to stabilize our planet’s rotation, holding Earth’s polar axis steady to within a few degrees. Without it, the current Earth’s tilt would vary chaotically by tens of degrees. Such large variationsmight not preclude life, but would lead to a vastly different climate.

The moon requires an improbable sequence of events:

Canup states that “No current impact model stands out as more compelling than the rest.” All are equally improbable, in other words. Indeed, they are:

It remains troubling that all of the current impact models invoke a process after the impact to effectively erase a primary outcome of the event — either by changing the disk’s composition through mixing for the canonical impact, or by changing Earth’s spin rate for the high-angular-momentum narratives.

Sequences of events do occur in nature, and yet we strive to avoid such complexity in our models. We seek the simplest possible solution, as a matter of scientific aesthetics and because simple solutions are often more probable. As the number of steps increases, the likelihood of a particular sequence decreases. Current impact models are more complex and seem less probable than the original giant-impact concept.

This is a good challenge to naturalism, but it lends support to one part of the habitability argument.

Previously, I blogged about a few of the minimum requirements that a planet must satisfy in order to support complex life.

Here they are:

  • a solar system with a single massive Sun than can serve as a long-lived, stable source of energy
  • a terrestrial planet (non-gaseous)
  • the planet must be the right distance from the sun in order to preserve liquid water at the surface – if it’s too close, the water is burnt off in a runaway greenhouse effect, if it’s too far, the water is permanently frozen in a runaway glaciation
  • the solar system must be placed at the right place in the galaxy – not too near dangerous radiation, but close enough to other stars to be able to absorb heavy elements after neighboring stars die
  • a moon of sufficient mass to stabilize the tilt of the planet’s rotation
  • plate tectonics
  • an oxygen-rich atmosphere
  • a sweeper planet to deflect comets, etc.
  • planetary neighbors must have non-eccentric orbits

This is a good argument, so if you want to learn more about it, get the “The Privileged Planet” DVD, or the book of the same name.

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How Earth-like are the 8.8 billion Earth-like planets from a recent estimate?

Previously, I blogged about a few of the minimum requirements that a planet must satisfy in order to support complex life.

Here they are:

  • a solar system with a single massive Sun than can serve as a long-lived, stable source of energy
  • a terrestrial planet (non-gaseous)
  • the planet must be the right distance from the sun in order to preserve liquid water at the surface – if it’s too close, the water is burnt off in a runaway greenhouse effect, if it’s too far, the water is permanently frozen in a runaway glaciation
  • the solar system must be placed at the right place in the galaxy – not too near dangerous radiation, but close enough to other stars to be able to absorb heavy elements after neighboring stars die
  • a moon of sufficient mass to stabilize the tilt of the planet’s rotation
  • plate tectonics
  • an oxygen-rich atmosphere
  • a sweeper planet to deflect comets, etc.
  • planetary neighbors must have non-eccentric orbits

Now what happens if we disregard all of that, and just classify an Earth-like planet as one which only has to potentially support liquid water at the surface? Well, you get a very high estimate of Earth-like planets.

Science journalist Denyse O’Leary responds to a recent estimate based on this questionable criterion, which placed the number of Earth-like planets at 8.8 billion.

Excerpt: (links removed)

A current official definition of habitable planets is “in the zone around the star where liquid water could exist,” but the ones discovered so far are unsuitable in many other ways.

Then a new cosmology term hit the media, “super-Earths.” It means “bigger than Earth,” but smaller than gas giant Neptune. Super-Earths could be the most numerous type of planet, in tight orbits around their star — which is actually bad news for life.Nonetheless, some insist, they may be more attractive to life than Earth is. Indeed, the Copernican Principle allows us to assume that some are inhabited already.

In reality, even the rocky exoplanets (known as of early 2013) that are Earth-sized are not Earth-like. For example, the Kepler mission’s first rocky planet find is described as follows: “Although similar in size to Earth, its orbit lasts just 0.84 days, making it likely that the planet is a scorched, waterless world with a sea of lava on its starlit side.” As space program physicist Rob Sheldon puts it, Earth is a rocky planet but so is a solid chunk of iron at 1300 degrees orbiting a few solar radii above the star. In any event, a planet may look Earth-like but have a very different internal structure and atmosphere.”

David Klinghoffer notes that the study is estimating that 8.8 billion number, but the actual number of Earth-like planets we can see is much lower.

He writes:

The study is supposed to be a major step forward because of its unprecedented accuracy:

For the first time, scientists calculated — not estimated — what percent of stars that are just like our sun have planets similar to Earth: 22 percent, with a margin of error of plus or minus 8 percentage points.

Oh! You see, they calculated. They didn’t just estimate.

Because there are probably hundreds of planets missed for every one found, the study did intricate extrapolations to come up with the 22 percent figure — a calculation that outside scientists say is fair.

Oh. They calculated in the sense of “extrapolating” to “come up” with a figure. In other words, they estimated. The figure of “8.8 billion stars with Earth-size planets in the habitable temperature zone” comes down a bit too when you talk about actual planets that have been observed instead of being merely conjectured and “calculated.”

Scientists at a Kepler science conference Monday said they have found 833 new candidate planets with the space telescope, bringing the total of planets they’ve spotted to 3,538, but most aren’t candidates for life.

Kepler has identified only 10 planets that are about Earth’s size circling sun-like stars and are in the habitable zone, including one called Kepler 69-c.

Ah hah. So from the initial, trumpets-blaring figure of 8.8 billion we’re down more realistically to 10. Not 10 billion, just 10. Meanwhile the silence from space continues absolutely unabated.

That’s the way it tends to go with stories like this, the blaring headline and the inevitable letdown.

One part of the AP press release makes the point that the estimate does not include all the minimum requirements for life. For example, you need an atmosphere, as I stated above. Do the estimated 8.8 billion Earth-like planets have an Earth-like atmosphere? How about an oxygen-rich atmosphere, do the 8.8 billion Earth-like planets have that?

NO:

The next step, scientists say, is to look for atmospheres on these planets with powerful space telescopes that have yet to be launched. That would yield further clues to whether any of these planets do, in fact, harbor life.

You know, after the whole global warming hoax, you would think that these headline writers would have learned their lesson about sensationalizing wild-assed guesses in order to scare up more research money. But a lot of true-believing naturalists are just going to read the headline and not the rest of the article, and they will never know that they’ve been had. Again. I love experimental science, but I don’t love the politicization of science. 

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Formation of life-permitting elements carbon and oxygen is fine-tuned

First, let’s review the structure of the fine-tuning argument.

The argument goes like this:

  1. The fine-tuning of the universe to support life is either due to law, chance or design
  2. It is not due to law or chance
  3. Therefore, the fine-tuning is due to design

Here are the facts on the fine-tuning:

  • Life has certain minimal requirements; long-term stable source of energy, a large number of different chemical elements, an element that can serve as a hub for joining together other elements into compounds, a universal solvent, etc.
  • In order to meet these minimal requirements, the physical constants, (such as the gravitational constant), and the ratios between physical constants, need to be withing a narrow range of values in order to support the minimal requirements for life of any kind.
  • Slight changes to any of the physical constants, or to the ratios between the constants, will result in a universe inhospitable to life.
  • The range of possible values spans 70 orders of magnitude.
  • The constants are selected by whoever creates the universe. They are not determined by physical laws. And the extreme probabilities involved required put the fine-tuning beyond the reach of chance.
  • Although each individual selection of constants and ratios is as unlikely as any other selection, the vast majority of these possibilities do not support the minimal requirements of life of any kind. (In the same way as any hand of 5 cards that is dealt is as likely as any other, but you are overwhelmingly likely NOT to get a royal flush. In our case, a royal flush is a life-permitting universe).

Carbon is that element that can serve as a hub, and oxygen is also a vital element, since it is a component of water, which is required for life. So both carbon (the hub of large molecules) and oxygen (a building block of water) are required for complex life of any imaginable kind.

Now for the study.

Mysterious Jen, who blogs at Victory Rolls and V8s sent me this amazing article on Science Daily about a new peer-reviewed study that supports the fine-tuning argument.

Here’s an excerpt:

Life as we know it is based upon the elements of carbon and oxygen. Now a team of physicists, including one from North Carolina State University, is looking at the conditions necessary to the formation of those two elements in the universe. They’ve found that when it comes to supporting life, the universe leaves very little margin for error.

Both carbon and oxygen are produced when helium burns inside of giant red stars. Carbon-12, an essential element we’re all made of, can only form when three alpha particles, or helium-4 nuclei, combine in a very specific way. The key to formation is an excited state of carbon-12 known as the Hoyle state, and it has a very specific energy — measured at 379 keV (or 379,000 electron volts) above the energy of three alpha particles. Oxygen is produced by the combination of another alpha particle and carbon.

NC State physicist Dean Lee and German colleagues Evgeny Epelbaum, Hermann Krebs, Timo Laehde and Ulf-G. Meissner had previously confirmed the existence and structure of the Hoyle state with a numerical lattice that allowed the researchers to simulate how protons and neutrons interact. These protons and neutrons are made up of elementary particles called quarks. The light quark mass is one of the fundamental parameters of nature, and this mass affects particles’ energies.

In new lattice calculations done at the Juelich Supercomputer Centre the physicists found that just a slight variation in the light quark mass will change the energy of the Hoyle state, and this in turn would affect the production of carbon and oxygen in such a way that life as we know it wouldn’t exist.

[...]The researchers’ findings appear in Physical Review Letters.

So that’s the latest research that supports the fine-tuning argument. But how effective is this argument really? Is it only admitted by theists, or do atheists accept the fine-tuning as well?

Is the fine-tuning real?

Yes, it’s real and it is conceded by the top-rank of atheist physicists. Let me give you a citation from the best one of all, Martin Rees. Martin Rees is an atheist and a qualified astronomer. He wrote a book called “Just Six Numbers: The Deep Forces That Shape The Universe”, (Basic Books: 2001). In it, he discusses 6 numbers that need to be fine-tuned in order to have a life-permitting universe.

Rees writes here:

These six numbers constitute a ‘recipe’ for a universe. Moreover, the outcome is sensitive to their values: if any one of them were to be ‘untuned’, there would be no stars and no life. Is this tuning just a brute fact, a coincidence? Or is it the providence of a benign Creator?

There are some atheists who deny the fine-tuning, but these atheists are in firm opposition to the progress of science. The more science has progressed, the more constants, ratios and quantities we have discovered that need to be fine-tuned. Science is going in a theistic direction. Next, let’s see how atheists try to account for the fine-tuning, on atheism.

Atheistic responses to the fine-tuning argument

There are two common responses among atheists to this argument.

The first is to speculate that there are actually an infinite number of other universes that are not fine-tuned, (i.e. – the gambler’s fallacy). All these other universes don’t support life. We just happen to be in the one universe is fine-tuned for life. The problem is that there is no way of directly observing these other universes and no independent evidence that they exist.

Here is an excerpt from an article in Discover magazine, (which is hostile to theism and Christianity).

Short of invoking a benevolent creator, many physicists see only one possible explanation: Our universe may be but one of perhaps infinitely many universes in an inconceivably vast multiverse. Most of those universes are barren, but some, like ours, have conditions suitable for life.

The idea is controversial. Critics say it doesn’t even qualify as a scientific theory because the existence of other universes cannot be proved or disproved. Advocates argue that, like it or not, the multiverse may well be the only viable non­religious explanation for what is often called the “fine-tuning problem”—the baffling observation that the laws of the universe seem custom-tailored to favor the emergence of life.

The second response by atheists is that the human observers that exist today, 14 billion years after the universe was created out of nothing, actually caused the fine-tuning. This solution would mean that although humans did not exist at the time the of the big bang, they are going to be able to reach back in time at some point in the future and manually fine-tune the universe.

Here is an excerpt from and article in the New Scientist, (which is hostile to theism and Christianity).

…maybe we should approach cosmic fine-tuning not as a problem but as a clue. Perhaps it is evidence that we somehow endow the universe with certain features by the mere act of observation… observers are creating the universe and its entire history right now. If we in some sense create the universe, it is not surprising that the universe is well suited to us.

So, there are two choices for atheists. Either an infinite number of unobservable universes that are not fine-tuned, or humans go back in time at some future point and fine-tune the beginning of the universe, billions of years in the past. I think I will prefer the design explanation to those alternatives.

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