When Chemists Speak Baloney About Peptides

Like some seedy honkytonk used-car sales lot where "anything goes," the world of so-called "science news" nowadays is a hall-of-mirrors "carnival barker" world in which truth is all mixed up with hype and misleading claims. These days most science news comes from press releases written by the copy writers of corporate and university press offices, who are notorious for making claims not warranted by anything found in the scientific papers they are promoting, and who often lack strong knowledge of the complex and deep topics being discussed. Moreover, quotes by professors in press releases are often wildly inaccurate. The professors know that the more paper citation counts they get, the more highly they are rated. Sadly, many a professor asked about his latest research will make some sensationalist claim that simply isn't true, to make his research sound like something much more worthy of attention and citation than it is. By reading my 47 posts with the label "overblown hype," you can find countless examples of lies and misleading statements that appeared in articles I found while reading the so-called "science news."

Some of the worst examples of phony-baloney "science news" comes when the topic of abiogenesis is discussed. Abiogenesis is the idea that life can naturally arise from non-life. Everything we know about the complexity and amount of organization in living things argues against this idea. Even the simplest living thing is a cell that requires hundreds of different types of protein molecules to exist and reproduce. Each of those types of protein molecules is a separate complex invention as unlikely to arise by chance as a well-written 100-word paragraph from a random arrangement of shells and pebbles and seaweed at a seashore.

There are no experiments supporting the idea of abiogenesis. No one has ever produced a living thing from any experiment realistically simulating lifeless early Earth conditions. No one has ever produced a functional protein molecule (one of the building blocks of one-celled life) from any experiment realistically simulating early Earth conditions. No one has ever even produced one of the building blocks of the building blocks of one-celled life (an amino acid) from any experiment realistically simulating early Earth conditions. The Miller-Urey experiment which produced some amino acids was not a realistic simulation of early Earth conditions, for reasons discussed in my post here. The apparatus used by the Miller-Urey experiment was a manufacturing device unlike anything that would have existed in the early Earth. We have had seventy years of lies from the mainstream press about the Miller-Urey experiment, claims that it revealed something that it did not actually reveal. 

The latest bit of untrue news in the long, long series of very misleading news stories about the origin of life is a pure baloney press release from Purdue University with the extremely untrue headline "The fountain of life: Water droplets hold the secret ingredient for building life." 

We read that Purdue University chemists have discovered a path by which two amino acids can form into a peptide. That is as unimpressive a result as "one plus one equals two." 

The basic facts are these:

(1) There are twenty types of amino acids used by the proteins in living organisms, with each amino acid being a particular arrangement of between 9 and about 25 atoms. 

(2) When two or a few amino acids combine, they form something called a peptide. 

(3) To produce the starting point of a functional protein molecule, you need hundreds of amino acids arranged in just the right way to form a very long molecule that is called a polypeptide.

(4) To produce a molecule with biological function, such a polypeptide has to somehow do a  very hard-to-achieve thing called folding, so that a very special and complex three-dimensional shape arises, which can serve as a functional protein molecule. We see one of those shapes in the visual below. 

(5) Just as it is not at all true that any old combination of hundreds of letters produces functional meaningful paragraphs, it is not at all true that any old combination of hundreds of amino acids produces a functional protein molecule. There is every reason to believe that within the set of all possible polypeptide chains, not even 1 in  1,000,000,000,000,000,000,000,000 are polypeptide chains that lead to functional protein molecules. Similarly, within the the set of all random character 400-character combinations, not even 1 in 1,000,000,000,000,000,000,000,000 result in meaningful, functional instructions. The number of combinations of amino acids that do not result in functional folding protein molecules is almost infinitely greater than the relatively tiny number of combinations of amino acids that do result in functional folding protein molecules like the one shown below, just as the number of combinations of letters resulting in unreadable nonsense is almost infinitely greater than the number of such combinations resulting in functional instructions. 

(6) A living cell capable of reproduction requires hundreds of different types of protein molecules, just as a complex computer requires hundreds of different subroutines, most being a well-arranged set of hundreds of individual characters. The amino acid sequence needed to make a protein is specified in a particular gene in the organism's DNA. Humans have about 20,000 genes, but one-celled microbes  require far fewer genes. A team of 9 scientists wrote a scientific paper entitled, “Essential genes of a minimal bacterium.” It analyzed a type of bacteria (Mycoplasma genitalium) that has “the smallest genome of any organism that can be grown in pure culture.” According to wikipedia's article, this bacteria has 525 genes consisting of 580,070 base pairs. The paper concluded that 382 of this bacteria's protein-coding genes (72 percent) are essential. So multiplying that 580,070 by 72 percent, we get a figure of about 418,000 base pairs in the genome that are essential functionality. This is all information that must be arranged in just the right way for the tiny microbe to be capable of self-reproduction. Even the simplest living thing capable of self-reproduction requires hundreds of protein molecules, and hundreds of genes specifying the amino acid sequence of such protein molecules. Each type of protein molecule has a unique sequence of hundreds of amino acids. 

One of thousands of protein molecule shapes (Credit: RCSB Protein Data Bank)

All that is pretty complicated, but nothing could be simpler than what the press release is reporting. It is reporting merely one amino acid combining with another amino acid to produce a mere peptide. Just like a two-character string such as "AB" doesn't get you anywhere if you are trying to produce software, a peptide of two amino acids doesn't get you anywhere if you are trying to make a living thing. By using the term "dipeptide" the scientific paper makes clear that all that was found was a peptide of merely two amino acids. A dipeptide is a molecule consisting of only two amino acids connected to each other. 

But the Purdue University press release quotes a chemist stating the following outrageous baloney:

" 'This is essentially the chemistry behind the origin of life,' said Graham Cooks. He is the Henry Bohn Hass Distinguished Professor of Analytical Chemistry in Purdue’s College of Science. 'This is the first demonstration that primordial molecules, simple amino acids, spontaneously form peptides, the building blocks of life, in droplets of pure water.'  " 

Hogwash. Bunk. Pure unadulterated baloney. The chemistry needed to start a living thing would be almost infinitely more complicated than the mere combination of two amino acids to make a peptide. It is not peptides that are the building blocks of one-celled life, but vastly more complicated molecules (protein molecules).  Claiming that you have produced "the chemistry behind the origin of life" by merely making a peptide from two amino acids is as pure baloney a statement as claiming that you wrote a good 100-page instruction manual  when you merely combined one letter (such as the character "A") with another letter, such as the character "B."  

Very eager to pick up page views that make money from people viewing ads on their web pages, mainstream online web sites these days always uncritically parrot whatever nonsense is being trumpeted by university press releases, no matter how transparently absurd the assertions are. So we heard many a web site uncritically parrot the rubbish in the Purdue University press release. One headline was "The Fountain of Life: Scientists Uncover the 'Chemistry Behind the Origin of Life.' " The Popular Science site had a nonsense headline of "Here’s how life on Earth might have formed out of thin air and water."  

Apparently the Popular Science writer has got the incorrect idea that the two amino acids that combined to make a lowly peptide were produced from scratch from water and thin air. That's impossible, because the amino acids involved (glycine and L-alanine) contain carbon atoms that are not found anywhere in water (H₂O) and thin air consisting of nitrogen and oxygen.  Given that the paper  makes no claim at all to have produced amino acids from scratch or through any natural process, we may presume with high likelihood that the scientists added to water some amino acids that were not naturally produced.  Referring to a highly artificial high-tech manufacturing processing involving "electrified nano-sprays that were blasted at a mass spectrometer," the Salon article on the experiment suggests that the amino acids were not naturally produced, telling us this: "The sprays were filled with two amino acids, glycine or L-alanine, and squirted out of an opening just a few millionths of a meter across." Such a manufacturing process is unlike anything that would have occurred in the natural world, where there are no electrified super-fast water jets aimed at microscopic holes. 

The word "spontaneous" used in the quote above by Graham Cooks is a word meaning "performed or occurring as a result of a sudden inner impulse or inclination and without premeditation or external stimulus." Instead of observing anything like any natural "spontaneous formation," the scientists produced the unimpressive combination of two amino acids using a high-voltage technique called electrospray ionization, which uses a very fancy piece of hi-tech equipment (like this) to produce chemical reactions. Claiming that the result from the use of such high-voltage equipment was "spontaneous" is as misleading as electrocuting an animal in an electric chair and then claiming the animal's death was "spontaneous." 

The same type of hogwash and baloney peddled by Graham Cooks in the quote above is given us by another chemist named Nick Lane. In a recent interview in Quanta Magazine, Lane states this bunk:

"So you have a random sequence of RNA that generates a nonrandom peptide. And that nonrandom peptide could by chance have some function in a growing proto-cell. It could make the cell grow better or grow worse; it could help the RNA replicate itself; it could bind to cofactors. Then you have selection for that peptide and the RNA sequence that gave rise to it. Although it’s a very rudimentary system, this means we’ve just entered the world of genes, information and natural selection."

This is nonsense. Peptides (combinations of only a few amino acids) don't produce biological functions. It requires vastly more complicated and vastly more hard-to-achieve molecules called proteins (consisting of hundreds of well-arranged amino acids) before you can get any biological benefit. It would be exponentially harder (like a billion trillion quadrillion times harder) for natural processes to produce a functional protein molecule than for natural processes to produce a mere peptide. And you can't get any so-called natural selection until you have a living, self-reproducing cell, which requires hundreds of different types of proteins, each consisting of very special arrangements of hundreds of amino acids, not just two or three of them. And how silly is it to claim that you have "entered the world of genes" from some event which merely formed a peptide? Genes are parts of a DNA molecule, something totally different (and vastly more complicated)  than a mere peptide. 

When origin-of-life theorists talk about "proto-cells" they mean merely fatty bubbles. Lane's insinuation that all you need is a proto-cell (a fatty bubble) and a peptide to get life rolling is every bit as false as claiming that a child can survive okay if it is born with only a tooth and a fingernail -- no brain, no heart, no stomach, no liver, no kidneys, but only a tooth and a fingernail. 

I can give you a good analogy for the baloney hogwash claims made in the Purdue University press release quoted above. Imagine if someone were to train his dog to move two wooden letter blocks together, training the dog to push the little blocks by using the dog's nose. Suppose that person were to then claim that this proved that dogs can write long useful instruction manuals, because when people write books it is "essentially the same" as the dog combining two letters with his nose. How should you respond to such a person? By saying something like this:

"What, do you think I'm the stupidest person in the world? Do you think I have an IQ of only 1 or 2 points?" 

Postscript: We get more of Nick Lane's baloney about life's origins in the interview here. It includes this false-as-false-can-be statement:

"What we are beginning to learn is that if we find carbon dioxide and hydrogen in a specific environment most of metabolism happens spontaneously. It recapitulates in the absence of genes and cells."

.

Metabolism is defined as "the chemical processes that occur within a living organism in order to maintain life." No metabolism has occurred in Lane's origin-of-life experiments, which have not produced life, have not produced genes, have not produced cells, have not produced proteins,  and have not even produced any of the building blocks of the building blocks of life (amino acids) in any experiment realistically simulating early Earth conditions. 

Scientists Keep Speaking Unrealistically About Life's Origin

The concept of abiogenesis is the idea that life can naturally arise from non-life. This is a concept that has zero basis in observational science or theoretical science. No one has ever done an experiment supporting the idea that life can naturally arise from non-life. There is no truth in claims such as claims that experiments such as the Miller-Urey experiment did anything to support claims about abiogenesis.  In multiple ways the Miller-Urey experiment failed to realistically simulate early Earth conditions; and the outputs of the Miller-Urey experiment (mere amino acids) were no more a living thing than a handful of nuts and bolts is a working digital computer. As described in my recent post "When Hi-Tech Manufacturing Is Passed Off as Evolution," some of the results that are being passed off these days as being supportive of the concept of abiogenesis are cases in which hi-tech manufacturing results are being passed off as examples of evolution, which is an example of extremely misleading speech.

Our scientists sometimes make wildly unrealistic statements on this topic.  An example can be found on the page here. An astronomer named Steven Vogt speaks about a planet called Gliese 581g, a possibly nonexistent extrasolar planet that may be in the "Goldilocks zone" around its star, neither too far from it nor too close to it. No one has even discovered either liquid water on this planet or oxygen in its atmosphere. We are not even sure that the planet exists, because the Wikipedia.org article on the planet states the following:

"Gliese 581g...unofficially known as Zarmina (or Zarmina's World), is an unconfirmed (and frequently disputed) exoplanet claimed to orbit within the Gliese 581 system, twenty light-years from Earth. It was discovered by the Lick–Carnegie Exoplanet Survey, and is the sixth planet orbiting the star; however, its existence could not be confirmed by the European Southern Observatory (ESO) / High Accuracy Radial Velocity Planet Searcher (HARPS) survey team, and its existence remains controversial. It is thought to be near the middle of the habitable zone of its star. That means it could sustain liquid water—a necessity for all known life—on its surface, if there are favorable atmospheric conditions on the planet." 

Even though the very existence of this planet is uncertain (as indicated by the statements above), Steven Vogt is quoted as saying that he is 100% sure that the planet contains life.  Below (from an article on www.space.com) is a quote that reveals a whole lot of wishful thinking going on:

" 'Personally,given the ubiquity and propensity of life to flourish wherever it can, I would say, my own personal feeling is that the chances of life on this planet are 100 percent,' said Steven Vogt, a professor of astronomy and astrophysics at the University of California, Santa Cruz, during a press briefing today. 'I have almost no doubt about it.'

His colleague, Paul Butler of the Carnegie Institution of Washington, in Washington, D.C., wasn't willing to put a number on the odds of life, though he admitted he's optimistic.

'It's both an incremental and monumental discovery,' Sara Seager, an astrophysicist at the Massachusetts Institute of Technology, told SPACE.com. Incremental because the method used to find Gliese 581g already has found several planets most of the known planets, both super-Earths, more massive than our own world outside their stars' habitable zone, along with non-Earth-like planets within the habitable zone.

'It really is monumental if you accept this as the first Earth-like planet ever found in the star's habitable zone,' said Seager, who was not directly involved in the discovery."

Vogt's statement was not one with any sound scientific basis. It is a statement based on his own personal preferences, as he reveals by confessing that he is speaking based on "my own personal feeling." The rationale given for the opinion makes no sense. It is not true that life is ubiquitous; it does not exist everywhere. No life exists on the moon. As best we can determine, there is no life on Venus. A recent article suggests that claims of a phosphine signal of life on Venus was just a false alarm. A poll of planetary scientists revealed that only a quarter of them think that life could exist now on Mars.  The propensity of life to flourish wherever it can is a different thing from the likelihood of life naturally arising, and the two things should not be confused. 

As for Seager's language, it was the type of speech that gives you the wrong idea. A planet on which life has not been discovered is referred to as an "Earth-like planet." No planet should ever be called Earth-like until the existence of life has been confirmed on that planet. 

There is the strongest reason why it is utterly unrealistic to estimate a 100% probability of life accidentally originating on some planet on which life has never been detected. The reason is that even the simplest microbial life involves a state of organization so vast that we should never expect it to be arising accidentally, even given trillions of planets of just the right type existing at just the right distance from a sun-like star. 

Natural selection does not fix the impossible odds prohibiting the natural origin of hundreds of genes and protein types needed at the very beginning, at the origin of life, before Darwinian evolution has started. A team of 9 scientists wrote a scientific paper entitled, “Essential genes of a minimal bacterium.” It analyzed a type of bacteria (Mycoplasma genitalium) that has “the smallest genome of any organism that can be grown in pure culture.” According to wikipedia's article, this bacteria has 525 genes consisting of 580,070 base pairs. The paper concluded that 382 of this bacteria's protein-coding genes (72 percent) are essential. Life can't get started until there arises in one tiny spot a vast amount of functional information, about as much functional information as in a 300-page technical manual.  We would never expect so much information to arise accidentally, even giving trillions of years and trillions of planets on which accidental chemical combinations can occur. 

Experiments have provided no support for claims such as Vogt's. In experiments realistically simulating early Earth conditions, there has never even arisen a single functional protein molecule. But many types of such very complex molecules would need to arise simultaneously for life to arise from non-life. Experiments realistically simulating early Earth conditions will produce neither the building blocks of one-celled life (protein molecules) nor the building blocks of the building blocks of one-celled life (amino acids and nucleotide base pairs). 

So why do people such as Vogt make claims such as he made? Probably what is going on is mainly ideology and psychology.  Faced with an unpleasant improbability, the human mind is prone to assert a 100% likelihood, rather than admit an improbability such a mind would prefer not to recognize.  Asserting such a 100% likelihood is a great way of kind of mentally squashing some possibility you don't want to recognize.  So, for example, on your wedding day you may tell yourself that there's a 100% likelihood that your spouse will always be faithful to you, rather than realistically conceding some small chance that some day your spouse might be unfaithful. 

Were scientists to realistically calculate the chance of life arising from non-life, they would have to say that such an origination would require some miracle of luck on the same order of someone throwing a deck of cards into the air and having them all form into a house of cards.  But many a scientist prefers not to recognize fortune so improbable in the past. The easiest way to cover-up such miracles of chance is to claim that they are inevitable. But that's as foolish as someone claiming that if you keep throwing decks of cards into the air, one day your toss will luckily form into a house of cards. When scientists such as Vogt say that they are 100% sure that a planet has life when we are not even sure that such a planet exists, that is a very good sign that what is going on is psychology, wishful thinking and ideology rather than realistic mathematical calculation. 

Quanta Magazine has a recent interview with origin-of-life researchers. We have more unrealistic talk and a conspicuous lack of straight talk. Jack Szostak says, "We used to think that life definitely started with just RNA, because we were thinking about ribozymes, RNA catalysts, RNA’s roles in modern cells." Then Szostak paints a portrait of the origin of life that senselessly leaves out the key ingredients of protein molecules. He states this:

"Okay, so, so I think we have to think about some environment on the surface of the Earth, some kind of shallow lake or pond where the building blocks of RNA were made and accumulated, along with lipids and other molecules relevant to biology. And then they self-assembled into lipid vesicles encapsulating RNA, under conditions where the RNA could start to replicate driven by energy from the sun. And that would allow Darwinian evolution to get started. So that the, some RNA sequences that did something useful for the protocell that they’re in would confer an advantage, those protocells would start to take over the population. And then you’re off and running, and life can gradually get more complex and evolve to spread to different environments, until you end up with what we see around us today." 

The idea that life can get started with just RNA and fatty bubbles (only a few of the many types of very complex molecules needed for even the simplest living thing) is utterly unrealistic silly talk, as goofy as saying that you can get a car by having only a steering wheel and an axle. The only reason scientists make these kind of goofy  statements is that they have no realistic explanations for how a living thing with all of its minimal requirements could have arisen from non-life. The long discussion in the interview includes no realistic talk of the difficulty of explaining the origin of very complex protein molecules, which is the principle difficulty of explaining the origin of life from non-life. It's kind of like if someone was discussing the accidental origin of automobiles, and forgot to mention the little difficulty of explaining the accidental origin of an engine. The discussion has some "bubble baby talk" in which someone tries to convince us that the ease of some fatty bubble splitting into two has some relevance to a cell dividing into two (it does not). 

Why is it that the quotation above does not mention protein molecules? Because explaining the origin of protein molecules is too hard for origin-of-life researchers. There is no factual basis to claims that you can get "off and running" with only RNA and some fatty molecules, and no self-reproducing cells packed with protein molecules. Such a thing has never been observed. No one has ever observed mere RNA and some fatty molecules evolve into a living thing. What we have here is more requirements underestimation, the perennial sin of theoretical scientists.  

A scientific paper has this to say about the RNA World theory promoted by Szostak:

"The 'RNA World' hypothesis suffers from a number of insurmountable problems of chemical and informational nature. The biggest of them are: (a) unreliability of the synthesis of starting components; (b) catastrophically increasing instability of the polynucleotide molecules as they elongate; (c) exceedingly low probability of meaningful sequences; (d) lack of the mechanism that would generate membrane-bound vesicles able to divide regularly and permeable to the nitrogenous bases and other RNA components; (e) absence of driving forces for the transition from the 'RNA world' to the much more complex 'DNA-RNA world'. Therefore, the 'RNA World' scenario is highly improbable."

The Quanta Magazine article includes an interview with a researcher named Betül Kaçar, who makes the extremely untrue and utterly preposterous claim that "life’s origins and early evolution created the blueprints for everything complex around us." To the contrary, there existed no blueprint for human anatomy or human cells in the first hundreds of millions of years of biological evolution.  There is still no known blueprint for human anatomy or human cells in any DNA molecule or cell. Contrary to the frequent misleading claims and insinuations of biologists, DNA only specifies low-level chemical information, not high-level anatomical information.  How the enormously complex hierarchical organization of human anatomy arises from the growth of a speck-sized ovum that does not specify such complexity is a wonder of origination utterly beyond the explanation of today's scientists.  

They don't claim flying horses -- just stuff more unbelievable

In related news, there was a recent story of Chinese radio astronomers reporting candidate signals from extraterrrestrial civilizations, but then retracting their claims.  This was very probably a case of picking up signals from earthly sources. The original report stated this (I've used Google Translate to get a translation):

"After launching the search for extraterrestrial civilizations, the 'China Sky Eye' has made important progress. A few days ago, Professor Zhang Tongjie, chief scientist of the China Extraterrestrial Civilization Research Group of the Department of Astronomy and Extraterrestrial Civilization Research Group of Beijing Normal University, revealed that his team used the 'Chinese Sky Eye' to discover several cases of possible technological traces and extraterrestrial civilizations from outside the earth...Zhang Tongjie said that these are several narrow-band electromagnetic signals different from the past, and the team is currently working on further investigation. 'The search for 'China Sky Eye' is a long one, and we have been working hard.'"

Since the history of SETI has been a history of false alarms, it is hard to get too excited about such a report. As a salon.com story makes clear, this is probably just another example of SETI researchers picking up unidentified earthly signals.

The Goofs in His "Evolution and Probability"

In his scientific paper “Evolution and Probability,” professor Luca Peliti raises the question of how evolution as described by Darwin could produce such wonders as the human eye. He then considers the problem of the origin of proteins. He states the following:

“Living cells have a repertoire of 20 amino acids and proteins are made of linear chains of amino acids (called polypeptide chains). A typical enzyme (a kind of protein whose function is to fasten, sometimes by several orders of magnitude, the unfolding of chemical reactions) is about a hundred amino acids long. If we suppose that only one particular amino acid sequence can make a functional enzyme, the probability to obtain this sequence by randomly placing amino acids will be of the order of one over the total number of amino acid sequences of length 100, i.e., 20¹⁰⁰ ≈ 10³⁰.”

Peliti is talking about a very important reality here, the difficulty of protein molecules forming by any Darwinian process. The problem is very severe, partially because of the very great number of different types of proteins in the human body. Humans have more than 20,000 types of protein molecules, specified by about 20,000 genes, each of which lists the amino acid sequence used by a protein. Each protein uses a different sequence of amino acids.

Peliti has committed two very serious errors in the passage quoted above. The first is that he has committed a careless math error in telling us that 20 to the hundredth power is equal to about ten to the thirtieth power. Twenty to the hundredth power is actually equal to ten to the one hundred and thirtieth power. Twenty to the hundredth power is equal to 1.2676506 X 10¹³⁰. In other words, 20¹⁰⁰ ≈ 10¹³⁰ rather than 20¹⁰⁰ ≈ 10³⁰ as Peliti stated. This difference is kind of all the difference in the world, because 10¹³⁰ is more than 1,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000 times larger than 10³⁰. If there was a chance of about 1 in 10³⁰ that a functional protein could appear by chance, that would be a likelihood very slim but perhaps something we might expect to occur, given countless million years for random trials. But if there was a chance of about 1 in 10¹³⁰ that a functional protein could appear by chance, that would be a likelihood so small that we would never expect it to happen in the history of the universe.

The screen shot below (from an online large exponents calculator) shows a conversion that corresponds to the one stated in the previous paragraph.

The second major error committed by Peliti in the passage quoted above is that he has seriously misstated the typical number of amino acids in a protein molecule or enzyme (an enzyme is a type of protein molecule). The number of amino acids in a human protein varies from about 50 to more than 800. The scientific paper here refers to "some 50,000 enzymes (of average length of 380 amino acids)." According to the page here, the median number of amino acids in a human protein is 375, according to a scientific paper. The difference between Peliti's suggestion that protein molecules such as enzymes have about 100 amino acids and the reality that they have a median of about 375 amino acids turns out to be a gigantically big difference when you calculate the probability of a protein forming by chance, a difference almost infinitely greater than the 375% difference between 100 and 375.

Let us do a calculation using the correct numbers and correct math. There are 20 amino acids used by living things. The median amino acid length of a human protein is 375 amino acids. So to calculate the chance of a set of amino acids randomly forming into the exact set of amino acids used by a functional protein such as an enzyme, the correct figure is 1 in 20 to the three-hundred-and-seventy-fifth power. This is a probability of about 1 in 10 to the four-hundred-eighty-seventh power. Very precisely, we can say that the chance of a random sequence of amino acids exactly matching that of a protein with 375 amino acids is a probability of 1 in 7.695704335 X 10⁴⁸⁷. That is a probability similar to the probability of you correctly guessing (with 100% accuracy) the ten-digit telephone numbers of 48 consecutive strangers. The calculation is shown in the visual below:

Now, for a protein such as an enzyme to function properly, it must have a sequence of amino acids close to its actual sequence. Experiments have shown that it is easy to ruin a protein molecule by making minor changes in its sequence of amino acids. Such changes will typically “break” the protein so that it will no longer fold in the right way to achieve the function that it performs. A biology textbook tells us, "Proteins are so precisely built that the change of even a few atoms in one amino acid can sometimes disrupt the structure of the whole molecule so severely that all function is lost." And we read on a science site, "Folded proteins are actually fragile structures, which can easily denature, or unfold." Another science site tells us, "Proteins are fragile molecules that are remarkably sensitive to changes in structure." But we can imagine that a protein molecule might still be functional if some minor changes were made in its sequence of amino acids.

Let us assume that for a protein molecule to retain its function, at least half of the amino acids in a functional protein have to exist in the exact sequence found in the protein. Under such an assumption, to calculate the chance of the functional protein forming by chance, rather than calculating a probability of 1 in 20 to the three-hundredth-and-seventh-fifth power, we might calculate a probability of 1 in 20 to the one-hundred-eighty-seventh power (187 being about half of 375). This would give us a probability equal to about 1 in 10 to the two hundred and forty-third power, a probability of about 1 in 10²⁴³. The calculation is shown below.

So even under the probably-too-generous assumption that perhaps only half of a protein's amino acid sequence has to be just as it is, we still are left with a calculation suggesting that a functional protein could never form by chance. The probability above is about the probability of you correctly guessing the 10-digit phone numbers of 24 consecutive strangers. It would seem that some miracle of luck would be required for a particular type of functional protein molecule to form. Since there are billions of different types of functional protein molecules in the biological world,  you need to believe in billions of miracles of luck to believe that such things appeared naturally. 

Peliti does get the math rather right in the excerpt below, in which he describes what he later calls a “garden of forking paths”:

“We can recast this argument in the following way. Let us suppose, following Dawkins... that 1000 evolution steps are necessary to obtain a working eye, and that at each step there are only two possibilities: the right or the wrong one. If the choice is made blindly, the probability of making the right choice at any step is equal to 1/2 . Then the probability of always making the right choice at every step is equal to 1/21000 ≈ 1/10³⁰⁰. It is clear that the fact that our lineage made the correct choice at each step looks nothing less than miraculous!”

The math here is reasonable. So we have two different ways of calculating things, and both have given us a likelihood of no more than about 1 chance in 10 to the two hundredth power. Such miracles of chance would need to happen not just once but very many times for the biological world to end up in its current state.

After raising this protein origin problem and the problem of the origin of complex biological systems like the vision system, Peliti attempts to address such origin problems. Peliti begins to reason like this:

“In the argument we just discussed we assumed that one does not know if one is on the right path until the end is reached. Let us suppose instead that each step made in the good direction provides a small advantage in terms of survival or fecundity to the being that makes it. More precisely, let us imagine to send in this 'Garden of forking paths' a group of, say, 100 individuals, who perform their choice (right or wrong) at each step, and then reproduce. Let us assume that those who make the right choice at the right moment have slightly more offspring than those who make the wrong one: for instance, that for each offspring of an individual who made the wrong choice, there are 1.02 offspring (on average) of one who made the right choice. Thus, after the first step, we shall have 50 individuals on the right side and 50 on the wrong side and, after reproduction, 102 on the right side and 100 on the wrong side. This is surely a very small difference: the fraction of individuals on the right path is 51% rather than 50%. However, if we wait a few generations, the fraction of individuals on the right side will increase: after 10 generations the ratio of the number of offspring of an individual who had made the right choice to that of one who made the wrong choice will be about 1.22, and after 100 generations it will be about 7.25.”

Peliti then goes further and further with such reasoning, eventually reaching the conclusion that something like an eye might appear after 300,000 generations. I need not discuss his full line of reasoning, and will simply note that Peliti's entire line of reasoning is fallacious because of the bad assumption that he has made at the beginning, the assumption that he states as, “Let us suppose instead that each step made in the good direction provides a small advantage in terms of survival or fecundity to the being that makes it.”

An assumption like this is what we may call a “benefit-with-every-step” assumption. Such an assumption can be visually represented like this:

Graph 1

The graph above shows a type of situation in which 10% completion yields 10% of the benefits of full completion, 20% completion yields 20% of the benefits of full completion, and so on and so forth, with 50% completion yielding 50% of the benefits of full completion, and 100% completion yielding 100% of the benefits of full completion.

A straight-line benefit calculation is suitable for a small minority of cases. For example, if you are a farmer who plants and harvests 10% of his farming field, you will get 10% of the benefit of planting and harvesting 100% of the field. And if you are a street vendor who sells 20% of the items in your vendor's wagon, you will get 20% of the benefit of selling 100% of the items in your wagon.

But it is obviously true that in life in general and in biology in particular, it is very often totally inappropriate to be using such a straight-line benefits calculation or to be making a benefit-with-every-step assumption. Here are some of the innumerable examples I could give to prove such a point:

1. Completing 30% of your SAT examination doesn't give you 30% of the benefit of completing 100% of the examination; instead it leaves you with a very bad score that doesn't do you any good at all.
2. Completing 50% of a suspension bridge across a river doesn't give you a bridge that is 50% as good as a full bridge; instead it leaves you with a bridge that is a suicide device because people driving across will find their cars falling into the river.
3. Completing 20% of an airplane doesn't give you something that flies 20% as fast or as high as a full airplane, but merely gives you something that doesn't fly at all.
4. Completing 20% of a television set doesn't give you something that gets 20% as many channels as a full TV set, but merely gives you something that doesn't display TV programs.
5. If you have 20% of a functional protein molecule, the molecule won't perform its function, and won't do anything.
6. If you build only 20% of a rocket designed to launch satellites, that rocket won't be able to reach orbit, and will produce no benefits at all.
7. A woman with 20% or 30% of her reproductive system won't be able to have 20% of a baby; instead, she won't be able to have any baby at all.
8. Having only one quarter of a circulatory system (such as only veins or only arteries or only half a heart) provides no benefit at all. 

We can call these type of cases late-yielding cases or “halfway yields nothing” cases. In all such cases, it is utterly inappropriate to use a benefit-with-every-step assumption or a straight-line benefit calculation, and it is utterly inappropriate to be evoking slogans such as “every step yields a benefit.” What type of graph would be appropriate to illustrate such cases? Rather than a straight-line graph, it would be a graph with a J-shaped line that stays flat for the first half of the graph, and then slopes up sharply. The graph would look rather like this:

Graph 2

The exact slope of such a curve would differ from one late-yielding situation to another, but in each case the curve would never be a straight-line curve but a curve rising sharply in the end stages, without any benefit in the earliest stages.

Now, which one of these two calculations would be appropriate to use when considering the case of the evolution of a vision system? Clearly the appropriate calculation would be like that shown in the “late yielding benefit calculation” graph (Graph 2), and not a calculation like that shown in the “straight-line benefit calculation” graph (Graph 1).

Let us ignore the red-herrings often thrown about when discussing such an issue, such as an appeal to the light-sensitive patches of earthworms. Humans are part of the chordates phylum, which is an entirely different phylum from the phylum of earthworms (the platyhelminthes phylum). No one believes that humans are descended from earthworms.

If we look at the fossil record of the phylum that humans belong to (chordates), we see no evidence that chordate eyes evolved from some mere light-sensitive patch such as on an earthworm. When considering the possible evolution of vision systems, we should be using something like a late-yielding benefit calculation and a “halfway yields nothing” assumption.

People very often speak as if “eyes=vision,” but such an assumption is false. For an organism to have vision, it is necessary to have a complex system consisting of many different things, including the following:

1. A functional eye requiring an intricate arrangement of many parts to achieve a functional end.
2. One or more specialized protein molecules capable of capturing light, each consisting of many amino acids arranged in just the right way to achieve a functional end.
3. An optic nerve stretching from the eye to the brain.
4. Extremely specialized parts in the brain necessary for effective vision.

All of these parts must be necessary for vision, so we clearly have here a situation that is not correctly described by an “every step yields a benefit” calculation. The correct assumption would be a “halfway yields nothing” assumption and a late-yielding benefits calculation.

We can give the name "the benefit-at-every-step fallacy" for the type of fallacy Peliti has committed by saying, "Let us suppose instead that each step made in the good direction provides a small advantage in terms of survival or fecundity to the being that makes it."  I can define the benefit-at-every-step fallacy as the fallacy of assuming that benefits will be yielded throughout a process that only yields benefits in its late stages.  Here is an example of such a fallacy (I'm not quoting here from Peliti's paper):

Dave: "If I slowly buy up a whole bunch of auto parts at the  junkyard, and assemble them into a car, in about 5 weeks I'll have a car I can sell for $1000. 1000 divided by 5 is 200. So I'll get an average of $200 a week, and that will pay my rent while I'm working on the car." 

Dave has committed here the benefit-at-every-step fallacy, just like Peliti.  Dave's labors will not actually yield any benefits until he has finished, or almost finished, the car he is working on.

A vision system is only one very complex thing that we would need to explain to naturally explain the origin of creatures such as humans. By far the biggest explanatory problem is explaining the origin of protein molecules. There are more than 20,000 different types of protein molecules in the human body, most specialized for some particular functional purpose. In the animal kingdom there are more than 10 billion different types of protein molecules, most of which are properly considered as complex inventions. The science site here estimates that there are between 10 billion and 10 trillion “unique protein sequences” in the animal kingdom. Most protein molecules have very hard-to-achieve folds necessary for their functionality. The science site here says “there are few common folds” in the protein universe. This means we have billions of complex biological inventions that we need to account for, for there are billions of different types of protein molecules in the natural world, each its own distinct complex invention.

When considering the appearance of protein molecules, we would have to use a late-yielding benefit calculation as shown in Graph 2 above, and not at all a straight-line benefit calculation as shown in Graph 1 above. It is certainly not true that the formation of 10% of a protein molecule gives you 10% of the benefit of the full molecule, or that the formation of 20% of a protein molecule gives you 20% of the benefit of the full molecule. It is instead usually true that having 50% of a protein molecule leaves you with a completely useless molecule. To be functional, protein molecules require complex hard-to-achieve folds. If you remove any 50% of their amino acid sequence, the protein molecules will not be functional, for reasons such as they cannot achieve the folds on which their functionality depends. Almost certainly, a large percentage of protein molecules will be nonfunctional if they have only 70% of their amino acids.  (See the end of this post for some scientific papers supporting these claims.)  As a biology textbook tells us, "Proteins are fragile, are often only on the brink of stability."

Indeed, a large percentage of protein molecules are not even independently functional if they have 100% of their amino acids, because of external functional dependencies of such protein molecules.  According to this source, between 20 to 30 percent of protein molecules require other protein molecules (called chaperone molecules) for them to fold properly.  Very many other protein molecules are not independently functional, because their function only arises when they act as team members in complex teams of proteins called protein complexes.  The answer to the question "what good is 50% of a protein molecule" is usually "no good at all," and in regard to a large fraction of protein molecules, the correct answer to the question "what good is 100% of a protein molecule" is "no good at all, unless there also exists one or more other protein molecules that the first protein molecule requires to be functional." 

All over the place in biology we see extremely complex innovations and intricate systems requiring many correctly arranged parts for minimal functionality, particularly when we look at the byzantine complexities and many "chicken or the egg" cross-requirements of biochemistry. That's why a physicist recently told us that even the simplest bacterium is more complex and functionally impressive than a jet aircraft. It is in general true that the more complex or intricate an innovation or system (biological or otherwise), the more likely that it falls under a late-yielding benefit calculation (as depicted in Graph 2) in which something like a "halfway yields nothing" assumption is correct, and the less likely that such an innovation or system falls under a "benefit at every step" calculation (as depicted in Graph 1) in which we can assume that the addition of each part produces a benefit.  It is a gigantic mental error to assume or insinuate that very complex  biological innovations should be typically described by a simplistic "benefit at every step" calculation such as depicted in Graph 1. But our ideologically motivated biologists have been making such an error for well over a century, and Peliti has merely repeated their error. 

Later in his “Evolution and Probability” paper, Peliti appeals to the concept of “selective pressure.” That term (also called "selection pressure") is simply a variation of "natural selection," a variation designed to impress us with the idea that something like physics is going on (even though nothing like that is at play).  

Here is a case where something a little like “selection pressure” might actually occur. Let us imagine a population (a group of organisms of the same species) where 10% of the organisms have some favorable trait that makes it more likely for them to survive and reproduce, and 90% of the organisms do not have such a trait. Then, over many generations, it might be that this trait might become more common in such a population, because those with the trait might reproduce more. In such a case, over many generations the percentage of the population with such a trait might increase. The 10% of the population with the trait might increase to 15%, then 20%, and so forth. One could use the term “selection pressure” to refer to such a tendency, although the term is actually doubly misleading; for there is no actual selection occurring (unconscious nature is not making a choice), and there is no actual pressure involved (pressure being a physical pushing force that is not occurring in this case).  The fact that "natural selection" does not actually describe a choice or selection is why Charles Darwin wrote in 1869,  "In the literal sense of the word, no doubt, natural selection is a false term."

But let us imagine some complex biological innovation that yields no benefit until more than 70% of it appears. It would be absolutely wrong and misleading to claim that the biological innovation had occurred because a “selection pressure” had pushed nature into forming such an innovation. During the first half of the imagined gradual formation process, there would have been no benefit from the appearance of 5% or 10% or 15% or 25% of such a biological innovation. So there would be no “selection pressure” at all that would have caused nature to pass through such stages.

But our biology dogmatists have constantly ignored such obvious truths, and have used the term “selection pressure” in an utterly inappropriate way. They will take some fantastically improbable biological innovation, and speak as if “selection pressure” pushed such a thing into existence. In reality, selection pressure would never occur in regard to any biological innovation until that innovation first appeared in some beneficial form. It is a complete fallacy to talk about “selection pressure” causing novel biological innovations whenever such innovations are late-yielding innovations that are nonfunctional in a fragmentary form.

Peliti is one of the biology theorists who has misused the concept of selection pressure. His error is shown in the passage below from his “Evolution and Probability” paper:

“We can summarize this discussion by stressing two main points: one, that an evolutionary history that appears extremely improbable a priori looks much more probable a posteriori, looking back from the arrival point, since a constant selective pressure has acted during the whole path, favoring advantageous variants with respect to disadvantageous ones.”

Here Peliti is again guilty of the "benefit-at-every-step" fallacy so often committed by biology dogmatists.  Because very complex biological innovations such as protein molecules and vision systems and reproductive systems usually do not provide any benefit when only small fractions of them exist (and very often do not provide any benefit when less than 60% or 70% of them exist), it is absolutely erroneous to assume that a “constant selective pressure has acted during the whole path” to produce complex innovations, while thinking along the lines of “every step provides a benefit.” There would typically be no selection pressure at all (and no benefit to survival or reproductive fecundity) until such extremely complex and hard-to-achieve biological innovations achieved a functional threshold, which would very often require fantastically improbable arrangements of matter that we would never expect to occur by chance (or by Darwinian evolution) in the history of the universe.  

Besides the fact that thinkers such as Peliti cannot credibly explain the origin of protein molecules such as those used in vision systems, there is the gigantic problem that no imaginable change in DNA can explain biological innovations such as vision systems, because the structure of such systems is nowhere specified in DNA. Contrary to the frequent mythical statements made about DNA being a blueprint for a human or a recipe for making a human, the fact is that DNA only specifies very low-level chemical information like the amino acid sequences of proteins. Not only does DNA not specify the structure of a human eye, it does not even specify the structure of any of the specialized cells used by the eye (such as the specialized cells used by cones and rods of the eye), or the structure of any other cells.  So any claim to explain the appearance of vision systems based on changes in DNA (with or without natural selection and with or without lucky random mutations) is futile.  The fact that DNA does not specify biological body plans or phenotypes is discussed very fully here. 

Through abused phrases such as "selection pressure," our biology theorists confuse us about probabilities.  The flowchart below helps to clarify the reality.  Consider some imagined path of biological progression.  The first question to ask is: was there a plan or idea matching the end result? If you think the answer is no, then go to the second question: was there a will or intention to improve the end result? If you think the answer to that question is no, then assume the progression occurred through a "random walk" effect like that of typing monkeys.  In the case of Darwinian evolution, there is no plan or idea for any of the results, nor is there any will or intention to achieve the results.  Darwinian evolution is properly described as a "typing monkeys" random-walk type of effect, with all the mountainous improbabilities associated with such a thing.  Our biologists often tell us that "evolution is a tinkerer," although that analogy is false and deceptive.  A tinkerer is an agent willfully attempting to improve something by using trial and error. There is no such willful agent present in Darwinian evolution. 

From an information standpoint, the vast amount of functional information in genomes is comparable to books in a library. The most accurate analogy for Darwinian evolution is the analogy of typing monkeys producing a large library of impressive works of literature (or functional information such as computer programs),  despite prohibitive odds against such a result. In fact, at the end of this recent essay, an evolutionary biologist ends up candidly comparing Darwinian evolution to typing monkeys.  The keystrokes of the monkeys are analogous to random mutations.  If you imagine one or more skyscrapers filled with typing monkeys, and a roving editor in each skyscraper searching for useful typed prose made by the monkeys, and making copies of such miracles of chance if they ever occur, with such a roving editor being analogous to natural selection, you will have a good analogy for the theory of Darwinian evolution. 

I discussed how fine-tuned and sensitive to changes protein molecules are.  Further evidence for such claims can be found in this paper, which discusses very many ways in which a random mutation in a gene for a protein molecule can destroy or damage the function or stability of the protein.  An "active site" of an enzyme protein is a region of the protein molecule (about 10% to 20% of the volume of the molecule) which binds and undergoes a chemical reaction with some other molecule.  Below are only a fraction of the examples of protein sensitivity and fragility cited by the paper:

"If a mutation occurs in an active site, then it should be considered lethal since such substitution will affect critical components of the biological reaction, which, in turn, will alter the normal protein function...Even if the mutation does not occur at the active site, but quite close to it, the characteristics of the catalytic groups will be perturbed....Changing the reaction rate, the pH, or salt and temperature dependencies away from the native parameters can lead to a malfunctioning protein....An amino acid substitution at a critical folding position can prevent the forming of the folding nucleus, which makes the remainder of the structure rapidly condense. Protein stability is also a key characteristic of a functional protein, and as such, a mutation on a native protein amino acid can considerably affect its stability....When a protein is carrying its function, frequently the reaction requires a small or large conformational change to occur that is specific for the particular biochemical reaction. Thus, if a mutation makes the protein more rigid or flexible compared to the native structure, then it will affect the protein’s function."

A very relevant scientific paper is the paper "Protein tolerance to random amino acid change." The authors describe an "x factor" which they define as "the probability that a random amino acid change will lead to a protein's inactivation." Based on their data and experimental work, they estimate this "x factor" to be 34%. It would be a big mistake to confuse this "x factor" with what percentage of a protein's amino acids could be changed without making the protein non-functional.  An "x factor" of 34% actually suggests that almost all of a protein's amino acid sequence must exist in its current form for the protein to be functional.  

Consider a protein with 375 amino acids (the median number of amino acids in humans).  If you were to randomly substitute 4% of those amino acids (15 amino acids) with random amino acids, then (assuming this "x factor" is 34% as the scientists estimated), there would be only about 2 chances in 1000 that such replacements would not make the protein non-functional.  The calculation is shown below (I used the Stat Trek binomial probability calculator). So the paper in question suggests protein molecules are extremely fine-tuned, fragile and sensitive to changes, and that more than 90% of a protein's amino acid sequence has to be in place before the molecule is functional. 

Figure 1 of the paper here suggests something similar, by indicating that after about 10 random mutations, the fitness of a protein molecule will drop to zero.