Tag Archives: Amino Acid

New software calculates the probability of generating functional proteins by chance

Apologetics and the progress of science
Apologetics and the progress of science

Here’s an article sent to me by JoeCoder about a new computer program written by Kirk Durston.

About Kirk:

Kirk Durston is a scientist, a philosopher, and a clergyman with a Ph.D. in Biophysics, an M.A. in Philosophy, a B.Sc. in Mechanical Engineering, and a B.Sc. in Physics. His work involves a significant amount of time thinking, writing and speaking about the interaction of science, theology and philosophy within the context of authentic Christianity. He has been married for 34 years to Patti and they have six children and three grandchildren. He enjoys landscape photography, antiques of various types, wilderness canoeing and camping, fly fishing, amateur astronomy, reading, music, playing the saxophone (alto), and enjoying family and friends.

Kirk grew up on a cattle and grain farm in central Manitoba, Canada, where he spent countless hours wandering around on his own in the forest as a young boy, fascinated with the plants and animals that are native to that region of the province. Throughout his teen years he spent six days a week in the summer working as a farm hand with cattle and grain. He left his father’s farm at the age of 19 to go to university.

Canada? Can anything good come out of Canada? Oh well, at least he’s not from Scotland. Anyway, on to the research, that’s what we care about. Code!

Summary of the article:

  • Biological life requires proteins
  • Proteins are sequences of amino acids, chained together
  • the order of amino acids determines whether the sequence has biological function
  • sequences that have biological function are rare, compared to the total number of possible sequences
  • Durston wrote a program to calculate the number of the probability of getting a functional sequence by random chance
  • The probability for getting a functional protein by chance is incredibly low

With that said, we can understand what he wrote:

This program can compute an upper limit for the probability of obtaining a protein family from a wealth of actual data contained in the Pfam database. The first step computes the lower limit for the functional complexity or functional information required to code for a particular protein family, using a method published by Durston et al. This value for I(Ex) can then be plugged into an equation published by Hazen et al. in order to solve the probability M(Ex)/N of ‘finding’ a functional sequence in a single trial.

I downloaded 3,751 aligned sequences for the Ribosomal S7 domain, part of a universal protein essential for all life. When the data was run through the program, it revealed that the lower limit for the amount of functional information required to code for this domain is 332 Fits (Functional Bits). The extreme upper limit for the number of sequences that might be functional for this domain is around 10^92. In a single trial, the probability of obtaining a sequence that would be functional for the Ribosomal S7 domain is 1 chance in 10^100 … and this is only for a 148 amino acid structural domain, much smaller than an average protein.

For another example, I downloaded 4,986 aligned sequences for the ABC-3 family of proteins and ran it through the program. The results indicate that the probability of obtaining, in a single trial, a functional ABC-3 sequence is around 1 chance in 10^128. This method ignores pairwise and higher order relationships within the sequence that would vastly limit the number of functional sequences by many orders of magnitude, reducing the probability even further by many orders of magnitude – so this gives us a best-case estimate.

There are only about 10^80 particles in the entire physical universe – 10^85 at the most. These are long odds. But maybe if we expand the probabilistic resources by buying more slot machines, and we pull the slot machine lever at much faster rate… can we win the jackpot then?

Nope:

What are the implications of these results, obtained from actual data, for the fundamental prediction of neo-Darwinian theory mentioned above? If we assume 10^30 life forms with a fast replication rate of 30 minutes and a huge genome with a very high mutation rate over a period of 10 billion years, an extreme upper limit for the total number of mutations for all of life’s history would be around 10^43. Unfortunately, a protein domain such as Ribosomal S7 would require a minimum average of 10^100 trials, about 10^57 trials more than the entire theoretical history of life could provide – and this is only for one domain. Forget about ‘finding’ an average sized protein, not to mention thousands.

So even if you have lots of probabilistic resources, and lots of time, you’re still not going to get your protein.

Compare these numbers with the 1 in 10^77 number that I posted about yesterday from Doug Axe. There is just no way to account for proteins if there is no intelligent agent to place the amino acids in sequence. When it comes to writing code, writing blog posts, writing music, or placing Scrabble letters, you need an intelligence. Sequencing amino acids into proteins? You need an intelligence.

Was early Earth’s atmosphere suitable for creating the building blocks of life?

Do the Miller-Urey experiments simulate the early Earth?
The Miller-Urey experiments

Biochemist Dr. Fazale Rana of Reasons to Believe offers some evidence.

Excerpt:

Today, the Miller-Urey experiment is considered to be irrelevant to the origin-of-life question. Current understanding of the composition of early Earth’s atmosphere differs significantly from the gas mix used by Miller. Most planetary scientists now think that the Earth’s primeval atmosphere consisted of carbon dioxide, nitrogen, and water vapor. Laboratory experiments indicate that this gas mixture is incapable of yielding organic materials in Miller-Urey-type experiments.

In May 2003 origin-of-life researchers Jeffrey Bada and Antonio Lazcano, long-time associates of Miller, wrote an essay for Science (May 2, 2003, pp. 745-746)commemorating the 50-year anniversary of the publication of Miller’s initial results.They pointed out that the Miller-Urey experiment has historical significance, but not scientific importance in contemporary origin-of-life thought. Bada and Lazcano wrote:

Is the “prebiotic soup” theory a reasonable explanation for the emergence of life? Contemporary geoscientists tend to doubt that the primitive atmosphere had the highly reducing composition used by Miller in 1953.

In his book Biogenesis, origin-of-life researcher Noam Lahav passes similar judgment:

The prebiotic conditions assumed by Miller and Urey were essentially those of a reducing atmosphere. Under slightly reducing conditions, the Miller-Urey reaction does not produce amino acids, nor does it produce the chemicals that may serve as the predecessors of other important biopolymer building blocks. Thus, by challenging the assumption of a reducing atmosphere, we challenge the very existence of the “prebiotic soup”, with its richness of biologically important organic compounds.

For many people, the generation of amino acids from simple chemical compounds thought to be present in early Earth’s atmosphere meant that life could originate all on its own without the need for a Creator. Work done on the early planetary conditions of Earth in the intervening decades between Miller’s famous experiment and his death, however, have invalidated this famous experiment and its support for an evolutionary explanation for life’s origin, in spite of what textbooks report.

The IDEA Center has a nice summary of origin-of-life research that explains why scientists no longer accept the idea that the building blocks of life can be formed by sparking the gasses that were present on the early Earth.

Miler and Urey used the wrong gasses:

Miller’s experiment requires a reducing methane and ammonia atmosphere, however geochemical evidence says the atmosphere was hydrogen, water, and carbon dioxide (non-reducing). The only amino acid produced in a such an atmosphere is glycine (and only when the hydrogen content is unreasonably high), and could not form the necessary building blocks of life.

Miller and Urey didn’t account for UV of molecular instability:

Not only would UV radiation destroy any molecules that were made, but their own short lifespans would also greatly limit their numbers. For example, at 100ºC (boiling point of water), the half lives of the nucleic acids Adenine and Guanine are 1 year, uracil is 12 years, and cytozine is 19 days (nucleic acids and other important proteins such as chlorophyll and hemoglobin have never been synthesized in origin-of-life type experiments).

Miller and Urey didn’t account for molecular oxygen:

We all have know ozone in the upper atmosphere protects life from harmful UV radiation. However, ozone is composed of oxygen which is the very gas that Stanley Miller-type experiments avoided, for it prevents the synthesis of organic molecules like the ones obtained from the experiments! Pre-biotic synthesis is in a “damned if you do, damned if you don’t” scenario. The chemistry does not work if there is oxygen because the atmosphere would be non-reducing, but if there is no UV-light-blocking oxygen (i.e. ozone – O3) in the atmosphere, the amino acids would be quickly destroyed by extremely high amounts of UV light (which would have been 100 times stronger than today on the early earth).This radiation could destroy methane within a few tens of years, and atmospheric ammonia within 30,000 years.

And there were three other problems too:

At best the processes would likely create a dilute “thin soup,” destroyed by meteorite impacts every 10 million years. This severely limits the time available to create pre-biotic chemicals and allow for the OOL.

Chemically speaking, life uses only “left-handed” (“L”) amino acids and “right-handed” (“R)” genetic molecules. This is called “chirality,” and any account of the origin of life must somehow explain the origin of chirality. Nearly all chemical reactions produce “racemic” mixtures–mixtures with products that are 50% L and 50% R.

Two more problems are not mentioned in the article. A non-peptide bond anywhere in the chain will ruin the chain. You need around 200 amino acids to make a protein. If any of the bonds is not a peptide bond, the chain will not work in a living system. Additionally, the article does not mention the need for the experimenter to intervene in order to prevent interfering cross-reactions that would prevent the amino acids from forming. That’s another problem with the origin of life – experiments show that getting the building blocks requires an intelligence to intervene.

Now keep in mind that even if you get the building blocks, you are left with the sequencing problem – but that’s another topic for another day.

Stephen C. Meyer lectures on intelligent design and the origin of life

A MUST-SEE lecture based on Dr. Stephen C. Meyer’s book “Signature in the Cell“.

You can get an MP3 of the lecture here. (30 MB)

I highly recommend watching the lecture, and looking at the slides. The quality of the video and the content is first class. There is some Q&A (9 minutes) at the end of the lecture.

Topics:

  • intelligent design is concerned with measuring the information-creating capabilities of natural forces like mutation and selection
  • Darwinists think that random mutations and natural selection can explain the origin and diversification of living systems
  • Darwinian mechanisms are capable of explaining small-scale adaptive changes within types of organisms
  • but there is skepticism, even among naturalists, that Darwinian mechanisms can explain the origin of animal designs
  • even if you concede that Darwinism can account for all of the basic animal body plans, there is still the problem of life’s origin
  • can Darwinian mechanisms explain the origin of the first life? Is there a good naturalistic hypothesis to explain it?
  • there are at least two places in the history of life where new information is needed: origin of life, and Cambrian explosion
  • overview of the structure of DNA and protein synthesis (he has helpful pictures and he uses the snap lock blocks, too)
  • the DNA molecule is composed of a sequence of proteins, and the sequence is carefully selected to have biological function
  • meaningful sequences of things like computer code, English sentences, etc. require an adequate cause
  • it is very hard to arrive at a meaningful sequence of a non-trivial length by randomly picking symbols/letters
  • although any random sequence of letters is improbable, the vast majority of sequences are gibberish/non-compiling code
  • similarly, most random sequences of amino acids are lab-proven (Doug Axe’s work) to be non-functional gibberish
  • the research showing this was conducted at Cambridge University and published in the Journal of Molecular Biology
  • so, random mutation cannot explain the origin of the first living cell
  • however, even natural selection coupled with random mutation cannot explain the first living cell
  • there must already be replication in order for mutation and selection to work, so they can’t explain the first replicator
  • but the origin of life is the origin of the first replicator – there is no replication prior to the first replicator
  • the information in the first replicator cannot be explained by law, such as by chemical bonding affinities
  • the amino acids are attached like magnetic letters on a refrigerator
  • the magnetic force sticks the letters ON the fridge, but they don’t determine the specific sequence of the letters
  • if laws did determine the sequence of letters, then the sequences would be repetitive
  • the three materialist explanations – chance alone, chance and law, law alone – are not adequate to explain the effect
  • the best explanation is that an intelligent cause is responsible for the biological explanation in the first replicator
  • we know that intelligent causes can produce functional sequences of information, e.g. – English, Java code
  • the structure and design of DNA matches up nicely with the design patterns used by software engineers (like WK!)

There are some very good tips in this lecture so that you will be able to explain intelligent design to others in simple ways, using everyday household items and children’s toys to symbolize the amino acids, proteins, sugar phosphate backbones, etc.

Proteins are constructed from a sequence of amino acids:

A sequence of amino acids forming a protein
A sequence of amino acids forming a protein

Proteins sticking onto the double helix structure of DNA:

Some proteins sticking onto the sugar phosphate backbone
Some proteins sticking onto the sugar phosphate backbone

I highly, highly recommend this lecture. You will be delighted and you will learn something.

Here is an article that gives a general overview of how intelligent design challenges. If you want to read something more detailed about the material that he is covering in the lecture above related to the origin of life, there is a pretty good article here.

UPDATE: There is a good breakdown of some of the slides with helpful flow charts here on Uncommon Descent.

Positive arguments for Christian theism

Stephen C. Meyer and Keith Fox debate intelligent design and evolution

From Justin Brierley’s “Unbelievable” podcast.

Details:

Stephen Meyer is a leading proponent of Intelligent Design who directs the Centre for Science and Culture at the Discovery Institute in Seattle. His [first] book “Signature in the Cell” claims to show that the DNA code is the product of intelligent mind, not naturalistic processes. Keith Fox is Professor of Biochemistry at Southampton University. He chairs the UK Christians in Science network but disagrees strongly with ID. They debate how life could have originated and whether design is allowed as an explanation in science.

Summary: (stuff in italics is my snarky paraphrase)

Meyer:

  • background and how he got interested in intelligent design
  • his research focus is on the origin of life – the first replicator
  • summarizes the history of origin of life studies
  • authored the book “Signature in the Cell”
  • the DNA enigma: where did the information in DNA come from?
  • naturalistic explanations of the DNA information have failed
  • but intelligent agents are known to be able to produce information
  • the best explanation of the information in DNA is that an intelligent agent authored it
  • Meyer’s book was named by atheist philosopher of science Thomas Nagel as a Times Literary Supplement Book of the Year in 2010
  • why is design so controversial? Many people think that Darwin explained why nature appears design
  • the Darwinian view is that nature can create the appearance of design using mutation and selection
  • however, Darwinian mechanisms cannot explain the origin of the first living cell, it assumes replication, and the origin of life is about where the first replicator comes from

Fox:

  • Meyer’s argument is not about the evolution of life after the first cell
  • Meyer’s case for design is about the origin of life
  • naturalists do not know a naturalistic explanation for the origin of life
  • there are a number of naturalistic hypotheses for the origin of life, like the RNA-first hypothesis
  • maybe in a few years one of them will turn out to be correct
  • what intelligent design is arguing from a gap in our current naturalistic knowledge to infer that God intervened in nature

Meyer:

  • that’s not what intelligent design is at all
  • the approach ID theorists use is the inference to best explanation
  • you evaluate all explanations, non-intelligent causes and intelligent causes
  • you prefer the best possible explanation
  • we know that minds are capable of producing information just like the information we find in DNA

Fox:

  • living cells replicate, so they have the ability to introduce mutations as they replicate and then some of those mutations can be selected
  • so maybe the process of replicating that living cells do created the first living cell
  • maybe the first living cell created itself, X brought X into being, self-creation, what’s irrational about that?

Meyer:

  • the issue is the origin of life – where did the first living cell come from?
  • you cannot appeal to the operations that a living cell can perform to explain the origin of the first living cell
  • there was no first living cell operating before the first living cell
  • there was no replication, mutation or selection before the first living cell
  • in fact, in my book I show that there is no known naturalistic mechanism that is able to produce the information needed for the first living cell
  • nothing can create itself, that is self-contradictory
Fox:
  • Well, you are just saying that because something is complex that God did it
Meyer:
  • Sadly, no. What I actually said needed to be explained was the information, not complexity
  • And we know from software engineering that the process of adding information to code is performed by programmers
  • in the absence of any adequate naturalistic explanation for information, we are justified in taking the explanation that we are familiar with – namely, intelligent agency – based on our uniform, universal experience of what causes information
Fox:
  • well, maybe we can appeal to the mutation and selection in existing living cells to explain the origin of the first living cell
  • maybe there were living cells before the first living cell, and then these other living cells created the first living cell
Meyer:
  • we can’t keep invoking mutation and selection when those processes are not operating prior to the origin of the first living cell
Fox:
  • well maybe some bare-bones self-replication molecule was a precursor to the first living cell
Meyer:
  • even to generate very limited replicator would require a large amount of information
  • the argument I am making is – where does the evolution come from?
Fox:
  • well, maybe we will think of an explanation for information that is naturalistic in 20 years
  • we’ve thought of explanations to things that were NOT information before
  • so maybe we will be able to think of something to explain information based on our ability to explain NOT information before

Moderator: Change topics: the Dover decision

Meyer:

  • the Discovery Institute opposed the policy that causes the trial
  • the wording of the statute was poor
  • the judge was completely wrong in his decision
  • young earth creationists used the phrase “intelligent design” to cover their agenda
  • intelligent design is an inference using the normal methods of science
Fox:
  • intelligent design is a science stopper because it stops looking for a naturalistic explanation
  • everything in nature must have a naturalistic explanation
  • everything has to be explained using matter and time and chance
  • it just has to be that way!!!!
Meyer:
  • well, what luck would you have explaining an effect like Mt. Rushmore?
  • can you explain that using matter,time and chance?
  • Mt. Rushmore was the product of intelligence, not wind and erosion
  • similarly, there is information in the cell, and we know that intelligence causes information
Fox:
  • So you are saying that we don’t understand and therefore an intelligence is necessary?

Meyer:

  • no I am saying we DO understand and we are making an inference based on that understanding
  • you are the one who is insisting on a material explanation because you pre-suppose materialism
  • we know that minds have causal powers, and we can infer mind as an explanation from information
Fox:
  • well nature is a seamless chain of material causes and effects
Meyer:
  • agents can act without violating the laws of nature
  • even humans can act as intelligent agents to create information in books, and they don’t violate the laws of nature
  • intelligent causes are real, and they explain effects in nature
Fox:
  • you’re trying to impose on science something to do with meaning and purpose
Meyer:
  • no that’s not what we’re doing, we’re inferring from from the fact that we ourselves are known causes of information to the fact that an intelligence cause is the best explanation for information in the cell
Fox:
  • but I am a materialist, I need a materialist explanation
Meyer:
  • mind IS an answer to the how question
  • we infer to mind in many other scientific disciplines, like cryptography, archaeology, etc.
  • a materialist might accuse an archaeologist of engaging in a “scribe-of-the-gaps” argument, but the best explanation of an artifact with information is a scribe
  • we are inferring that mind is the cause from the nature of the effect: information
Moderator: is it appropriate to call DNA “information”

Fox:

  • well DNA is just a molecular polymer, any reference to information is just by analogy
Meyer:
  • DNA is a molecular polymer, but it also exhibits the property of specified complexity
  • the arrangement of bases, which function as machine instructions in a software program, for performings task in the cell
  • we have observed that the property of specified complexity always comes from an intelligence
Fox:
  • well, maybe there are other sequences that would work, so maybe it’s really not uncommon to develop functioning sequences by chance alone, without an intelligence
Meyer:
  • you can measure how precise the functional specificity is in DNA and proteins

Moderator: is Shannon information the same as functional information

Meyer:

  • Shannon information refers to the sequences of digits or symbols that do not necessarily have any function, i.e. – a four character string QSZX has as much Shannon information as WORD. However, only the latter is functional against the pattern of the English language. There are arrangements of DNA bases and amino acids that have the same number of symbols/characters as a functional sequence would have, but they have no biological function – they do not exhibit specified complexity
Fox:
  • Well, maybe there are lots and lots of sequences of DNA and proteins so that it is fairly easy to get a functional one by chance

Meyer:

  • DNA sequences that are functional are extremely rare, protein sequences are even more rare
  • this is not my opinion, this is what the research shows – functional protein sequences are rare
Fox:
  • well maybe there are other functional sequences that are occur before the first functional sequence that are precursors to the first functional sequence
  • maybe there are billions of years of replication, mutation and selection before the first replication, mutation and selection

Meyer:

  • you can’t get to the first selectable functional sequence by appealing to precursor selectable functional sequences – there are no selectable functional sequences before the FIRST one
  • you have to get the first selectable functional sequence by chance alone, because there is nothing to mutate or select before the first replicator
  • the chance hypothesis has been rejected because the minimal amount of information for the simplest replicator is too high to get by chance alone, given the resources, including time, that are available

Moderator: Keith are you confident that naturalism will be able to substantiate these naturalism-of-the-gap speculations that you offer in response to Meyer’s actual science that we have today? 

Fox:

  • well, it is hard to know for sure because it was just a fluke event
  • but there’s nothing irrational or unscientific or miraculous about it – the fluke would have a material explanation
  • there is nothing that we can detect that would implicate God, my speculations about a fluke which I cannot observe or measure or test would all be compatible with an atheistic worldview that omits God as a causal entity

Meyer:

  • where are those material processes that could account for this fluke then?
  • the whole point of this argument is that the information in DNA transcends the material components in the sequence
  • it’s the arrangement of the material parts/letters/characters/symbols/instructions that needs to be explained
Fox:
  • Well, I just have a different philosophy of science that rules out intelligent causation a priori

Meyer:

  • Yes, that’s the difference between us – you pre-suppose that all explanations of natural phenomena must exclude intelligent causes

There is a bit more where Meyer talks about how parts of the cell are implementations of various design patterns (Gang of Four design patterns) that are used by software architects who design software.

Find more posts on Stephen C. Meyer here.

Stephen C. Meyer lectures on intelligent design and the origin of life

A MUST-SEE lecture based on Dr. Stephen C. Meyer’s book “Signature in the Cell“.

You can get an MP3 of the lecture here. (30 MB)

I highly recommend watching the lecture, and looking at the slides. The quality of the video and the content is first class. There is some Q&A (9 minutes) at the end of the lecture.

Topics:

  • intelligent design is concerned with measuring the information-creating capabilities of natural forces like mutation and selection
  • Darwinists think that random mutations and natural selection can explain the origin and diversification of living systems
  • Darwinian mechanisms are capable of explaining small-scale adaptive changes within types of organisms
  • but there is skepticism, even among naturalists, that Darwinian mechanisms can explain the origin of animal designs
  • even if you concede that Darwinism can account for all of the basic animal body plans, there is still the problem of life’s origin
  • can Darwinian mechanisms explain the origin of the first life? Is there a good naturalistic hypothesis to explain it?
  • there are at least two places in the history of life where new information is needed: origin of life, and Cambrian explosion
  • overview of the structure of DNA and protein synthesis (he has helpful pictures and he uses the snap lock blocks, too)
  • the DNA molecule is composed of a sequence of proteins, and the sequence is carefully selected to have biological function
  • meaningful sequences of things like computer code, English sentences, etc. require an adequate cause
  • it is very hard to arrive at a meaningful sequence of a non-trivial length by randomly picking symbols/letters
  • although any random sequence of letters is improbable, the vast majority of sequences are gibberish/non-compiling code
  • similarly, most random sequences of amino acids are lab-proven (Doug Axe’s work) to be non-functional gibberish
  • the research showing this was conducted at Cambridge University and published in the Journal of Molecular Biology
  • so, random mutation cannot explain the origin of the first living cell
  • however, even natural selection coupled with random mutation cannot explain the first living cell
  • there must already be replication in order for mutation and selection to work, so they can’t explain the first replicator
  • but the origin of life is the origin of the first replicator – there is no replication prior to the first replicator
  • the information in the first replicator cannot be explained by law, such as by chemical bonding affinities
  • the amino acids are attached like magnetic letters on a refrigerator
  • the magnetic force sticks the letters ON the fridge, but they don’t determine the specific sequence of the letters
  • if laws did determine the sequence of letters, then the sequences would be repetitive
  • the three materialist explanations – chance alone, chance and law, law alone – are not adequate to explain the effect
  • the best explanation is that an intelligent cause is responsible for the biological explanation in the first replicator
  • we know that intelligent causes can produce functional sequences of information, e.g. – English, Java code
  • the structure and design of DNA matches up nicely with the design patterns used by software engineers (like WK!)

There are some very good tips in this lecture so that you will be able to explain intelligent design to others in simple ways, using everyday household items and children’s toys to symbolize the amino acids, proteins, sugar phosphate backbones, etc.

Proteins are constructed from a sequence of amino acids:

A sequence of amino acids forming a protein
A sequence of amino acids forming a protein

Proteins sticking onto the double helix structure of DNA:

Some proteins sticking onto the sugar phosphate backbone
Some proteins sticking onto the sugar phosphate backbone

I highly, highly recommend this lecture. You will be delighted and you will learn something.

Here is an article that gives a general overview of how intelligent design challenges. If you want to read something more detailed about the material that he is covering in the lecture above related to the origin of life, there is a pretty good article here.

UPDATE: There is a good breakdown of some of the slides with helpful flow charts here on Uncommon Descent.

Positive arguments for Christian theism