This is not a simple or straight forward question. It is the question that Meyer addresses in his 7th chapter. I think I found this the most difficult chapter in the book.
Meyer discusses the nature of “historical sciences” such as geology and paleontology and evolutionary biology and argues that they use different methods to “experimental sciences” such as physics and chemistry. He states that Stephen Jay Gould accepted this distinction and argued that historical scientific theories were testable by analysing their “explanatory power” (Gould, “Evolution and the Triumph of Homology”) Gould describes the process of testing in historical sciences as seeking “consilience”. Consilience is the situation where many facts can be explained well by a single proposition or theory. Gould he says argues that historical sciences depend upon the knowledge of the laws of nature to make inferences about the past.
Meyer then asks whether a design hypothesis can be formulated as a historical scientific theory about what happened in the past.
Historical scientists cite the occurrence of an event or series of events in the past as the explanation for some observable phenomenon in the present. Historical scientists use a distinctive mode of reasoning. Using their knowledge of cause and effect relationships historical scientists “calculate backwards” and infer past conditions and causes from present conditions and causes.
This type of reasoning is called “abductive” reasoning as opposed to inductive(in which a universal law is established from repeated observations) or deductive (in which a particular fact is deduced by applying a general law to another particular case. Abductive logic was first described by Charles Sanders Pierce
Despite the tentative nature of abductive reasoning we do make conclusive inferences about the past.
A conclusion of abductive reasoning is certain if we cannot explain the currently observed facts without the past cause. An abductive conclusion is established by showing that it is either the best or the only explanation of the effects in question.
To address this problem in geology Thomas Chamberlain proposed a method of “multiple working hypotheses. This is also known as “inference to the best explanation”
Peter Lipton is associated with this way of reasoning arguing that it is used both in science and ordinary life. Discovering certain particular marks in fresh snow we infer that a person with snow shoes has passed this way. Lipton argued that the ability to explain particular facts sometimes mattered more than predictive success in the evaluation of a particular hypothesis.
The problem with this method of assessing explanations is exactly how we judge which is the best explanation as opposed to the explanation we like the best.
Sunday, May 23, 2010
What is the relationship of ID to Science? Is it Science?
Image from here
In his sixth chapter of “Signature in the Cell” Meyer presents the view that the scientific enterprise is much wider than “doing experiments.”
Kekule famously “discovered” the structure of benzene while having a daydream about snakes seizing their own tails.
I turned my chair to the fire [after having worked on the problem for some time] and dozed. Again the atoms were gamboling before my eyes. This time the smaller groups kept modestly to the background. My mental eye, rendered more acute by repeated vision of this kind, could not distinguish larger structures, of manifold conformation; long rows, sometimes more closely fitted together; all twining and twisting in snakelike motion. But look! What was that? One of the snakes had seized hold of its own tail, and the form whirled mockingly before my eyes. As if by a flash of lighting I awoke... Let us learn to dream, gentlemen.
Meyer uses the example of Watson and Crick who relied on other people’s experimental results and their own model building to present the structure of DNA. Once they had the idea…it was obviously right!
Copernicus, Newton and Einstein are among the most famous scientists but none of them were outstanding in terms of their laboratory experiments.
Darwin is not a famous scientist because of his experimental results on seed dispersal or worms or movement in plants.
Meyer reminds us that for the early days of science intelligent design was not a controversial or career breaking interest. A. N. Whitehead is quoted:
“There can be no living science unless there is a widespread conviction in the existence of an Order of Things, in particular, of an Order of Nature.”
This Whitehead argues was provided by the Christian belief in the rationality of God.
Steve Fuller has amplified Whitehead’s observation. Science began because theists believed that an intelligent God made the universe to be intelligible to human beings made in his image.
Why has intelligent design which was so important in the origin of science become so completely rejected from modern science?
Sunday, March 28, 2010
The experiment that launched evolution.
"Charles Darwin did little experimental science. He did make several descriptive studies of barnacles and worms and some experimental studies about how species spread through seed dispersal and other processes. Yet his masterpiece, On the Origin of Species by Means of Natural Selection, contains neither a single mathematical equation nor any report of original experimental research. Yet he formulated a great scientific theory."
Stephen Meyer - Signature in the Cell p139
Stephen Meyer - Signature in the Cell p139
The Axe-Meyer Axis.
This is an attempt to state more clearly what I tried to say before...
How is Axe's published work relevant to ID?
Past posts for reference:
I was thinking...
J.Mol.Biol- 2000 -301-585-595
Controversial paper
Appearance of design
Making a functional protein from scratch is difficult. This is relevant in two situations(a) In a prebiotic soup making a protein to help stabilise or increase the function of a precellular replicon.
(b) after the origin of life the development of a brand new structural or functional protein which enhances the reproductive capacity of the organism.
The following argument is my version of what Stephen Meyer says on p206 and following in Signature in the Cell.
Most functional proteins are over 150 amino acids long. The average is estimated at around 300 amino acids long. With 20 different amino acids a protein 150 amino acids long gives a very large number of possible sequences - 10195 (which is a pretty big number)
Firstly in a prebiotic soup with an abundance of amino acids there are a number of possible ways in which amino acids can link up- however to get a folding protein we need peptide bonds. The probability of forming a peptide link is about 1 in 2.
To get a 150 amino acid molecule with peptide bonds the whole way along will be a probability of 1 in 1045.
Secondly in a prebiotic soup there will be 2 optical isomers of each amino acid. All the functional proteins in nature use only L isomers.
To get a 150 amino acid molecule with only L isomers the probability is also 1 in 10 45.
Thirdly there are constraints in terms of the exact order of amino acids that will produce a protein that can fold into a globular shape with the possibility of having a function.
Fourthly there are constraints in terms of the exact order of amino acids that will produce a protein that has a function.
The fourth issue was investigated by Robert Sauer in the late 1980's at MIT. Cassette mutagenesis was used to examine the tolerance to sequence change at a number of locations in a variety of proteins.
The results showed that the probability of acheiving a functional sequence in several small proteins was very low. In other words there are very few different combinations of amino acids that allow the function to be maintained.
The chance of hitting on one of these by chance was about 1 in 1063.
Doug Axe was interested in Sauer's work and began to wonder if he had underestimated how much protein sequences can vary and still retain function.
He developed a more rigorous mechanism to test this. The results in a paper published in 2004 were particularly important. On the basis of these results Axe was able to demonstrate that the ratio of functional sequences to non functional sequences for the enzyme beta-lactamase was 1 functional sequence to every 1 x1077.
Axe's work also allowed him to calculate the probabilities of finding any functional sequence amongst the possible sequences. This was done by looking at the probability of sequences being able to form stable folds (a necessary pre-requisite for stable 3D structure)
On the basis of his work he calculated the ratio of sequences able to form stable 3D structures to those which were not able to as 1 to 10 74.
A comparison of these odds:
The odds of finding a 150 amino acid sequence able to fold into a stable 3D shape is equivalent to finding a single marked atom out of all the atoms in a a billion Milky Ways (that is the galaxy[this is the star system rather than the chocolate bar] rather than the chocolate bar)
These are unpromising odds to say the least.
For a functional protein in a prebiotic soup the odds are considerably worsened.
For a complex of functional proteins occuring at the same time the odds are also considerable worsened.
The odds of a 150 amino acid protein with stable 3D shape in a prebiotic soup is 1 in 10 to 164 this is well below the entire probabalistic resources of the entire history of the entire universe.
How is Axe's published work relevant to ID?
Past posts for reference:
I was thinking...
J.Mol.Biol- 2000 -301-585-595
Controversial paper
Appearance of design
Making a functional protein from scratch is difficult. This is relevant in two situations(a) In a prebiotic soup making a protein to help stabilise or increase the function of a precellular replicon.
(b) after the origin of life the development of a brand new structural or functional protein which enhances the reproductive capacity of the organism.
The following argument is my version of what Stephen Meyer says on p206 and following in Signature in the Cell.
Most functional proteins are over 150 amino acids long. The average is estimated at around 300 amino acids long. With 20 different amino acids a protein 150 amino acids long gives a very large number of possible sequences - 10195 (which is a pretty big number)
Firstly in a prebiotic soup with an abundance of amino acids there are a number of possible ways in which amino acids can link up- however to get a folding protein we need peptide bonds. The probability of forming a peptide link is about 1 in 2.
To get a 150 amino acid molecule with peptide bonds the whole way along will be a probability of 1 in 1045.
Secondly in a prebiotic soup there will be 2 optical isomers of each amino acid. All the functional proteins in nature use only L isomers.
To get a 150 amino acid molecule with only L isomers the probability is also 1 in 10 45.
Thirdly there are constraints in terms of the exact order of amino acids that will produce a protein that can fold into a globular shape with the possibility of having a function.
Fourthly there are constraints in terms of the exact order of amino acids that will produce a protein that has a function.
The fourth issue was investigated by Robert Sauer in the late 1980's at MIT. Cassette mutagenesis was used to examine the tolerance to sequence change at a number of locations in a variety of proteins.
The results showed that the probability of acheiving a functional sequence in several small proteins was very low. In other words there are very few different combinations of amino acids that allow the function to be maintained.
The chance of hitting on one of these by chance was about 1 in 1063.
Doug Axe was interested in Sauer's work and began to wonder if he had underestimated how much protein sequences can vary and still retain function.
He developed a more rigorous mechanism to test this. The results in a paper published in 2004 were particularly important. On the basis of these results Axe was able to demonstrate that the ratio of functional sequences to non functional sequences for the enzyme beta-lactamase was 1 functional sequence to every 1 x1077.
Axe's work also allowed him to calculate the probabilities of finding any functional sequence amongst the possible sequences. This was done by looking at the probability of sequences being able to form stable folds (a necessary pre-requisite for stable 3D structure)
On the basis of his work he calculated the ratio of sequences able to form stable 3D structures to those which were not able to as 1 to 10 74.
A comparison of these odds:
The odds of finding a 150 amino acid sequence able to fold into a stable 3D shape is equivalent to finding a single marked atom out of all the atoms in a a billion Milky Ways (that is the galaxy[this is the star system rather than the chocolate bar] rather than the chocolate bar)
These are unpromising odds to say the least.
For a functional protein in a prebiotic soup the odds are considerably worsened.
For a complex of functional proteins occuring at the same time the odds are also considerable worsened.
The odds of a 150 amino acid protein with stable 3D shape in a prebiotic soup is 1 in 10 to 164 this is well below the entire probabalistic resources of the entire history of the entire universe.
Thursday, March 18, 2010
The appearance of Design.
The universe itself and living organisms in particular have the appearance of being designed. Human intelligence from very early times has concluded from this appearance of design that there must be a designer.
Darwin’s theory was an alternative seeking to explain the appearance of design without an actual designer.
In terms of biology ID writers suggest three key areas for investigation that interest me.
1. The origin of life itself.
2. The origin of new functional proteins
3. The origin of interdependent proteins where multiple proteins are fine tuned for a particular function and all are required simultaneously for minimal function.
With regards to area 1 I am interested in working through Stephen Meyers recent book – Signature in the Cell.
With regards to area 2 the key research is the investigation of the relative quantities of functional to non-functional proteins amongst all possible proteins. How easy is it to produce an entirely new functional protein? I am not talking about variants within a protein family but the production of an entirely new structure with a new function with no amino acid sequence homology to any other functional protein.
One way to investigate this is to ask how easily protein structure and function degrades when you change one or more amino acids around the active site of an enzyme or elsewhere in its structure.
This gives an increasingly clear picture of the size of the islands of protein functionality in the vast ocean of possible protein amino acid sequences.
It is this kind of experiment that Doug Axe did at Cambridge.
Some previous posts on this:
How big is the hole?
I was thinking..
Axe's paper
Axe's paper
Which Golf Course?
Darwin’s theory was an alternative seeking to explain the appearance of design without an actual designer.
In terms of biology ID writers suggest three key areas for investigation that interest me.
1. The origin of life itself.
2. The origin of new functional proteins
3. The origin of interdependent proteins where multiple proteins are fine tuned for a particular function and all are required simultaneously for minimal function.
With regards to area 1 I am interested in working through Stephen Meyers recent book – Signature in the Cell.
With regards to area 2 the key research is the investigation of the relative quantities of functional to non-functional proteins amongst all possible proteins. How easy is it to produce an entirely new functional protein? I am not talking about variants within a protein family but the production of an entirely new structure with a new function with no amino acid sequence homology to any other functional protein.
One way to investigate this is to ask how easily protein structure and function degrades when you change one or more amino acids around the active site of an enzyme or elsewhere in its structure.
This gives an increasingly clear picture of the size of the islands of protein functionality in the vast ocean of possible protein amino acid sequences.
It is this kind of experiment that Doug Axe did at Cambridge.
Some previous posts on this:
How big is the hole?
I was thinking..
Axe's paper
Axe's paper
Which Golf Course?
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