Just trying to simplify the arguments of Axe in his review paper...
If we take E.coli as our model then the average length of a functional protein is around 300 amino acids.
If the protein is longer or if a number of different proteins are required to act in concert then the problem is made worse.
The number of possible sequences to be sampled to find functional proteins of this moderate size is vast...
There are two ways of reducing the sparse sampling problem.
(a) The number of possible sequences with a particular function is very large. Sequence space is rich in function.
(b) The functional sequences are in some way linked- once you have one function it is easy to jump to the next.
Axe argues that experimental results indicate that (a) is not big enough to solve the sparse search problem....
I will look at what he says about (b) next week!
Sunday, September 26, 2010
Tuesday, August 17, 2010
The Case Against a Darwinian Origin of Protein Folds
One of the paragraphs from the conclusion of Douglas Axe's recent article:
Clearly, if this conclusion (A dawinian search is insufficient to find new protein folds) is correct it calls for a serious rethink of how we explain protein origins, and that means a rethink of biological origins as a whole. Drawing on some of the points developed here, I presented an earlier version of this case several years ago to two prominent experts in the field. Bothered by my conclusion, both felt that it must be in error. When the three of us met for a discussion, they had their own hunches about where my reasoning might have gone wrong. Interestingly, though, after perhaps two hours of heated discussion neither agreed with the other’s hunch, and we ended up at a polite but dissatisfying impasse. I left with the distinct impression that my conclusion was being rejected not because it was unfounded but because it was unwelcome.
Sunday, June 13, 2010
Is intelligent design a possible cause of the origin of biological information?
In his 7th chapter 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 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.
What makes an explanation the best?
1. A good explanation is causal.
2. A good explanation for a particular event is something which provides a “causal difference” in the outcome.
Historical scientists use the principle of causal adequacy. Causes that are known to produce the effect in question are better explanations. Charles Lyell expressed this as – “explanation of the past by causes now in operation.” Michael Scriven described this method as “retrospective causal analysis.” The candidate cause must provide independent evidence showing itself able to produce this effect on other occasions.
When there is only one possible cause for a particular effect the solution to the problem of what really happened is easy. This situation is where historical scientists can infer a uniquely plausible cause. For example an archaeologist who knows that scribes are the only known cause of linguistic inscriptions will, when they find a tablet containing ancient writing infer scribal activity. Where a particular past cause is known to be necessary to produce a subsequent effect, the occurrence of the effect is taken as sufficient to establish the occurrence of the cause.
Where there is more than one possible cause the situation is more difficult. In this case scientists will look for additional evidence that can help distinguish the explanatory power of the remaining explanations. They will look for additional facts for which there is only one adequate causal explanation. In practice the process of determining the best explanation involves examining a list of possible hypotheses. These will be compared for their known causal powers against the relevant evidence and then, like a detective, the scientist will progressively eliminate inadequate explanations until only one is left.
A second way of addressing this problem is to ask which of the adequate causes was actually present at the time of the event in question. Thus two criteria are needed:
1. causal adequacy
2. causal existence
To meet the second criteria historical scientists must show that the proposed cause is not only able to produce the event in question but that it was actually present at the right time and in the right place.
There are two ways of doing this
1. Showing the presently acting course must have been present in the past because this cause is the only known cause of the effect in question.
2. By examining a wider class of facts to show that only one other possible cause explains the whole collection.
Michael Scriven summarises situation. To establish a causal claim a historical scientist
1. needs to show that his proposed cause was present
2. that his proposed cause able to produce the effect under study
3. there is an absence of evidence of other possible causes.
Many scholars think that Charles Darwin structured his argument in the Origin to show that natural selection was both causally adequate and had causal existence. His theory of universal common descent could not be tested by predicting future outcomes under controlled experimental conditions. It could be demonstrated to be right by showing that it could explain already known facts in a more adequate fashion.
The question is now whether a case for an intelligent cause can be formulated and justified in this way. Is intelligent design a possible historical scientific explanation for the origin of biological information? Is it possible to formulate a case for intelligent design as an inference to the best explanation for the origin of biological information?
It is possible to conceive of the purposeful acts of an intelligent agent is a causal event. This clearly represents a known and presently acting adequate cause for the origin of information.
Our uniform and repeated experience indicates that intelligent agents produce information rich systems.
What causes now in operation produce digital code or specified information? Is there a known cause of the origin of such information? What does our uniform experience tell us?
Intelligent design must qualify at least as a possible scientific explanation for the origin of biological information.
Is intelligent design the only known or adequate cause of the origin specified information? If so then the past action of designing intelligence will be established as the strongest and most logically compelling form of historical inference.
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 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.
What makes an explanation the best?
1. A good explanation is causal.
2. A good explanation for a particular event is something which provides a “causal difference” in the outcome.
Historical scientists use the principle of causal adequacy. Causes that are known to produce the effect in question are better explanations. Charles Lyell expressed this as – “explanation of the past by causes now in operation.” Michael Scriven described this method as “retrospective causal analysis.” The candidate cause must provide independent evidence showing itself able to produce this effect on other occasions.
When there is only one possible cause for a particular effect the solution to the problem of what really happened is easy. This situation is where historical scientists can infer a uniquely plausible cause. For example an archaeologist who knows that scribes are the only known cause of linguistic inscriptions will, when they find a tablet containing ancient writing infer scribal activity. Where a particular past cause is known to be necessary to produce a subsequent effect, the occurrence of the effect is taken as sufficient to establish the occurrence of the cause.
Where there is more than one possible cause the situation is more difficult. In this case scientists will look for additional evidence that can help distinguish the explanatory power of the remaining explanations. They will look for additional facts for which there is only one adequate causal explanation. In practice the process of determining the best explanation involves examining a list of possible hypotheses. These will be compared for their known causal powers against the relevant evidence and then, like a detective, the scientist will progressively eliminate inadequate explanations until only one is left.
A second way of addressing this problem is to ask which of the adequate causes was actually present at the time of the event in question. Thus two criteria are needed:
1. causal adequacy
2. causal existence
To meet the second criteria historical scientists must show that the proposed cause is not only able to produce the event in question but that it was actually present at the right time and in the right place.
There are two ways of doing this
1. Showing the presently acting course must have been present in the past because this cause is the only known cause of the effect in question.
2. By examining a wider class of facts to show that only one other possible cause explains the whole collection.
Michael Scriven summarises situation. To establish a causal claim a historical scientist
1. needs to show that his proposed cause was present
2. that his proposed cause able to produce the effect under study
3. there is an absence of evidence of other possible causes.
Many scholars think that Charles Darwin structured his argument in the Origin to show that natural selection was both causally adequate and had causal existence. His theory of universal common descent could not be tested by predicting future outcomes under controlled experimental conditions. It could be demonstrated to be right by showing that it could explain already known facts in a more adequate fashion.
The question is now whether a case for an intelligent cause can be formulated and justified in this way. Is intelligent design a possible historical scientific explanation for the origin of biological information? Is it possible to formulate a case for intelligent design as an inference to the best explanation for the origin of biological information?
It is possible to conceive of the purposeful acts of an intelligent agent is a causal event. This clearly represents a known and presently acting adequate cause for the origin of information.
Our uniform and repeated experience indicates that intelligent agents produce information rich systems.
What causes now in operation produce digital code or specified information? Is there a known cause of the origin of such information? What does our uniform experience tell us?
Intelligent design must qualify at least as a possible scientific explanation for the origin of biological information.
Is intelligent design the only known or adequate cause of the origin specified information? If so then the past action of designing intelligence will be established as the strongest and most logically compelling form of historical inference.
Sunday, May 23, 2010
Is ID Science?
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.
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.
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?
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