Wednesday, December 15, 2010

What is Intelligent Design?

It is the area of science that studies the signs of intelligence.
Intelligent agents produce artifacts that other intelligent agents can recognize as the products of intelligence.
These artifacts may include:
1. Complex information


2. Multiple parts functioning together which have an irreducible core.

Sunday, October 17, 2010

Shortcuts to new protein folds.

There are some possible shortcuts.
1. The changes that are known to occur which change how specific an enzyme is for a particular reaction thus allowing it to use a slightly different chemical.
These are where a small change in the structure of an existing protein means that it can use a slightly altered substrate.
Examples of this kind of change are the oscillations in the antibiotics battle.
People discover an antibiotic --> microbes die
a microbe develops resistance by a small change in protein structure --> people die
People develop a slightly changed antibiotic --> microbes die.
In these cases there is a shortcut to other similar functions by a relatively small number of mutations.
(Usually it is this kind of change that is presented as evidence for evolution.)
Why aren’t this kind of shortcuts sufficient to reassure us that evolution can solve the problem?
Not all proteins have this kind of relationship with each other. Protein databases have 1777 classes of structural domains These are the “superfamilies” of protein structures. There may be recognisable similarities between domains within a superfamily … but the superfamilies themselves are not related.
Even if all the proteins within a superfamily can be derived from one original sequence this does not explain the origin of all the 1777 plus classes of superfamily.
2. If a relatively few changes causes a change in function and this is followed by subsequent sequence divergence in the new protein. Axe considers an example of this from PA Alexander published in PNAS….. and argues that this will not get us very far.
3. If proteins are made up of a relatively small set of “chunks” rather like a lego kit. This would simplify the problem of building a new protein superfamily. Gene fusion events can be used to build a new structure.
But Axe states that…”The binding interfaces by which elements of secondary structure combine to become units of tertiary structure are predominantly sequence dependent, and therefore not generic.”
Thus enzymes with an identical function and 50% sequence similarity do not have chunks which are interchangeable. Even when this similarity is increased to 90% equivalent chunks are not interchangeable. Graziano and his co-workers constructed and tested a huge library of 10^8 variants of gene segments and found none that formed a folded structure.


Sunday, September 26, 2010

The Origin of Protein folds

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!

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.