The Lenski Experiments

In the Lenski experiment the E.Coli cells grown in the presence of oxygen gained the ability to transport citrate across the membrane. The allowed them to utilize citrate as a carbon source and provided a selective advantage in the conditions of the experiment.

In the absence of oxygen with another suitable source of energy the E.coli cells are able to transport and use citrate.

The mutation(s) that occurred in the Lenski experiment therefore allowed (unusually) the transport of citrate across the membrane in the presence of oxygen.

As far as I am aware the detailed molecular story of what happened in this particular case has yet to be unravelled. It seems that at least two different mutations must occur for this ability to be conferred.

As far as I am aware no new proteins are involved. The most likely explanations are a loss of the usual control of the anaerobic citrate transport system or a mutation in a protein that transports a similar molecule

What is significant from these results is that even for this small modification in an existing protein 31,500 generations were required with a population size of about 5 million. This was in the presence of the heaviest selection pressure possible.

Behe argues that this work is consistent with his arguments regarding the limit of evolution.

Behe’s discussion of the Lenski work.

A recent Scientific American article on the Lenski experiment. (HT to Psilo)

How big is the hole?

In an earlier post I likened the production of a protein with a new function to a blind man playing golf. One commenter wondered how large the hole was. I thought of this again while reading Stephen Meyer's recent book "Signature in the Cell". He presents the figure of 1 out of 10^74 as the number of possible proteins 150 amino acids long which have any function whatsoever. If this is correct then the hole is very small indeed...roughly equivalent to finding a single marked atom blindfold from all the atoms in the milky way. This figure also assumes that all the amino acids are left handed and only peptide bonds are formed.

Change in Comments Policy

Visitors will have noticed that there has not been much activity here for some time. This was because I have been unable to devote sufficient time to dealing with hostile comments. As a result of the increasingly unpleasant nature of these comments I have (reluctantly) decided to have only moderated comments.

For a comment to be published it must:
-be directly relevant to the post
-contain no bad language
-be polite

The God Delusion

I am reading Dawkin's book with the above title. A couple of thoughts occurred to me as I read the chapter entitled "Why there is almost certainly no God."

1. If Darwin was correct in highlighting the discovery of a complex organ which cannot be produced by numerous slight successive modifications as a real possible falsification of his theory then we cannot simply rule out any such proposed organ as a "God of the gaps" argument. If the God of he gaps protest is permitted then the possible falsification has gone. If the falsification is a genuine possible one then we must allow for the existence of real gaps.

2. Dawkins argues that an intelligent designer must be more complex than the evidence of his design and therefore requires a further explanation of an even higher level of complexity. He seems to indicate that this is a sort or killer punch as if the rule of the universe is that all complexity must necessarily come from simplicity. However the fact that he spends time on other arguments seems to indicate that he is not entirely happy that his killer blow has actually killed.

Self Organisation is the Answer

From an interesting Telegraph article here.

"Evolution on its own doesn't look like it can make the creative leaps that have occurred in the history of life," says Dr Seth Bullock, another of the conference's organisers. "It's a great process for refining, tinkering, and so on. But self-organisation is the process that is needed alongside natural selection before you get the kind of creative power that we see around us.

Is Science atheistic?

“Some say God is living there. I was looking around very attentively, but I did not see anyone there. I did not detect either angels or gods…. I don’t believe in God. I believe in man—his strength, his possibilities, his reason.” (Titov USSR)

The question that interests me is whether atheistic scientists are willing to acknowledge that a clear line can be drawn between science and atheism. Can one be just as committed to science and yet believe in the reality of God, spirits, miracles and special revelation or is an atheistic, materialistic world view the only real position that a true scientist can take.

1. Is science intrinsically atheistic? Atheistic science is the true un-encrusted form whereas theistic science is a primitive medieval form of science prior to its emancipation to full grown materialism.

2. Can the tools of science be seen as a valuable toolbox which can be used usefully within a variety of philosophical contexts and presuppositions but has limited value in actually testing those contexts and presuppositions.

3. Can the results and evidence produced by the toolbox of science be seen in different ways according to the presuppositions and philosophical contexts of the individual scientist? Do the presuppositions and philosophical context of the scientist affect the way in which the data is interpreted and put together? Do the presuppositions and philosophical context predispose individual scientists to particular interpretations of the evidence?

Institutionalised Idolatry

One of the key blindspots of atheistic scientists it seems to me is their inability to distinguish between beliefs based on evidence and beliefs based on presupposition. There seems to be the assumption that any "religious" position is antagonistic to some kind of "normal" view of any civilised democracy. The "normal" view of any civilised democracy is of course secular humanism - atheism- the worship of man as the highest authority. What they seem to have missed and be apparently completely blind to is that this secular humanism is just as much a "religious" position and faith as any other "religious" position. Its assumed "normal" and superior status is just another kind of religious orthodoxy seeking to impose its dogmas upon a society. Many people including top scientists seem to be entirely blind to this.

I thought Geoffrey Lean's article very perceptive.

Tail on the Donkey

I was thinking about Intelligent Design and I thought of the old children’s game that we used to play – Pin a tail on the donkey. The children competing would be blindfolded and each would be given a tail with a pin in it. They would have to guess the correct position of the donkey and pin the tail where it was supposed to go. Get the tail in the right place and you are a winner.

This is a bit like finding a protein that works by random mutation. The protein that works is the donkey with the tail in the right place.

The key variables are the size of the available space for your pin and the number of people trying to stick the pin in the right place.

Of course there is not just one right sequence that works and gives a selective advantage and there are of course many more players in protein building than children at a party. However the key question is - how realistic is it to think that random mutation and natural selection are sufficient tools to build all the proteins and protein combinations that are required to explain biology as we know it?

If we made our illustration realistic….

• How big would the board space be for sticking the pins in?
• How big would the area be that give a selective advantage?
• How many tails need to be stuck on how many donkeys at once?
• How many children do we need on the board to make life as we know it a realistic achievement for chance mutation and natural selection?

These are the big questions for ID research. One would have thought that biologists would agree that these are really exciting questions to be asking. This is the area where there is a real possibility for the main mechanism proposed for evolution to be falsified and shown to be unrealistic. That surely makes this research great science and exciting science.

That is the sort of research that Doug Axe is trying to do…. But it isn’t being funded by the usual biology funding pathways. He has developed a good method. He has published good work in the field. When you mention that he works in the Biologic Institute to the Darwin faithful at best you get a sneer at worst a snarl and curses!

You could put his decisions down to one big weird publicity stunt or say that the fellow has lost his marbles or you could say that there is more going on in modern molecular biology than a disinterested pursuit of the truth…wherever it leads.

I have a hunch that it isn’t just a publicity stunt and that his marbles are pretty much all present and correct and that he might be right and he might be able to demonstrate that he is right. I hope so and wish him well!

The Biologic Institute.

I have been following Douglas Axe's work with interest (see here and here) so I was very keen to look at the website of the Biologic Institute. This is the research institute that is funded by the Centre for Science and Culture which Douglas Axe is in charge of.

On the research page there are reports of what they have been working on and descriptions of the research which has been or is shortly to be submitted for peer review. "The difficulty of interconverting the functions of structurally similar enzymes" is one of the areas in which I will be interested.

The sad part of the story is why such an institute is needed at all. The work that Douglas Axe has done and the systems that he has set up should be supported in the usual way without the need to set up a separately funded institute.

How do Scientists use the word “Theory”?

I have heard many people who believe in Creation say “But evolution is only a theory.”
What they mean is that in denying the evolutionary view of life they are not denying proven facts.

The difficulty is that the statement includes two words which are used in very different ways and the statement is therefore open to serious misunderstanding.

I explained why I believe that distinguishing between micro and macro evolution here.


I want to set out a few thoughts about the word “theory” here.

It is a word with multiple senses from relatively loose to very tight and is therefore a source of confusion.

In ordinary speech it is used in the following ways:
Speculative suggestion which provides an explanation for one or more observations. The Shorter Oxford dictionary has this description: “An unsubstantiated hypothesis; a speculative (esp. fanciful) view.
Theory vs Practice – In theory how something should be done – Abstract knowledge and speculative thought. A scheme of how to do something including all the rules and principles to be followed- eg a theory about bringing up children.
A hypothesis that has been confirmed or established by experiments or observations and is accepted as accounting for known facts.
In science the word has a set of more specialised meanings.
There seem to be two dimensions of use of the word “Theory” in Science.

Its reach – how high in the hierarchy of scientific knowledge is it?
“a comprehensive explanation”
The oxidative stress theory of Ageing is of a much lower order in Biological Theories than the theory of evolution.

Its validity – how certain are we that it is correct?

There are five ways the word is used in science:

1. The NAS definition of scientific theory indicates that the use of the word theory should be reserved for the very highest level of validity:

“supported by many facts gathered over time” “so well established that no new evidence is likely to alter them”
Tests – Logical consistency, How throroughly it explains data and how broadly it can be applied.
The Panspermia theory of the origin of life on earth is of much lower validity than Theory of DNA being the coding molecule for the production of proteins in the cell.


The NAS has attempted to define the word theory as having a very wide reach and the highest possible standard of validity.

“In science, the word theory refers to a comprehensive explanation of an important feature of nature that is supported by many facts gathered over time.”
“Some scientific explanations are so well established that no new evidence is likely to alter them. The explanation becomes a scientific theory.”

However though the NAS clearly uses the word like this in some of its publications this is not a comprehensive definition covering all uses of the word in the current professional scientific literature. On its own this is actually a misleading definition and is therefore unhelpful. It does not relect the real usage of the word in science.



2. It is used for a confirmed hypothesis.
e.g. New theory confirms that genetic kin recognition is inherently unstable, explaining its rarity.
3. It is used for an unconfirmed hypothesis or for one of several competing hypotheses.
e.g. here
4. It is used for explanations which have been shown to be incomplete or even wrong.
e.g The Ether Theory for the propagation of light.
Newtons theory of motion ie it is not a complete theory and does not work well near the speed of light.
5. Theoretical speculation currently unverifiable- String Theory or Theories of Everything.

Now in what way is ID a scientific theory and in what way is it not?

I would answer
1. No
2. No
3. Yes
ID is one of several competing hypotheses for the origin of biological complexity.
4. No
5. No

Other references:
http://en.wikipedia.org/wiki/Theory

http://www2.ncseweb.org/kvd/experts/behe.pdf
(9.6MB includes large images)

Realistic Cooption.

It seems clear to me that, at the very least, Behe’s book “Darwin’s black box” stimulated interest in, thinking about and probably research into - the origin of complex integrated biological systems.

As I understand it the current Miller/Matzke etal explanation for the origin of the rotary motor propulsion systems in bacteria is a series of cooption events.


Function 1 (1 or more proteins)

↓

← Function 2 (1 or more proteins)
↓

Function 3 (2 or more proteins)

There is an assumption that all the proteins which form the motor have all been collected and modified from other purposes in the bacterial cell. In the words of the New Scientist article- it was “cobbled together.” Some of the proteins in the motor have not been found to have any homologues elsewhere but let us assume that homologies for all the proteins will be found at some point.

My big question is whether this explanation is realistic. Obviously we can imagine it happening providing if we try hard enough. The big question that remains to me is whether this is just wishful thinking. Is it realistic to imagine this happening? How can we know when a series of imagined cooption events is realistic or not.

Obviously if we find compelling examples of intermediate stages this helps but is there a way in which we can test whether our evolutionary imaginations are being kept within realistic limits?

Outboard motors made without design.

The New Scientist has a piece announcing the death of the flagellum as the great champion of the demonstrations of design in biology.

It is a well written piece and gives a useful summary of the response of Darwinists to Michael Behe's argument of Darwin's Black box.


The arguments can be summarised:

1. There are lots of different flagellum like systems. If there was a designer he would not design this more than once

[This makes the assumption that people who believe in design do not believe in any evolution at all. It is a theological argument which claims to be able to see into the mind of God and say what he would or would not do.]

2. There are strong homologies of the flagellum proteins with the proteins of the Type 3 secretory system(T3SS). (Workers acknowledge that the T3SS probably came from the flagellum rather than the other way around.)

3. There are homologies with many of the other proteins suggesting that many of the flagellum proteins may have been co-opted from other functioning structures.

The conclusion is...
"this abundance of homology provides incontrovertible evidence that bacterial flagella are cobbled together from recycled components of other systems - and vice versa - through gene duplication and diversification. In other words, they evolved."

To my mind that is just rubbish.
Most of the proteins showing some homology to other proteins does not prove that it is reasonable to think that the blind watchmaker made it without any help.

"Evolutionary biologists have put their house in order. It's time for their opponents to do the same." Doolittle

This is about as close as Darwinists go to saying that Behe made an important point in his book!

I am afraid that I still think that it is reasonable to conclude that the bacterial flagellum could not be assembled in the way that these champions of the fight against "unreason" maintain. [Unreason = any vestige of a conviction that intelligence is required for the origin or diversity of life]

It is a pretty cheap response to Behe's argument to present the whole problem as essentially concluded in favour of a blind watchmaker simply by showing that many of the proteins in the flagellum have sequence similarity to other bacterial proteins.

The big questions that still remain in my mind are these:

1. Is it reasonable to think that there is a pathway from these proteins doing something else to their specific function in the flagellum that we see today.

2. Is it reasonable to think that the proteins that are required but which have no known homologies could also arrive to allow the flagellum to function.
3. Is it possible to get to a clear answer for the above two questions. Is it possible to test whether Darwinists are simply excercising too much faith in the power of the blind watchmaker or not.


I am aware that Darwinists are good at imagining long pathways of functioning machines with gradually increasing complexity...but how do we know if they are reasonable or not? Should I believe them until someone demonstrates it is impossible or should I disbelieve them until someone demonstrates it is possible?

Maybe a simple thought experiment will clarify what I mean...

Let us imagine a machine which does something useful (but is not a motor)which contains all but 4 of the proteins needed to make a motor.

Let us imagine that those four proteins are busy doing something else in the boring but busy immobile bacterium.

Let us imagine that those four proteins have all duplicated and the duplicate of each is busy accumulating point mutations etc such that they can no longer perform the function the blind watchmaker made them for.

Let us imagine that the times are good- all the economic indicators for bacteria are favourable - it is a real baby boom and the population is rocketing!

My question is - How big are the targets that these four proteins are aiming for? (please excuse the teleological nature of the sentence!)

Is it reasonable to think of all four hitting the target at the same time?

Is that a reasonable scenario or do Darwinists imagine the co-option of one protein at once? With each addition providing selective advantage??

Who adjudicates fairly what is reasonable here? The champions of reason of course.

Freak spaghetti arrangement?

Synthetic Life.

Spontaneous living cells in a test tube from simple ingredients?
Well no …..not quite…. we supply the carefully made membranes….oh and the 36 enzymes…. Oh and also the ribosomes…..oh and also the genetic information! But we are nearly there!

At least this is the illusion that some origin of life researchers seek to indicate.

Dr. Giovanni Murtas from the Synthetic Biology and Supramolecular Chemistry group at RomaTre University says:

"We can prove at this point that we can have protein synthesis with a minimum set of enzymes - 36 at the moment."

The fluescent green colouring indicates that these "primitive cells" can synthesize a protein from the supplied genetic information.

According to the guardian account this result “will teach us about the earliest stirrings of life in Earth’s primeval slime some 3.5bn years ago.”

Yerrr sure!

I would have thought that to any unbiased observer this result simply reminds us all that there is no hope that the primeval slime…no matter how exotic and how many billion years you give it will ever produce a living organism with minimal information and functioning protein machinery.

The information to specify such elegant structures as these does not hang around in primeval slime waiting for 36 enzymes and a few ribosomes to arrive.


I am not against this kind of work at all... I applaud it! What I am against is giving the impression that the solution to the problem of the origin of life is nearly solved and it is just a matter of time before we crack it.

Melanie Phillips - Life in a random Universe?

"Moreover, since science essentially takes us wherever the evidence leads, the findings of more than 50 years of DNA research — which have revealed the almost unbelievable complexity of the arrangements which are needed to produce life — have thrown into doubt the theory that life emerged spontaneously in a random universe."

See the whole piece here.

Science Vs Religion.

Publication of Steve Fuller’s Dissent over Descent has been delayed until Spring 2008. However, in the meanwhile, he has just published another book relating to ID, Science vs Religion? Intelligent Design and the Problem of Evolution (Polity). You can peek inside the book by going to the Amazon website.

Fuller will be speaking at the Leeds University conference, ‘Darwinism after Darwin’, on 3-5 September. This includes an appearance on a panel discussing Richard Weikart’s controversial From Darwin to Hitler (Palgrave), with Weikart as respondent. For more information about this conference, which is open to the public, see the website: http://www.darwinismafterdarwin.com/

Darwin or Design.

Jason Rennie, the young Australian producer of the on-line ‘thesciphishow’, has released ‘Darwin or Design’, 9.5 hours of interviews with various people on either side of this controversy.

The links to these interviews are here.


An overview of Evolution
Chapter 1 : PZ Myers, An overview of Evolution and ID 15:48
Chapter 2 : Sean Carroll, What is Evo Devo ? 20:17
Chapter 3 : Nick Matzke, Can the Flagella Evolve ? 29:27

Design in the ID advocates own words
Chapter 4 : Salvador Cordova, What is ID ? 20:20
Chapter 5 : Mike Behe, What is Irreducible Complexity ? 17:51
Chapter 6 : Angus Menuge, Agency and how to identify it 18:28
Chapter 7 : Guillermo Gonzalez, The Privileged Planet 17:26
Chapter 8 : Joey Campana, Does ID research actually exist ? 26:17
Chapter 9 : James Shapiro, Sentient Cells ? 33:50
Chapter 10 : Mike Gene, What is Front Loading ? 23:37

ID's critics
Chapter 11 : Elliot Sober, ID and the Philosophy of Science 10:46
Chapter 12 : Scott Turner, The problem of Design 24:02
Chapter 13 : Glenn Morton, Can ID work in Biology ? 15:19
Chapter 14 : Ryan Nichols, Are ID and Theology Inseperable ? 14:28
Chapter 15 : Georgia Purdon, Isn't ID just Creationism in Disguise ? 21:44

ID, The Philosophy of Science, History and The Law
Chapter 16 : David Livingstone, Evolution and Christianity, The History 32:37
Chapter 17 : Del Ratzsch, Can ID be Science ? 25:38
Chapter 18 : Massimo Pigliucci, Evolutionary Epistemology and ID 28:34
Chapter 19 : Henry Schaefer, Science and Religion 14:40
Chapter 20 : Donald McConnell, Intelligent Design, Creationism and The Law 34:42
Chapter 21 : Steve Fuller, ID & Social Epistemology 19:11

ID in the Wild
Chapter 22 : John Davison, The Price of Dissent 35:26
Chapter 23 : Denyse O'Leary, ID & The Media 22:51
Chapter 24 : Geoff Simmons, Darwinism, ID & Medicine 27:40
Chapter 25 : Rob Sawyer, Calculating God 25:27

Expelled!

A trailer for this film due to be released on Darwins birthday (February 12th next year) is now available here.

Press release is here.

It looks interesting!

Separation of Science and Religion

The separation of the religious and the scientific means in the end the separation of the religious and the true; and this means that religion dies among true men.

(James Denney - Studies in Theology 1894)

Teaching Intelligent Design is the perfect recipe for mass producing suicide bombers!

This is apparently what Harry Kroto (an otherwise intelligent fellow) seriously believes!

The Education Guardian included this extract from Sir Harry Kroto’s (Francis Eppes professor in the department of chemistry and biochemistry at Florida State University) “Can the Prizes Still Glitter? The Future of British Universities in a Changing World” published by Agora.

Do I think there is any hope for UK? I am really not sure. It is beyond belief that in the 21st century, our prime minister and the Department for Education and Skills are diverting taxpayers' money to faith-based groups intent on propagating culturally divisive dogma that is antagonistic to the secular, enlightened philosophy that created the modern world.

It is a scandal that the present system is enabling a car salesman to divert significant government funds to propagate dogma such as "intelligent design" in our schools. State funds are also being used to support some schools that abuse impressionable young people by brainwashing them into believing that non-believers will burn for all eternity in the fires of hell. This policy is a perfect recipe for the creation of the next generation of homegrown and state-educated suicide bombers.

I think there is every likelihood that the lack of scientifically educated and aware young people in the UK will result in ever poorer performance on a global scale, and a takeover by the next generation of young Chinese and Indians, ravenous for the scientific knowledge that will free them from the shackles of present poverty levels. They are being actively encouraged by their governments, who understand that the future lies in a scientific education based on doubt and questioning, rather than on belief.

It is truly disturbing that a well-funded cohort of religious groups - aided, abetted and condoned by the Labour government - is undermining our science education. If they achieve any more success in their subversion of the intrinsic secular safeguards embodied in our democratic institutions and our educational system, there can be no doubt there is major trouble ahead. So my final message is: "Do Panic!"

Harry Kroto is a brilliant scientist. However as an example of what he describes as “the enquiring mindset” he leaves a great deal to be desired with regards to the influence of his own materialist mindset on his convictions about those who disagree with his philosophy.

It is scarcely credible that a well educated scientist feels that he can write such patently ridiculous, offensive, ill informed, vitriolic gibberish.

If he feels as strongly about this as he appears to from this extract then at the very least he ought to get his facts straight! Being passionate about something is one thing. Being passionate about and publishing your passionate rhetoric without checking your facts is the quickest way to make yourself and your cause appear ridiculous.

1. What evidence is there that a traditional Christian education produces a higher proportion of suicide bombers than an atheistic, materialistic, relativistic one or any other sort of education? Presumably Kroto lumps all religious education together as being equally destructive. If you are religious then you are a secret member of the Taleban. So much for a carefully nuanced and a meticulously researched piece of prose!
2. What evidence does he have that a particular car salesman is in favour of teaching any intelligent design or creationism in science lessons let alone that he is diverting government funds for this purpose?
3. What right has he got to claim all the improvements in the modern world as the natural children of “secular, enlightened philosophy” (which presumably means materialism)?
4. What evidence does he have that there is “brainwashing” taking place in any UK state school?
5. Since when did the UK become a secular materialist state?

I share Prof Kroto’s concern for improved science education at the university level in the UK. However I do not think that insisting upon an ideological commitment to materialism like the bad old days of the USSR is the way to catch up with the US where there is considerably more creationism and intelligent design than in the UK.

Evolution becomes fact.

"For many years it was possible to doubt the validity of Darwin's theory, but skepticism is not a tenable position today."

Cynthia Russett, Darwin in America 1976, p210

When did this transition take place? What were the key discoveries that resulted in this transition?

Science and Materialism.

I was interested in this quote from Martin Redfern's article.

"Everyone is entitled to their beliefs, but what annoys Eugenie Scott is the way in which the received wisdom of Genesis is given equal or higher status to scientific evidence; and the way in which the latter is used selectively.

'In the card game of creationism, the Bible trumps science every time,' she says.

But in her game, science is dealt a hand that is purely materialistic. Ideas of a supernatural being belong in a different game, be it philosophy or theology."

Fuller Dissent.

Steve Fuller has a new book out:

I have pre-ordered a copy so I will be interested in his view of this controversy on this broad canvas. I wonder if his arguments will include things like this?

Methodological Naturalism

Just over a year ago Paul Nelson posed this question here

"Ask oneself a simple question. Suppose life actually were designed by a nonhuman intelligence -- would methodological naturalism allow us to discover that? If the answer is no, then methodological naturalism hinders scientific discovery and dictates the shape of reality as thoroughly as philosophical naturalism. If the answer is yes, then methodological naturalism is superfluous and says nothing more than that science should be empirical and testable."


Do you agree?

Questions....

1. Is Methodological naturalism (MN) an essential commitment for scientific progress?
2. Is MN falsifiable? Could MN be false? How would we know?
3. Is the origin of life without intelligence reasonable without a prior commitment to MN? Is it acceptable scientifically to think that the origin of life requires an intelligent agent?
4. Is MN significantly different from philosophical naturalism? Are MN and consistent Theism compatible?

Douglas Axe - J.Mol.Biol.(2000) 301, 585-595

Thanks to "Smokey" for the paper.
Previous blog post here.
This paper examines the idea that there are many amino acid residues in an enzyme which almost act as non-specific spacer residues and the nature of their side groups is almost completely irrelevant to the enzyme function. The only requirement is that the external residues be polar and the internal ones be hydrophobic (the binary code hypothesis). The paper argues that this idea is erroneous. Axe’s arguments rely on data from two different, unrelated enzymes.

Firstly, several amino acids are exchanged with several other very similar amino acids on the surface of the molecule and away from the active site and the effects measured. When roughly 1 in 5 of these residues is changed this results in complete loss of function in both enzymes examined.

Secondly, hybrids are constructed between two different versions of B-lactamase enzymes using various combinations of their surface sections. All of these hybrids are inactive.

Axe concludes that homologues that share less than 2/3 sequence identity should be considered as distinct designs with their own set of optimising features.

These results were surprising as they followed similar experiments where the hydrophobic core or an enzyme was systematically replaced and the conclusion was that general hydrophobicity was the only requirement for these core residues.

It was expected that the surface residues distant from the active site would show an even greater degree of tolerance to change than the hydrophobic core residues.

Axe compares the two hybrid situations with two functionally equivalent linguistic messages where exchanges between the non-conserved letters is functionally disastrous.

Away for a few days.

I will not be around for a few days so I will look at comments when I get back.

Inside the Cell.

David Goodsell is a biochemist who is also an excellent artist. He has combined these skills in the production of beautiful paintings which seek to portray an idea of the molecular biology of the cell. More of his illustrations are here. He kindly gave me permission to use these pictures here:

This picture shows part of a bacterium.

(Can you spot the motor? :-) )

This one shows a section across a red blood cell with the blood serum outside the cell.

This is an enlargement of a small part of the same picture.

This picture shows an HIV virus particle under attack from the immune system.

(Thanks to Tony Jackson for the original link.)

"Strong indications of design."

Nick Jackson of the Independent interviews Stuart Burgess who argues that there are "strong indications of design" in the four bar linkage of the knee joint. The report is here.

The making of "The Root of All Evil."

In response to this question:
Why have you not engaged in public debate with Alister McGrath, Mary Midgley, Michael Ruse, Keith Ward, or indeed anyone else who would present you with a serious challenge? JAMES RADFORD, By e-mail
Richard Dawkins replied:
The producers of my Channel 4 documentary [Root of All Evil?] invited the Archbishop of Canterbury, the Cardinal Archbishop of Westminster and the Chief Rabbi to be interviewed by me. All declined, doubtless for good reasons. I don't enjoy the debate format, but I once had a public debate with the then Archbishop of York, and The Observer quoted the verdict of one disconsolate clergyman as he left the hall: "That was easy to sum up - Lions 10, Christians nil."
(from here)


Alistair McGrath gives a somewhat different slant...
Dawkins and I both love the sciences; we both believe in evidence-based reasoning. So how do we make sense of our different ways of looking at the world? That is one of the issues about which I have often wished we might have a proper discussion. Our paths do cross on the television networks and we even managed to spar briefly across a BBC sofa a few months back. We were also filmed having a debate for Dawkins's recent Channel 4 programme, The Root Of All Evil? Dawkins outlined his main criticisms of God, and I offered answers to what were clearly exaggerations and misunderstandings. It was hardly rocket science.
For instance, Dawkins often compares belief in God to an infantile belief in Santa Claus or the Tooth Fairy, saying it is something we should all outgrow. But the analogy is flawed. How many people do you know who started to believe in Santa Claus in adulthood?
Many people discover God decades after they have ceased believing in the Tooth Fairy. Dawkins, of course, would just respond that people such as this are senile or mad, but that is not logical argument. Dawkins can no more 'prove' the non-existence of God than anyone else can prove He does exist.
Most of us are aware that we hold many beliefs we cannot prove to be true. It reminds us that we need to treat those who disagree with us with intellectual respect, rather than dismissing them - as Dawkins does - as liars, knaves and charlatans. But when I debated these points with him, Dawkins seemed uncomfortable. I was not surprised to be told that my contribution was to be cut. The Root Of All Evil? was subsequently panned for its blatant unfairness. Where, the critics asked, was a responsible, informed Christian response to Dawkins? The answer: on the cutting-room floor.
(from here)

Comments.

The comments section at IDintheUK has been entirely uncensored up till now (apart from really foul comments and obvious advertising.) I would like it to remain like this. I have learned a lot from the very high quality of comments from people on both sides of this argument. This seems to me a great benefit of this kind of site.

In order for this to continue it does require some self discipline on the part of the commenters.

Generally you have responded well to previous pleas.

I would like people to feel free to comment under whatever name they like and to be able to comment annonymously if they so choose. I think that part of good blog behaviour is to respect that choice. Attacks on another commenter because of their background and percieved or actual bias are to be avoided- it is the arguments about the data and its interpretation that we should focus on.

Please try to avoid overly emotive language- I know that many commenters feel very very strongly about this area - It is good to feel strongly about truth and to expose what is not true ruthlessly and energetically. However resorting to the red card "LIAR" is rarely helpful in my experience. Even if you are convinced that someone is deliberately and knowingly lying it is better to suggest that they may be mistaken first and point to the evidence. If you must make an allegation of deliberate, knowing deception please make sure you have a cast iron case and please try to do it as little as you possibly can.

The Dawkins Delusion.

I have noticed several pieces about this odd phenomenon. Bill Dembski seems to have got hold of a very strange interview with Dr Terry Tommyrot, available here. Another interesting report of a discussion on the same subject is here.

Possible Pathways for the evolution of intracellular transport.

In his book “Darwin’s Black Box Behe made the claim with regards to the cellular transport systems that:
"A search of the professional literature and textbooks shows that no one has ever proposed a detailed route by which such a system could have come to be."

Some commenters here have argued that Behe is being intentionally deceptive they argue that there is an abundance of published material – shelf loads of it - that give a clear outline of how a pathway transporting a newly synthesized protein to an intracellular compartment could arise.

Some suggestions were given as to where I should start – (I acknowledge that they were probably hurriedly put together sources by scientists who are very busy doing more important work than arguing with me and I do appreciate the attempt to provide me with the references.)

http://www.mrc-lmb.cam.ac.uk/myosin/Review/Reviewframeset.html

This is sequence comparisons in the myosin superfamily looking at homologies between the different types of myosin molecules in different organisms.

http://www.pnas.org/cgi/content/full/103/10/3498
This is the attempted production of a phylogenetic tree comparing different types of myosin molecule.

The Richards and Cavalier Smith Nature paper is similar and suggests that the most primitive eukaryotes had three types of myosin from which all eukaryotic myosins come but that does not really help me.

This gives 111 delightful titles but not really what I am after. They are mainly phylogenetic trees and studies of sequence similarities. Behe accepts that there are an abundance of this kind of study.

What I am after is a simple step by step process whereby a single transport system from protein translation completion to function in a separate compartment can arise. It does not have to be a DVD of the process happening just a suggestion of some of the useful steps along the way.
I am thinking of the kind of thing that Matt Inlay produced in response to Behe’s Immunology chapter (here) or Nick Matzke’s response to the flagellum chapter ( here)


Tony’s scenario:
This problem concerns the way proteins are targeted to the mitochondria. These organelles (again, they’re shown in your diagram) are responsible for supplying a major fraction of the cell’s energy needs. They are distantly descended from free-living bacteria that began a symbiotic relationship with an early eukaryote. As part of that evolutionary history, mitochondria still retain a small genome which encodes a few of the proteins required by the organelle. However, over evolutionary time there has been a general drift towards more and more mitochondrial genes being transplanted to the nucleus. Mitochondrial proteins produced from such nuclear genes somehow have to get to their correct organelle. How do they do that? It turns out that such proteins contain, right at the start of their amino acid sequence, a so called ‘targeting signal’ made of about the first ten or so amino acids and which docks with import machinery in the mitochondrion. A mitochondrial gene newly transplanted into the nuclear genome must acquire this signal or it risks turning into a pseudogene. So how easy is it to acquire a functioning targeting signal? Some years ago a clever experiment was performed to find out. It’s a neat example of how our intuitive ‘gut feelings’ about these issues can lead us badly off-course. The scientists took a gene for a mitochondrial protein, then replaced its normal targeting signal with random DNA sequences sized to encode between about ten and thirty amino acids. They then determined what fraction of these random sequences acted as functioning mitochondrial targeting signals for the protein.What do you think the answer was? One in ten million? Or some other Dembski number perhaps? Actually, they got a remarkable 3 to 5%! Subsequent work with more truly random and uniformly-length sequences increased this estimate still further. Evidently, it’s almost ridiculously easy to evolve working targeting signals. One more point is worth making here. Because the results were so striking and the way the experiment was conducted was so elegant, this work is rather well known in the field. It was published in 1987 – almost ten years before Behe wrote his book. Yet he tells us with a straight face that no experiments have been done to address the evolutionary origins of protein traffic!


Tony’s point here is that the ID code for the mitondrial car park is pretty easy to forge. The fellow checking the ID’s is a pretty sloppy fellow and a great variety of ID sequences will do.

However let us imagine that this putative mitochondrial gene is the very first one to complete the journey into the cell’s genome. Let us also assume that the appropriate insertion of DNA occurs of the correct length and with the approximately correct sequence. Is this all that is required for the newly made protein to find its way into the mitochondrion? Is it just a single rough ID sequence that is needed or are other modifications required in the mitochondrial genome and elsewhere in the cell?

Molecular Meccano

Described by some researchers as a strange form of molecular “lego” and by others as “molecular basket weaving” the beautifully shaped propeller like molecules of clathrin have a crucial role in the cell’s internal distribution network. Another description in the literature is “groovy” which I think is about right! A single clathrin complex is made up of 3 light chains together with 3 heavy chains

to form the propeller like structure called a “triskelion” meaning three-legged.
These 3 legged units can be attracted to a membrane by a variety of different molecular structures on the surface of the membrane. As they are attracted they begin to associate

and as they associate they begin to bend the membrane inwards. The structure grows to form a complete and beautiful basket or cage around a little blister of membrane which is eventually pinched off to form a separate bubble inside the membrane.

At this point the clathrin complexes can be removed and reused elsewhere.

The diagram below is adapted from here (thanks to Dr. Tony Jackson)

A Quicktime Movie is here showing the assembly of a clathrin coated vesicle. (You may have to wait a little time for it to load.)

A Flash animation of the budding off of a clathrin vesicle is available here.