The Bathroom Wall

| 261 Comments

With any tavern, one can expect that certain things that get said are out-of-place. But there is one place where almost any saying or scribble can find a home: the bathroom wall. This is where random thoughts and oddments that don’t follow the other entries at the Panda’s Thumb wind up. As with most bathroom walls, expect to sort through a lot of oyster guts before you locate any pearls of wisdom.

The previous wall got a little cluttered, so we’ve splashed a coat of paint on it.

261 Comments

Troll writes

Why not take a 200 aa protein (for example) and see how many proteins can be randomly changed before it loses some function - and how many before it loses all function?

Please tell us how we know that the protein has lost “all function”? That’s Question #1 for you. When you provide an answer that shows you have some understanding about molecular biology, I’ll take you more seriously.

Well now, I’m not the one who is trying to convince people that evolution is plausible. You want to convince me? Then put something relevant in the area of verifiability: don’t just make up stories about how something “might” have happened. Also, I’m not an evolutionary biologist - or for that matter, a biologist at all, so I expect biologists who have something to prove to present me with research to demonstrate the truth of their hypotheses.

However, I’m happy to give it a go. In prokaryotic cells, a single RNA polymerase enzyme catalyses all RNA synthesis. There is plenty of it about to experiment on, presumably. Rates of reaction can be measured in standardised conditions. What is the effect of one change on the rate of reaction? Ten changes? A hundred?

Then following on, how uniform is this enzyme across all prokaryotic cells? Is there a gradual improvement pathway that would allow selection to work from a version of the enzyme that is specified all but (say) 10 amino acids? How close to the “right” sequence would this enzyme have to be for a darwinian mechanism to work on it? What this would mean is that the proto-enzyme should be partially effective at catalysing RNA synthesis, and a random change that leads to a greater correspondence with the enzyme as we see it today should improve the reaction rate. Isn’t this basically the evolution model proposed by neo-darwinism?

Incidentally, this is a necessary but not sufficient step to demonstrating that RNA polymerase might have evolved - because if this occurs, it is the last and easiest fraction of the process. You still have to get that already well-specified protein to appear from somewhere, and an optimistic estimate of the proportion of proteins with any function across the space of poly-amino-acid sequences has already been suggested above at 1 in 10^11. (Incidentally, you have asked what I mean by “all function” - what does the author of the paper cited above mean by “any function”?) If you like, this demonstrates micro-evolution at the level of proteins - micro-evolution is accepted by creationists - it would be a bad design that didn’t allow creatures to adapt to changing environments anyway. The big question of macro-evolution at the protein level is still there, but it’s a start.

Creationist Troll wrote

Oddly enough with regard to the correspondence between language and genes - it wasn’t the creationists that started it - it was Dawkins, with METHINKSITISLIKEAWEASEL - which has been demonstrated to be a flawed analogy in various ways - firstly because the target sequence was designed - and secondly because as we can all now see, language is nothing like genes. So of course, you’ll be making sure that Dawkins doesn’t reproduce that analogy in future issues of “The Blind Watchmaker” and any instance where it is quoted will be clarified, in the same way that Haeckel’s embryos are not reproduced, and the peppered moth as case showing natural selection is identified as a flawed experiment, in all biology textbooks.

In fact, Dawkins made it quite clear in the first editionwhat the ‘METHINKS’ example was meant to illustrate, and it wasn’t biological evolution in general; it was the advantage conferred by cumulative selection over non-cumulative stochastic search. Period. And it is still an excellent illustration of that difference. Misrepresentations of it as demonstrating anything else are just that, misrepresentations, regardless of who makes them, evolutionist or creationist.

RBH

I’m glad that has been cleared up, then. So we can derive from this that there is an acceptance by Richard Dawkins that it is hopeless to produce sentences (or proteins) by completely stochastic means, even if the frequency of occurrence of “functional” proteins (definition not given) is as high as 1 in 10^11. (Before you criticise this analysis, I realise I’m not specifying whether this is DNA bases or amino acids, but the difference is less than an order of magnitude). In actual fact, I know that Dawkins accepts this - he talks about upper bounds in improbability based on the number of possible planets in the universe (if I remember right - I am writing without the advantage of a library to hand), and it was the whole thesis of “Climbing Mount Improbable”. The ID community is much more generous, I believe - Dembski is prepared to accept as a lower bound of improbability one in the product of the number of (?) Planck intervals from the beginning of the universe and the number of protons in the universe.

However, granting that this is simply a representation of the advantage of cumulative selection, we then need to consider whether METHINKS is a fair analogy for biological cumulative selection - because the pro-evolution community (particularly non-biologists) have certainly used it in that way.

In the analogy, Dawkins allows a randomly changed letter to convey a selective advantage if it corresponds to the target string. The target string, however, was specified in advance - by Dawkins - or by Shakespeare, arguably. (Dawkins communicates well, but I prefer the immortal bard any day!)

However, one - if we didn’t know what the target string was (if METHINKS wasn’t specified in advance), would random changes to the string allow us to get any closer to “functionality” - a meaningful string? Starting from a random series of bases with (say) a 5% correspondence with a target sequence, is there actually a selective advantage in going to a 10% correspondence? Or a 25% correspondence? For 200 aa’s, we are talking about going from the (expected random number of) 10 being right to 20 or 50 being right. Even an extra 10 aa’s being right would be pretty unusual. OK - we have lots of cells to try this out in - but on the other hand, mutation rates need to be pretty conservative, or any existing specification will be lost long before new specification appears. Will there be a selective advantage in going from 5 to 10%? You need this for macro evolution - production of large scale new features. At the end of the day, if we are talking about probabilities too small then it will be irrelevant whether (as per the disputes with Meyer’s paper above) the Cambrian explosion took place over 40 My or 4000 My - this is, after all, only two of the orders of magnitude of improbability that we are having to deal with.….

Two - the research that I outlined above with (say) prokaryotic RNA-polymerase would attempt to establish that this process of cumulative selection could work at the “higher” end - once you have a 90% (95%? 99%?) specified protein, mutation and natural selection will provide a mechanism for selection to a protein that is completely specified - that is, as tailored to its role as those that we see in cells now. At the end of the day, this is considered to be the engine of evolution. There ought to be research that demonstrates that this can occur. Because if it can’t even be shown to work at the higher end (be an engine for micro-evolution at the protein level, if you like), then there is no way that we can take seriously the stories that are told about it being the engine for macro-evolution.

What we have in METHINKS is what would appear to be an “icon of evolution” - you are saying that the sole point of reference for Dawkins was to show that cumulative selection works. Well, fine, but you don’t need a degree to know that - even a three year old knows that intuitively anyway - it’s the same as the process that we go through when we do a jigsaw puzzle (sorry, dunno if it’s called the same in the US). What Dawkins appears to show is that a series of random changes to DNA bases in a gene can lead “within a very few generations” to a highly specified gene. Even the choice of his words in the way he wrote it were designed to reinforce this perception. Perhaps if the limitations of the analogy were made clear each time it was referred to, it would confuse fewer people - both evolutionists and non-evolutionists.

It is worth bearing in mind that many people who are non-evolutionists now didn’t start off that way - regardless of how you thunder against teaching of creation in schools, this hasn’t been the dominant scientific worldview for over a generation - probably the best part of 100 years at the level of universities. The reason most people give up on evolution is because they suddely realise that they don’t have any evidence for it.

What we have in METHINKS is what would appear to be an “icon of evolution” - you are saying that the sole point of reference for Dawkins was to show that cumulative selection works. Well, fine, but you don’t need a degree to know that - even a three year old knows that intuitively anyway - it’s the same as the process that we go through when we do a jigsaw puzzle (sorry, dunno if it’s called the same in the US).

It is something every three year old knows intuitively, but the vast majority of creationist or ID proponents have somehow managed to forget or deny.

aCTa Wrote:

Perhaps if the limitations of the analogy were made clear each time it was referred to, it would confuse fewer people - both evolutionists and non-evolutionists.

It’s amazing how many ID advocates are unaware that Richard Dawkins very clearly and forthrightly enumerated the reasons why the “weasel” program was not a complete or exact simulation of biological evolution. It’s more amazing still how often ID advocates offer “clarifications” that were already present in Dawkins’s discussion as if they are introducing some new and valuable contribution to the discussion. This phenomenon of communal ignorance and communal chutzpah is simply stunning.

Maybe if the ID advocates could be persuaded to read the original materials for comprehension rather than quote-mining opportunities, there would be less confusion. It’s a radical proposal, I know…

There’s no way to determine what percentage of randomly generated amino acid strings would form a functional structure. But plenty of evidence says that it’s high. Much higher than the naive creationist calculation requires.

Hey Troll

That was some wonderful dissembling above. But how about you answer the question I posed for you? Here it is again (because I know your memory works):

Please tell us how we know that the protein has lost “all function”? That’s Question #1 for you.

Above you mentioned something about “Rates of reaction can be measured in standardised conditions.” You mean rates of all conceivable molecular events that involve the protein in question, don’t you? If you don’t mean that, then please explain what you mean. I’m trying to understand your larger point that proteins must have been designed by alien beings.

And fyi – the burden is on *you*, my friend. You are the one making the nonsensical claim and admitting that you don’t know dick about molecular biology. You’re lucky that I give you the time of day, much less engage you in discussions about aspects of science that you aren’t prepared to understand.

Troll Wrote:

The reason most people give up on evolution is because they suddely realise that they don’t have any evidence for it.

Which is the worst reason since it does not take much time to look at the actual evidence. Of course if one were to rely on creationist resources one may indeed come to such a conclusion. Meyer’s paper comes to mind in this context where he failed to do what a review article should.

For starters see 29+ Evidences for Macroevolution The Scientific Case for Common Descent by Douglas Theobald

Evolution is self evident, the (relative importance of) mechanisms may be open to discussion but ID provides NO scientifically relevant approaches

Wesley - it’s amazing how many non-biologists reproduce Dawkins’ argument as though it is the mechanism for evolution, having failed to observe the caveats that he so clearly enumerated.

Jon Fleming - No, creationists and ID proponents don’t dispute the value of cumulative selection. What they are saying is that it does not provide a mechanism to allow macroevolution to occur, because there is no selective advantage for a protein until it is already very highly specified. I attached some guessed numbers earlier on - I would hazard a guess that a protein needs to be 80%+ specified before single mutations will convey a selective advantage. A random amino acid sequence will only have a 5% correspondence to the specified protein. That’s a mighty big cliff on Mount Improbable before you can reach the gentle slope of mutation and natural selection. Even assuming that there are several hundred ways of skinning a cat, this still only reduces the improbability by several orders of magnitude.

Of course you might be lucky, and get highly specified proteins by chance over and over again. But we don’t like that idea, do we, because it’s indistinguishable from there being a designer. Or an anthropic universe. Not sufficiently materialistic.

GWW - I may not be a Dr, but I did a first year degree course in cell biology, so I know enough to have some idea of what papers are about. I also did chemistry, physics and maths in the first year, and then I did a two year degree in computer science, so I also have some clue about systems modelling and analysis.

I’m not saying that proteins were designed by alien beings - “directed panspermia” and the idea that life actually originated somewhere else in the universe are not creationist or ID concepts.

I can’t tell you when a protein has lost function unless you first tell me what it means for it to have function - as per the paper cited above. I can give you a stab at a definition, which would work out something like as follows. If a protein is an enzyme associated with assisting a reaction pathway under the normal environmental conditions in which it is found, then a mutated version of the protein has lost some relative functionality if under the same conditions the rate of reaction has decreased. It has lost some absolute functionality if under all conceivable environmental conditions the rate of reaction has decreased. Of course, the two are different - if the protein works better in some circumstances, this might help evolution. However, there are some modifications which might mean that the protein will simply not function as it did before at all. A protein has lost all functionality if the rate at which the reaction/process proceeds is at or close to the background rate.

But, hey, I’m the guy who knows nothing about molecular biology. Why should I be trying to tell you what the definitions are? This process (mutation/natural selection) is the foundation of evolution. Surely a better definition has already been written? Surely, in fact, the research exists to show these final stages of natural selection at work on amino acid sequences - possibly even within organisms?

Steve - your statement was so lacking in any substance that it was a waste of bandwidth. Not only have you failed to specify what a “high” percentage is in the vaguest terms, you have failed to specify how high the naive creationist estimates are, and you have failed to specify how high would actually be of any use. This is just vague hand-waving. I’ve already suggested that I don’t think that there is a selective advantage in carrying 10^11 amino acids per random protein to be produced with any functionality - and the likelihood of a protein having a functionality which is of use to an organism hasn’t been estimated either.

Pim - as far as evidence for macroevolution is concerned, there are alternative analyses of the evidence offered in Theobald’s paper cited above. For example, the issue of suboptimum design is often cited - but no consideration is made by evolutionists of the design trade-offs that are always made, or the intention of the designer. Also, a lot of the supposed “sub-optimum” designs, like vestigial organs, and “junk DNA” turn out not to be within a few decades. Of course, that’s only one of the 29+, but I have to work and tend to my family as well - I’m not paid to wrangle ideas. (“that’s for the best”, chorussed the assembled masses! :-) )

aCTa Wrote:

Wesley - it’s amazing how many non-biologists reproduce Dawkins’ argument as though it is the mechanism for evolution, having failed to observe the caveats that he so clearly enumerated.

Really? Let’s see your citations. On the old “One, two, three, many” scale, you should be able to come up with four confirmed cases with no difficulty if your claim has merit.

To head off the usual “You first!” response, I will go first and point out several instances where the careful criticism that Dawkins gave of his own program is overlooked.

When it comes to antievolutionists spouting nonsense about Dawkins’s “weasel”, it’s pretty easy to come up with cases.

Dembski manages to mess up two out of three “steps” in “weasel”: http://www.asa3.org/archive/evoluti[…]10/0310.html

Royal Truman manages to mischaracterize “weasel” in much the same way as Dembski: http://www.answersingenesis.org/docs/4057.asp

Werner Gitt doesn’t get it, either, pointing out the fixed target after Dawkins had already done so: http://www.answersingenesis.org/cre[…]4/weasel.asp

Ey and Batten fail to note Dawkins’s criticisms of “weasel”: http://www.answersingenesis.org/hom[…]_program.asp

Jon Saboe fails to note that Dawkins had already brought up the unrealistic element of having a target fixed in advance: http://www.evolutionisdead.com/weasel_frame.php

Phillip Johnson comes close to crediting Dawkins with having delimited his own program, but then goes on to ask how any intelligent people could think that such a mechanism explains evolution: http://66.102.7.104/search?q=cache:[…]et&hl=en

Raymond Hendrix points out the distant ideal target but never mentions that Dawkins was the first to produce that criticism: http://www.puretolerance.com/chapter8.htm

And as a special bonus, in the “OK, smarty-pants, you were honest in your self-criticism, therefore your argument is rubbish” category, we have Paul Nelson holding forth: http://origins.swau.edu/q&a/evo[…]ions/q9.html

The majority of these people that I’ve cited are well-known, high-profile antievolutionists. Let’s see how “aCTa” does in establishing his counter-claim and who it is that he ends up citing, if he in fact comes up with any examples of people pushing “weasel” as a grand verification of biological evolution without caveat.

I will likely be moving this whole sub-thread to the Bathroom Wall later. We seem to have digressed pretty far.

Troll writes

A protein has lost all functionality if the rate at which the reaction/process proceeds is at or close to the background rate.

You left out the word “relative”, troll. Put the word “relative” back in, go to the post where you made your original claim, and reconsider your argument. Thanks.

No, creationists and ID proponents don’t dispute the value of cumulative selection. What they are saying is that it does not provide a mechanism to allow macroevolution to occur, because there is no selective advantage for a protein until it is already very highly specified.

Claims that cumulative selection “does not provide a mechanism to allow macroevolution to occur” based on arm-waving and argument from ignotace is disputing the value of cumulative selection.

Sorry, Wesley, but I agree with the person who replied to you. If it makes you feel better, call me stupid.

Quote from Dembski cited above:

(1) Start with a randomly selected sequence of 28 capital Roman letters and spaces (thats the length of METHINKS IT IS LIKE A WEASEL); (2) randomly alter all the letters and spaces in the current sequence that do not agree with the target sequence; (3) whenever an alteration happens to match a corresponding letter in the target sequence, leave it and randomly alter only those remaining letters that still differ from the target sequence.

As far as I can remember, that is pretty much exactly the procedure that Dawkins envisages. Would you like to describe the procedure that Dawkins did follow to make clear how that description diverges? Evidently I am not the only one unconvinced by what you said.

aCTa Wrote:

Sorry, Wesley, but I agree with the person who replied to you. If it makes you feel better, call me stupid.

Let’s say “lazy” instead. If aCTa had bothered to open a copy of The Blind Watchmaker or even read the thread in question all the way to the end, he would have found out I was right.

The point of disparity that taints Dembski’s version of “weasel” (both his steps 2 and 3) I mentioned in that thread:

There is rather a large conceptual difference between treating “correct” letters as immune to mutation and treating all letters as equally likely to mutate. I continue to see this as a problem.

Here, by the way, is the text of the final message in that thread that aCTa references:

Richard Wein Wrote:

Oh dear. Maximum embarrassment. ;-)

I’ve just taken a trip down to the public library to re-read the relevant section of TBW. (They only had a reference copy in stock, so I couldn’t bring it home with me.) It turns out my memory of the Weasel model was faulty. Wesley was right. Both Dembski and I were wrong.

My aplogies to Wesley and all whose time I’ve wasted.

Richard Wein (Tich)

I’m glad that aCTa agrees with the person who responded to me, who also agrees that I was right.

I didn’t write my bit until I had re-examined The Blind Watchmaker and corresponded with Dawkins to make sure that there were no other editions of TBW that gave a different description of “weasel”. In other words, I did my homework.

Say, aCTa, where’s the citations backing up your claim about biologists using “weasel” as a verification of evolution without caveat? Having some difficulty finding what doesn’t exist, perhaps?

Could someone help me get a handle on some creationist terminology here? They’ve got new ones, Fully-Specified Protein, and Partially-Specified Protein. Having a little exposure to proteins, i have no idea what these terms mean, or how they could mean anything important. But maybe someone can help me clear up my misunderstandings.

Here’s one protein I’ve worked with:

1 msynnpyqle tpfeesyeld egssaigaeg hdfvgfmnki sqinrdldky dhtinqvdsl 61 hkrlltevne eqashlrhcl dnfvaqatdl qfklkneiks aqrdgihdtn kqaqaensrq 121 rflkliqdyr ivdsnykeen keqakrqymi iqpeatedev eaaisdvggq qifsqallna 181 nrrgeaktal aevqarhqel lkleksmael tqlfndmeel vieqqenvdv idknvedaql 241 dveqgvghtd kavkcarkar knkircwliv faiivvvvvv vvvpavvktr

And here’s a slightly different one I’ve worked with:

1 msynnpyqle tpfeesyeld egssaigaeg hdfvgfmnki sqinrdldky dhtinqvdsl 61 hkrlltevne eqashlrhsl dnfvaqatdl qfklkneiks aqrdgihdtn kqaqaensrq 121 rflkliqdyr ivdsnykeen keqakrqymi iqpeatedev eaaisdvggq qifsqallna 181 nrrgeaktal aevqarhqel lkleksmael tqlfndmeel vieqqenvdv idknvedaql 241 dveqgvghtd kavksarkar knkircwliv faiivvvvvv vvvpavvktr

They only differ by two serines. In yeast cells, they each perform the exact same function. So by this new terminology, are they both fully specified? Or is one, but not the other? Or neither? And why? How could anyone say they’re “fully specified” if they are immune to certain changes in the specification?

Syntax Error: mismatched tag at line 17, column 17, byte 5259 at /usr/local/lib/perl5/site_perl/5.12.3/mach/XML/Parser.pm line 187

Syntax Error: mismatched tag at line 9, column 2, byte 542 at /usr/local/lib/perl5/site_perl/5.12.3/mach/XML/Parser.pm line 187

This just seems so appropriate today.

Well, you wonder why I always dress in black, Why you never see bright colors on my back, And why does my appearance seem to have a somber tone. Well, there’s a reason for the things that I have on.

I wear the black for the poor and the beaten down, Livin’ in the hopeless, hungry side of town, I wear it for the prisoner who has not committed any crime, But is there because he’s a victim of the times.

I wear the black for those who never read, Or listened to the words that Ghandi said, About the road to happiness through peace and empathy, Why, you’d think he’s talking straight to you and me.

Well, we’re doin’ mighty fine, I do suppose, In our streak of lightnin’ cars and fancy clothes, But just so we’re reminded of the ones who are held back, Up front there ought ‘a be a Man In Black.

I wear it for the sick and lonely old, For the reckless ones whose bad trip left them cold, I wear the black in mournin’ for the lives that could have been, Each week we lose a hundred fine young men.

And, I wear it for the thousands who have died, Believing that the Lord was on their side, I wear it for another hundred thousand who have died, Believing that we all were on their side.

Well, there’s things that never will be right I know, And things need changin’ everywhere you go, But ’til we start to make a move to make a few things right, You’ll never see me wear a suit of white.

Ah, I’d love to wear a rainbow every day, And tell the world that everything’s OK, But I’ll try to carry off a little darkness on my back, ’Till things are brighter, I’m the Man In Black

Johnny Cash

I don’t want my grandchildren to die in Iraq, or any other hellish place. I don’t want a “war President” who goes to war when he wants to. I want a “peace President” who only goes to war when he (or she) has to. I don’t sleep well at night knowing that for some people, the death of Americans is a moral imperative. This is too important to ignore. Please don’t.

After someone mentioned that a comment had been moved to the previous Bathroom Wall I went looking for it, but I couldn’t find it.  It was buried too deep in the archives to come up easily.

How about a permanent front-page link to it, as long as it’s always going to be receiving new stuff?

Specified complexity is a somewhat meaningless term to attach a probability to our ignorance. In other words it is not based on a positive observation but merely describes what we do not know. But things get worse, information and specified information can arise quite easily under the processes of selection and variation as has been shown many times in various papers (Adami, Schneider, Lenski et al). The problem is that concepts of information and complexity are used in a meaningless manner. On the one hand we have claims by ID proponents of information and on the other hand of specified complexity without much of an attempt to link the two. Information in the more commonly used sense of Shannon information can be shown to easily arise, the problem is that when the probabilites increase CSI has by definition to decrease so in other words, natural processes by definition cannot generate CSI. But on the other hand CSI is often confused with information which CAN be generated by natural processes. And through the process of equivocation and invocations of handwaving, the creationist argument is made. So any claims that confuse the terms of information (regulatory information) and specified complexity are based on poorly defined terms, equivocation. Once these terms are placed within the correct context it is easy to show that CSI is a meaningless concept to replace our ignorance and that such concepts as law of conservation of CSI or design inferences are based on flawed premises, faulty theoretical foundations. No wonder that these concepts have failed to provide any foundations for scientific hypotheses and have failed to be scientifically relevant. So let’s, in name of the search for truth, reject the attempts to confuse information and CSI/specified complexity and focus on the real arguments which are: Can the increase in information in the genome be explained by natural processes. And the answer is at least in principle yes. So lets do the hard work and focus on real scientific hypotheses. And no, Intelligent Design, contrary to claims by some of its proponents is not really scientific.

The Bathroom wall has a perminate link on the front page. Right side of the page. There are a number of boxes The first is Description

Then second is Information in that box the 5th item from the top is The Bathroom Wall

To find previous “The Bathroom Wall”s simply drill throuth them from the first post in each “The Bathroom Wall” by clicking on the link provided.

Creationists suck.

Specified complexity does not describe what we do not know. In fact, my understanding is that it is completely the opposite. The amount of information in a system can be measured - that is the amount of information required to specify this system and not a different one. Obviously from a darwinian perspective, the amount of information is linked directly to the genetic material available. What hasn’t been measured is the information that is coded in non-genetic areas - such as spatially within an organism. Neo-darwinists ignore these factors; Meyer has referred to them, but only to point out they are there, I believe. There is enough CSI in the genome to keep us going for now.

Steve wrote

That protein I mentioned is a yeast SNARE called SSO1. Typical protein. You have several mutants of it in yourself, actually. You could change about 220 of the 290 amino acids and get a functionally equivalent protein.

Thanks for that, that is the first response that has addressed the questions that I was trying to ask. Since I seem to be an alien species here, give yourself a masters in xenolinguistics!

Now, you have said, “typical protein”. In what regard? Its size? The fact that only 25% of its peptides are relevant to its function? Could you change any 220 peptides of the 290? If there are 70 specific sites that are relevant, then in effect rather than a (ballpark) 29020(1049) range of polypeptide space to find this peptide in, you have a 7020 (1036) space. Plus an order of magnitude or two I suppose for the fact that the size of the protein is presumably relevant. A big improvement - a probability 13 orders of magnitude bigger. Though still pretty unlikely to crop up at random - a lot less likely than the 1011 for any functionality quoted above. (!!! I do hope I got those brackets right!)

I suppose it is possible for some of those 70 “active” amino acids to substitute for amino acids with a similar nature - hydrophobic, or whatever? Again, that might help raise the probability.

I noticed on a quick search for abstracts related to this protein that it was considered noteworthy that different places where it cropped up were so divergent in genetic terms. Would this imply that this is not typical of proteins with the same function? Are they normally not as able to be varied as this?

Traffic demons suck.

Syntax Error: mismatched tag at line 41, column 2, byte 2933 at /usr/local/lib/perl5/site_perl/5.12.3/mach/XML/Parser.pm line 187

OK, one more bit now…

aCTa Wrote:

Specified complexity does not describe what we do not know. In fact, my understanding is that it is completely the opposite. The amount of information in a system can be measured - that is the amount of information required to specify this system and not a different one.

“Specified complexity”, in one sense, does indeed not describe what we do not know. That sense is the one in which one recognizes that no complete, correct, and successful application of Dembski’s full framework for detecting “specified complexity”, his “generic chance elimination argument” with use of his “universal small probability”, has ever been published. As such, “specified complexity” does not as yet describe anything at all.

The “measurement” in “specified complexity” concerns what Dembski calls “complexity”, and is derived from the maximum probability of origin of the event in question if it were due to non-agent causation. The amount of information required to “specify” the event is not utilized to quantify Dembski’s “specified complexity”. “Specification”’s part in “specified complexity” is a Boolean; either an event is “specified” or it is not in Dembski’s framework, and the math involved in determining whether “specification” holds does not play any further role in “specified complexity”.

Using the amount of information required to specify an event is, in fact, the basis of “specified anti-information” (SAI), an alternative methodology derived in Elsberry and Shallit 2003. SAI has the advantage over “specified complexity” of being readily applied to real world problems. But SAI does not lead to an inference of agent causation.

From http://www.antievolution.org/cgi-bi[…]2;t=78;st=10 :

The existence of a minimal program/input pair that results in a certain output indicates that there exists an effective method for production of the output. Since effective methods are something that are in common between intelligent agents and instances of natural computation, one cannot distinguish which of the two sorts of causation might have resulted in the output, but one can reject chance causation for the output. We haven’t so much repaired specification as we have pointed out a better alternative to it.

This leads me to a claim about Dembski’s design inference: Everything which is supposedly explained by a design inference is better and more simply explained by Specified Anti-Information.

SAI identifies an effective method for the production of the output of interest. The result of a design inference is less specific, being simply the negation of currently known (and considered) regularity and chance. The further arguments Dembski gives to go from a design inference to intelligent agency are flawed. On both practical and theoretical grounds, SAI is a superior methodology to that of the design inference.

I ‘saw this’ on the bathroom wall in my local EvC web ring:

For a good time trashing misguided creationist apologetics on the philosophy of science argument, call 555-Get-A-Grip. Or visit this Blog.

Wesley: Firstly, I sincerely hope the surgery goes well. Do you want me to pray for you? I guess not .… but all the best, anyway. I’m sorry that you feel that this discussion is a bit trivial in the light of what’s coming up.

I wrote:

Wesley - it’s amazing how many non-biologists reproduce Dawkins’ argument as though it is the mechanism for evolution, having failed to observe the caveats that he so clearly enumerated.

You wrote:

aCTa, by the way, still has jack concerning his claim about “many” biologists using “weasel” as a proof of biological evolution without caveat.

You misquoted or misrepresented me - as you can see above, I specifically said “non-biologists”. And for the record, you were in any case taking what I had written out of its wider context - which was as an echo of a quote from you - more a rhetorical point than an argument that I expected to have to defend - because from the way you wrote this:

It’s amazing how many ID advocates are unaware that Richard Dawkins very clearly and forthrightly enumerated the reasons why the “weasel” program was not a complete or exact simulation of biological evolution.

.… I assumed that you were also speaking rhetorically. I didn’t expect the Spanish Inquisition! (Nobody expects the Spanish Inquisition) (Sorry, that may not mean anything to you)

However, whilst Dawkins may have been clear that his model was not a complete or exact simulation etc, he evidently felt that it had something to tell us about evolution. Yet the key issue in the text at this stage (if I remember right) was can mutation/natural selection - the blind watchmaker - produce something more than a random process can? This model was then given - apparently to address this question - but the point is that the watchmaker is not blind in this model! So Dawkins - you say deliberately, and I can’t say otherwise, since I don’t have TBW to hand - was not dealing with the issue that followed from the text.

I didn’t realise at the time that you were so concerned to defend Dawkins’ honour. I’m sorry if people misrepresent his work, but there are people who have taken what he wrote there (one of the bits they think they can understand) and use it as an argument for evolution. I can’t give frinstances, I’m afraid - books that I find helpful, I pass onto other people, and I live in a house in suburbia, with no conveniently-attached university library or bookshop. I’m not sure which book I may have read the “classic” example in - but it was a quotation from a philosopher who basically argued for evolution using this example. It may have been “Does God believe in Atheists?” by John Blanchard.

Also, I still think your approach is a little disingenuous. Basically, you aren’t saying ID’ers and creationists are wrong and that METHINKS is a model for evolution - you are agreeing that it isn’t a model for evolution, and saying that this is what Dawkins was trying to get across. So you aren’t saying that the creationists and ID’ers are wrong in their conclusions, in this area, just wrong in their methodology. I’m not going to get stroppy with you for saying I said “biologists” when I actually said “non-biologists” - but this has more impact on the sense of my argument than the errors of people in misrepresenting Dawkins have on theirs. Maybe had Dawkins not put the model in the context in which he put it, then he wouldn’t be in the situation of people misinterpreting its role.

So when creationists and ID’ers show that this model doesn’t work, you make lots of noise and say, “You’ve got it wrong”. But what you mean by that isn’t that the model works as an analogue for evolution - it’s that they aren’t quoting Dawkins properly. But everybody thinks that what you are saying is that the model does work as an analogue for evolution, because that is the issue they are trying to get across.

I had no problem parsing your comment, BTW. The problem was you were referring to a block of text that was half a quote from somebody else - and the quotation that you then gave wasn’t in the block of text that you had referred to at all.

I don’t have time for more. Best wishes, again.

In comment #8216

Wesley Esberry Wrote:

Hmmm. Giving that I’ll be undergoing major surgery within a week, …

Best of luck—and best wishes for a painless and rapid recovery.

And aCTa has yet to provide even a single citation to support his counter-claim that “many” biologists use the “weasel” program as a proof of biological evolution without caveat.

Actually, his counter-claim was that many non-biologists “reproduce Dawkins’ argument as though it is the mechanism for evolution” (comment #8117). Of course, that doesn’t alter the fact that he has failed to provide the requested citation of even a single non-biologist doing what he claimed.

In comment #8051

A Creationist Troll, apparently Wrote:

Oddly enough with regard to the correspondence between language and genes - it wasn’t the creationists that started it - it was Dawkins, with METHINKSITISLIKEAWEASEL

Oh, creationists have been peddling silly arguments from imaginary analogies between language and the genetic code from long before Dawkins published his weasel example in 1986. See, for example, page 110 of The Creation of Life, by A.E. Wilder Smith D.Sc., Ph.D., Dr.es. Sc., F.R.I.C., first published in 1970.

From the Humanist Manifesto 2

FIFTH: The preciousness and dignity of the individual person is a central humanist value. Individuals should be encouraged to realize their own creative talents and desires. We reject all religious, ideological, or moral codes that denigrate the individual, suppress freedom, dull intellect, dehumanize personality. We believe in maximum individual autonomy consonant with social responsibility. Although science can account for the causes of behavior, the possibilities of individual freedom of choice exist in human life and should be increased.

SEVENTH: To enhance freedom and dignity the individual must experience a full range of civil liberties in all societies. This includes freedom of speech and the press, political democracy, the legal right of opposition to governmental policies, fair judicial process, religious liberty, freedom of association, and artistic, scientific, and cultural freedom. It also includes a recognition of an individual’s right to die with dignity, euthanasia, and the right to suicide. We oppose the increasing invasion of privacy, by whatever means, in both totalitarian and democratic societies. We would safeguard, extend, and implement the principles of human freedom evolved from the Magna Carta to the Bill of Rights, the Rights of Man, and the Universal Declaration of Human Rights. EIGHTH: We are committed to an open and democratic society. We must extend participatory democracy in its true sense to the economy, the school, the family, the workplace, and voluntary associations. Decision-making must be decentralized to include widespread involvement of people at all levels — social, political, and economic. All persons should have a voice in developing the values and goals that determine their lives. Institutions should be responsive to expressed desires and needs. The conditions of work, education, devotion, and play should be humanized. Alienating forces should be modified or eradicated and bureaucratic structures should be held to a minimum. People are more important than decalogues, rules, proscriptions, or regulations.

It might oversimplify things to attribute the deaths in communist regimes to communism. But if you were, along with aCTa, to attribute those deaths along with those killed by Nazis to Humanism then you would be lying. Humanism is a distinctive philosophy, amongst whose core values are commitments to the value of the individual, and to fully democratic societies and as such is completely antithetical to either communism or fascism. aCTa’ tawdry game has all the intellectual merit of attributing the deaths and tortures of the inquisition to Islam as a proof that Islam is a murderous religion.

Tom Curtis

Sorry, I was not sufficiently specific. I was using humanism not in the formal philosophical sense, but in the sense of a general worldview that starts from the perspective that there is nothing higher than human beings - that people are only accountable to themselves (and the state is an extension of this). Marxism is humanistic not because it derives from the Humanist Manifesto but because at its core is the imposition of a new ruling working class. Fascism (in the general sense) is humanistic because it has as its highest good the power of a particular group of people.

However, I’m personally not convinced that, despite the high values that formal humanism proclaims, it has a great deal to show for itself. From a Christian perspective, I would argue that the Tower of Babel was the ultimate humanist enterprise - which God deliberately confounded.

I think it is interesting that the humanist manifesto offers euthanasia, whereas Christians throughout the world (though not all of them) consider part of their Christian service working for people who are affected by HIV, Downs, terminal illness etc.

Steve Benson has a nice editorial cartoon that can be seen here:

http://www.comics.com/editoons/bens[…]0041207.html

That Benson cartoon is awesome. It’s as good, as blaming Hitler on Humanism is fucking stupid.

aCTa,

Fer chrissakes, this wouldn’t be another of your assaults on modernism, would it? Only now, instead of “modernism”, or “rationalism”, you’ve decided to call it “humanism”. All the worlds ills may be laid at the feet of modernism/rationalism/humanism/etc..ism. If we’d only kept that old-time religion, I mean pre-modern worldview, everything would be hunky-dory, right? Just like in the good old days of the Inquisition, no doubt.

Auto-da-fe? What’s an auto-da-fe? It’s what you oughn’t to do but you do anyway.

Fascism (in the general sense) is humanistic because it has as its highest good the power of a particular group of people.

This is about as wrong as it is possible to be. Fascism puts the interests of the state and/or the race above the individual, completely contrary to the dictates of humanism. Your statement reveals a tremendous ignorance of either fascism or humanism, or likely both.

And then there’s this:

However, I’m personally not convinced that, despite the high values that formal humanism proclaims, it has a great deal to show for itself.

This is distressingly similar to your previous absurd claims about rationalism. Take a look about you. Show me a modern first-world government whose laws are not greatly influenced by humanist concerns. Republicanism? Freedom of religion? Civil liberties in general? Ethics? The only nations which are governed according to your beloved pre-modern, pre-humanist, non-rationalist worldview are third-world theocracies like the Taliban. That is something to aspire to. For all your talk about the power of the pre-modern worldview, I find it hard to believe that you would actually want to live in the pre-modern world.

BTW, nice try on the euthanasia cheap-shot. Yes, we humanists support the right to euthanasia because we’re too lazy and selfish to care for sick people, and we wish they’d just kill themselves and make life easier for everyone. You’ve certainly got our number.

Do you guys know about CafePress? They let you make t-shirts, coffee mugs, mousepads etcetera using logos or designs you provide; I’d buy a mug and I’m sure others would too. You could donate the proceeds to NCSE, or buy yourselves a beer for that matter. Keep up the good work.

Oklahomans for Excellence in Science Education has established a web site for fighting the evolution deniers in Oklahoma.

OESE is a non-profit educational organization that promotes the education of the public about the methods and values of science and advocates excellence in the science curriculum.

The formation of OESE was prompted by the attempts in the Oklahoma State Textbook Committee in 1999 and in the Oklahoma Legislature each year since to diminish the teaching of evolution by the introduction of creationist textbook disclaimers to be inserted into any textbook used in public schools that discussed evolution

List of such sites for other states

. List of low-volume, moderated email lists for new on anti-evolutionist activities for each of the 50 states plus Canada

—- Anti-spam: replace “user” with “harlequin2”

Oklahomans for Excellence in Science Education to fight evolution deniers? If that’s what the aim is, then what’s the matter with just saying what you aim to do in your name, rather than implying that you have a wider brief? Like “Oklahomans against evolution deniers”? I suppose it’s just like NCSE, really, isn’t it? After all, the creationists are such a dissembling lot - you need to be just as dishonest if you want to win arguments with them, don’t you?

Earlier, I wasn’t advocating a theocracy. What I am saying is that any government which starts by having a high view of humans and their power ends up as totalitarian. Democracy doesn’t work because it ensures that the majority get their way - it works (or at least should work!) by preventing extremists from taking power. That’s why Churchill said, “Democracy is the worst political system - apart from all the others.”

So what sort of political system am I advocating, as a Christian? Well, none, really; Christianity doesn’t (or shouldn’t) have a political agenda. It teaches people to live lawful lives as far as they are able; and it teaches Christians in authority to seek to use that authority justly. It also teaches that “from one man, God made every nation so that they would seek him and perhaps find him” - in other words, the nations are ultimately in God’s hands (although people are responsible for the way in which they use their abilities and position). It teaches that the ultimate end of the universe is that one day, everybody will accept that Jesus is God’s chosen king to rule over everybody, everywhere, forever - the ultimate theocracy - and that the model of that eschatological order is (or should be) the local church.

Oklahomans for Excellence in Science Education to fight evolution deniers? If that’s what the aim is, then what’s the matter with just saying what you aim to do in your name, rather than implying that you have a wider brief? Like “Oklahomans against evolution deniers”? “Oklahomans against Creationists”? I suppose it’s just like NCSE, really, isn’t it? After all, the creationists are such a dissembling lot - you have to be dishonest to win arguments with them, don’t you? :-P

Earlier, I wasn’t advocating a theocracy. What I am saying is that any government which starts by having a high view of humans and their power ends up as totalitarian. Democracy doesn’t work because it ensures that the majority get their way - it works (or at least should work!) by preventing extremists from taking power. That’s why Churchill said, “Democracy is the worst political system - apart from all the others.”

So what sort of political system am I advocating, as a Christian? Well, none, really; Christianity as an entity doesn’t (or shouldn’t) have a political agenda. It teaches people to live lawful lives as far as they are able; and it teaches Christians in authority to seek to use that authority justly. It also teaches that “from one man, God made every nation so that they would seek him and perhaps find him” - in other words, the nations are ultimately in God’s hands, and exist for his purposes (although people are responsible for the way in which they use their abilities and position). It teaches that the ultimate end of the universe is that one day, everybody will accept that Jesus is God’s chosen king to rule over everybody, everywhere, forever - the ultimate theocracy - and that the model of that eschatological order is (or should be) the local church, not the nation or para-church organisations.

With regard to euthanasia, however well-intentioned the humanist manifesto is, the fact is that once even the removal of care becomes an option, there is a danger that it will rapidly become an expectation, and then a pressure - there was an article in the Times the other day about a disabled woman who was ill in intensive care, with every expectation of getting better, but to whom it was suggested on separate occasions by separate doctors that, if she stopped breathing, she might not wish to be revived.

Incidentally, there were many things that were in the humanist manifesto that I have no problem with. For example, the fact that people are more important than rules; the importance of “local government” and so on.

aCTa,

Earlier, I wasn’t advocating a theocracy. What I am saying is that any government which starts by having a high view of humans and their power ends up as totalitarian.

That’s a pretty strong statement. Does that mean that most first-world nations are on the slippery slope to totalitariansism? Actually, I’m willing to entertain the idea that my country is on such a slope, but I’m pretty sure it has nothing to do with humanism. Really, aCTA, what is your basis for this claim? Humanism is diametrically opposed to totalitarianism. I would propose that a government which puts any interest above that of the individual is in danger of succumbing to totalitarianism. This interest can be the state (Fascism), the party (Communism), or religion (Theocracy). Surely you aren’t trying to say that a belief in a higher power somehow prevents the rise of totalitarianism? Because that would be silly.

Smokey you nailed it. I didn’t understand this topic until I read an essay similar to yours by Cathy Young. The fact is, you can subvert human rights in pursuit of a variety of ideologies. And in the end, the horrors of totalitarianism and theocracy and such are measured by how far they diverge from good, humanistic values.

The “good, humanistic” values that you espouse are the ones that you borrowed from the Bible, in many cases. The difference is that - sorry, we’re back here again - you’re using them without an epistemological foundation.

Are many first-world nations heading towards totalitarianism? Yes, I’d argue they probably are. We are within a couple of decades of criminalising many religiou s communities - and probably many of the people here would assent with this criminalisation!!! - over issues like: should a religiou s community be able to choose not to employ somebody on grounds of their morality? Which leads to: should religiou s communities be licensed? We all have to have child protection policies; we all have to do police checks before employing people - or even allowing them to do voluntary work. Now the thing is, these things aren’t inherently wrong - but just think for a minute! Can’t you see how much freedom has been taken away from you, “for your own good”? And we have all just accepted it!! You don’t have to be terribly enlightened to see what has happened in the States under the doublethink label of the “Patriot Act” is extremely worrying - and again, most people think it is a good thing!

What about the media? The “totalitarian” authorities aren’t just those in parliaments - they are the people who control channels of communication. Have you heard what was going to happen to “Stupid White Men” as a book shortly before some librarians got to hear about it? The channels of free expression are still there - but for how much longer?

Remember that totalitarian states rarely oppress the majority. They rule with the consent of the majority - and oppress the minority. You may be happy with that - you may be in the majority. But if in twenty years’ time you find yourself wondering where exactly your free society went, you might want to remember what you read here.

Oddly enough, I think that blogging (a highly individualistic pursuit) is one of the latest tools that we have to escape from authoritarianism.

To go back to humanist values, again, my Grandpa was a socialist who fought against fascism, and ended up exiled from his home country for many years in the twentieth century - a far more direct experience of realpolitik than anybody on this forum (me included) is ever likely to have, fortunately. He used to say to dad: “Marx said, ‘If you won’t work, you shouldn’t eat.’” Dad pointed out to him: “Yes, but the Bible said that first.”

You may be wondering why a space regularly features in a phrase in that post. I am wondering why Yew Ess Space See Oh Emm should be regarded as questionable content. But there you go.

Syntax Error: not well-formed (invalid token) at line 11, column 1, byte 1031 at /usr/local/lib/perl5/site_perl/5.12.3/mach/XML/Parser.pm line 187

I thought some folks here might get a kick out of this article on the Skeptical Inquirer website.

A writer for the Skeptical Inquirer visited Hovind’s creationist theme park in Florida and wrote a review of it for the SI.

Young-earth creationist Kent Hovind has built a dinosaur-filled theme park in the Florida panhandle and claims to prove that evolution is bunk. A visit there shows that it is definitely a fantasy land.

See Stupid Dino Tricks: A Visit to Kent Hovind’s Dinosaur Adventure Land

Don’t forget Marshall Hall at fixedearth.com -> evolution denial + rotating/orbiting earth denial.

apparently he’s got a time machine too, because at the very bottom it says “©1997-2005 Marshall Hall”

Syntax Error: mismatched tag at line 10, column 111, byte 2427 at /usr/local/lib/perl5/site_perl/5.12.3/mach/XML/Parser.pm line 187

Syntax Error: not well-formed (invalid token) at line 5, column 8, byte 452 at /usr/local/lib/perl5/site_perl/5.12.3/mach/XML/Parser.pm line 187

aCTa,

If “Nobody is good enough to go to heaven,” does that mean that the place is entirely deserted and all them sweet sounding harps are just laying around gathering dust with their strings sagging? What a pity. Where then is the incentive toward moral behaviour?

Have you ever pondered how much of the bible is borrowed from the Torah, and how much of the Torah is borrowed from …

News of the weird in the natural world …

In case anybody is interested, there are a couple of Op-Ed articles in the San Francisco Chronicle today concerning ID/evolution. One is written by Stephen Meyer and John Angus Campbell, of the DI, titled Students should learn to assess competing theories.

The other is by Robert Sapolsky, a neurology professor at Stanford, titled Regardless of how it works, evolution is for real.

About this Entry

This page contains a single entry by Prof. Steve Steve published on October 1, 2004 3:15 PM.

I Was a Token Darwinist was the previous entry in this blog.

A Smithsonian Anti-Science Museum? is the next entry in this blog.

Find recent content on the main index or look in the archives to find all content.

Categories

Archives

Author Archives

Powered by Movable Type 4.361

Site Meter