In Search of the Protocell - The Work of Jack Szostak

The origin of life problem is perhaps the most important question to ever have been the focus of scientific scrutiny. The only other question that I think rates of similar importance is the origin of the universe. Both questions have special obstacles to overcome before any answers are within sight. 

The Miller-Urey experiment of the 50s was a lightningrod for research into this question, but the euphoria caused by the viewpoint that the answers were near quickly receded once the scope of the problem was realized and it was decades before the excitement was rekindled in the scientific world. It's no surprise that the search is a difficult one. Remember, researchers are trying to compress the millions of years that undoubtedly were required for nature to give life a kick start into the lifespan of humans. Couple this with only a limited knowledge of what the conditions were at the time life started except in the grossest terms with the possibility that trace elements may be essential for the synthesis of life greatly compounds the issue. Anyone thinking that if life arose through naturalistic processes means it should be both easy, and that a mere 50 years of research should have resulted in the creation of protolife really doesn't have a good grasp of the scope of the problem. 

The molecules of life in the prebiotic world were all over the place, and not just on this planet. We know this not only from the Miller-Urey experiment itself, though we now think were the conditions at the time were somewhat different (which does not change the conclusions drawn from that experiment, or from similar ones which simulated what we now think the conditions at the time were), but meteorites have been found with complex organic molecules which could have seeded a barren Earth with the raw materials for the synthesis of life. Amphiphilic molecules (molecules possessing both water-loving (hydrophilic) and water-hating (hydrophobic) regions) have been generated by a variety of means simulating conditions found naturally: ultraviolet radiation of ice particles in the vacuum of space and at hydrothermal vents. Such molecules would provide the first cell membranes. 

A plan for synthesizing life was put forward by Szostak in 2001. It is based on a heterotophic model (cell structure first) rather than on an autotrophic one (metabolism first). First, create a spontaneously-replicating membrane through which small molecules can diffuse but bar larger molecules synthesized from these precursors from escaping. Next, create a replicase - a molecule mediating polymerization of a second molecule - a template containing protogenetic information to be copied.  The template could be RNA complimentary in sequence to the replicase or an unfolded replicase. RNA molecules can be encapsulated in vesicles and the whole cell self-assemble. This compartmentation inevitably results in the replicase component being subject to variation and natural selection.

Under the right conditions, amphiphilic molecules in solution can form micelles, or vesicles. This is similar to what soap, another amphiphilic class of molecules, does. Soap molecules (in the correct range of concentrations) cling together to form balls with the water-loving heads facing outward. In the case of vesicles, the molecules stand tail-to-tail with their hydrophilic heads facing outward from both the inner and outer surfaces of the ball. 

These vesicles would provide microenvironments for retaining and protecting primitive oligonucleotides (short sequences of RNA or DNA, typically of less than 20 bases). It is unlikely that early cell membranes would be made up of the same types of molecules which make up those in modern cells: phospholipids. Membranes made up of phospholipids are far too efficient at keeping out negatively charged ribonucleotides. Modern cells have evolved specific transport proteins to take in nutrients, but the earliest cells would have had no such mechanism available to them. 

Rather, the earliest cells would have used less efficient amphiphilic molecules, such as fatty acids, through which small molecules like ribonucleotides (such as uridine monophosphate, which make up RNA) could pass accross by simple diffusion. One hypothesis for both vesicle formation and RNA synthesis is respectively the interaction of fatty acids and ribonucleotides with clays. There is a growing body of evidence that this is a viable mechanism by which both of these process could happen. The clay montmorillonite has long been known to be able to catalyze RNA from activated ribonucleotides, but it can also greatly increase the rate of formation of fatty acid vesicles. The clay has a positively charged surface which attracts and concentrates the negatively charged fatty acids and thus facilitates their formation. Fatty acid membranes are also permeable to magnesium, a divalent cation necessary in many biochemical reactions and itself increases membrane permeablilty to negatively charged ribonucleotides. 

The surprise is that vesicles created in the presence of montmorillonite will also incorporate clay particles! It was immediately obvious to Szostak that this provides not only a mechanism for vesicle formation, but a method of synthesizing RNA oligonucleotides from ribonucleotides which diffuse through the membrane. Oligonucleotides formed within the vesicle are unable to escape the interior and are trapped. (As an aside, it also provides an explanation as to why L- rather than D-amino acids are utilized in protein synthesis. D- and L-amino acids are non-superimposable versions of each other, rather like the mirror image of your hand is not superimposable on your physical hand. Amino acids synthesized in an isotropic medium would be an equal (racemic) mixture of both optical isomers. These optical isomers have exactly the same physical properties bar one - each rotates the plane of polarized light in opposite directions. However, catalysis by a surface breaks the symmetry and one optical isomer would be selected over the other. It just so happens that L-amino acids were the ones selected. For sugars like glucose, it is the D-optical isomer that is used in biochemical reactions.)

Not only will these vesicles form, they have been shown to be able to spontaneously grow and divide in a series of elegant experiments. It was found that if the high vesicle concentration decreased by slowly adding a dilute solution of fatty acids, the vesicles would actually grow rather than just form new micelles. Vesicle division can be accomplished by extruding them through a polycarbonate filter. This likely happens by elongating the micelles so that they are no longer spherical and resealing after being pinched-off. As confirmation of this, vesicles preloaded with fluorescent dye were run through a filter released the dye into the medium in amounts only slightly greater than what was predicted for this mechanism of division. Had complete membrane disruption and reformation of vesicles occurred, the entire contents of the micelles would have been dumped into the medium. Vesicle division thus strongly resembles cellular division via budding and their formation, growth and division require no complex machinery at all, only raw physical forces. This is consistent with our current hypotheses on how early cell membranes must have formed. It even supplies a means for the first genetic material to have been generated through ribonucleotide uptake and mineral-catalyzed oligonucleotide formation.

Now our good friend Darwin steps in. Vesicles under osmotic stress due to their encapsulated contents need to decrease osmotic pressure by increasing their volume (and hence their surface area) by capturing fatty acids. Either that, or explode, dumping their contents. They do this by stealing fatty acids from other vesicles. But this is not a random process. The encapsulated contents have something to say about how well a vesicle will relieve the stress. Thus, we have what may have been the first example of biological competition! In the paper which covers this research (Chen, 2004), however, the competition was purely for stealing fatty acids from isotonic micelles (that is, vesicles not under osmotic stress). In other words, they feed. Once a truly replicating protocell is synthesized, a goal not yet reached, natural selection will become paramount in importance. The replicase can easily mutate through random mutation (since there are no error correcting mechanisms yet) and those which replicate better than others, eat other vesicles more efficiently and, as a consequence, divide more often will become more prevalent. Sounds like evolution to me.

So, when vesicles divide, how can the genetic material split into two as well? This is a Holy Grail in abiogenesis research. Some RNA can act like enzymes (another tantalizing clue to the origin of bioactive molecules). Such RNA molecules are known as ribozymes. Hammerhead ribozymes, which can catalyze cleavage and ligation of RNA molecules, are thought to be important in an RNA world and allow a mechanism for self-replication in the presence of magnesium. Encapsulated hammerhead ribozymes perform this self-cleavage as well, a necessary first step in this line of study. Research continues in developing a truly self-replicating protocell, and the results to date are highly encouraging. Activated nucleotides permeating across amphiphilic membranes have been shown to non-enzymatically replicate - this is key - encapsulated DNA templates. It just remains to fill in the lines.

When all is said and done, is this going to show us how abiogenesis occurred? Maybe. Note the language that Szostak uses: "model protocell vesicles", "prebiotically plausible membrane", etc. It's very careful language. What these experiments and others give us is a possible pathway, not necessarily the pathway. Perhaps autotrophic and heterotrophic abiogenesis are not either/or propositions and both are possible but only one historically occurred. Unless someone invents a time machine that can take us back to that point in time (current theoretical designs can only take us - well, actually only particles, not us - back in time to the point at which the machine was turned on), it is unlikely that we will be at all confident in having found the pathway. But this is not the point. The point is to find a plausible mechanism whereby abiogenesis could have occurred naturally, and we are well on our way there.  

Sometimes the journey is more important than the destination.

References:

Szostak JW, Bartel DP, Luisi PL, Synthesizing Life, Nature 409387-390 (2001)

Hanczyc MM, Fujkiawa SM, Szostak JW, Experimental Models of Primitive Cellular Compartments: Encapsulation, Growth, and Division. Science 302:618-622 (2003)

Chen IA, Roberts RW, Szostak JW, The Emergence of Competition Between Model Protocells. Science 305:1474-1476 (2004)

Chen IA, Salehi-Ashtiani K, Szostak JW, RNA Catalysis in Model Protocell Vesicles, JACS 127:13213-13219 (2005)

Mansy SS, Schrum JP, Krishnamurthy M, Tobe S, Treco DA, Szostak JW, Template-directed Synthesis of a Genetic Polymer in a Model Protocell, Nature [Epub ahead of print] (2008)

Is Evolution the Drunken Man as Behe claims?

I was listening to the latest episode of 'The Things That Matter Most' with Dr. Michael Behe, the man that put forth the idea of Irreducible Complexity (IC), as guest. Wow. Some of the worst arguments for Intelligent Design (ID) I've heard to date. It's no wonder that his colleagues at Lehigh University have disowned him.

I've blogged on the many problems of the IC concept before and, even though it is impossible to believe that Behe has never heard of the complete and utter refutations by others with far more expertise than I (little-known people such as Richard Dawkins, Ken Miller, PZ Myers, Jerry Coyne,....), he continues to espouse this idea. Even his mousetrap has been found to be reducible. I'm sorry, Dr. Behe, but this makes you a dishonest broker. 'Irreducible complexity is this fancy phrase that all it means is that you've got a machine like a mousetrap... that has a number of different parts all of which are required [for it] to work.' The mousetrap is a red herring because I have yet to see a mousetrap replicate. Since the primary mechanism by which Natural Selection is removed, the analogy is false one.

Behe arbitrarily declares that structures serving other functions can't be co-opted to be brought together for a new function. 'Even if you are hoping to use those things [parts] for something else, like a doorstop, a doorstop has nothing to do with catching mice.' What's he done here? He's concocted a straw man (hardly original) of Evo. He presumes that catching mice (function) is something not only desirable, but a necessary end point. But function is something we ascribe to a system - the genes themselves do not care what or even whether they provide a function, only that they impart survival value.

So, what we should always be looking for is whether a genetic change imparts a survival advantage, not whether the change maintains function. The latter is simply irrelevant. DNA does not care about any one of its gene's functions, or whether there even is a function for it, only the effect of the gene on survival probability. To illustrate this using the mousetrap example, let's say that a cell contains the parts that are required for the mousetrap and the catching a mouse results in an increase in the chances of survival. If bringing some of the parts together confers some survival advantage (or is benign in terms of survival) then the changes will tend to be passed on to the next generation. In other words, bringing two parts together can increase the chances of survival more than the parts being separate. Then, in a future generation, another part gets added, conferring even more survival value, and so on. Thus, structures better and better suited to survival are produced. Here's the kicker: the function of the early versions of the mousetrap need not even have involved catching mice at all so long as some net survival advantage was gained by combining parts! When looked at in these terms, there is no basis on which to deny the base of the mousetrap to have originally served as a doorstop!

At some point, the functions of the structure changed from whatever they were to by catching mice. This is immediately apparent to anyone familiar with Natural Selection and Behe's poster child for ID, the bacterium flagellum. When Behe artificially rules out functional change the flagellum seems 'irreducible', but he provides no good reason that we should accept omitting such evolutionary paths to this structure. He is simply invoking an artificial restriction that he claims Evolution can not violate (yet it clearly can and does) simply because it makes IC look good and for no other reason that anyone can fathom.

Does the Type III secretory system, which comprises part of the flagellum motor, lose its function when combined with another part on its way to powering the flagellum? Quite probably. Does this matter? Not at all if a net advantage is gained.

For all his philosophizing he has yet to perform a single experiment to confirm irreducible complexity. I can think of a number of experiments off the top of my head to test the validity of IC. One is simply looking at the parts of a complex structure such as the bacterium flagellum and seeing if the parts have analogous structures in related organisms. That the individual proteins of the flagellum are completely conserved and have wholly different functions in related bacteria does not bode well for IC at all and clearly points to an evolutionary process. Why would you, if you wanted to design a mousetrap as opposed to evolve it, use a blender? I think if you wanted to make a mousetrap you would do what is already done - create the individual parts specific to the task.

The blood clotting cascade, another of Behe's examples, can also be tested as to whether it fits the IC model. In this case, we do not have a single structure composed of several proteins, but a series of biochemical reactions. Ideally, one would like to be able to remove one or more enzymes catalyzing reactions in the cascade. Can this be done? Absolutely. Genetically engineering mice to inactiveate genes is routine these days. Dr. Behe has never even suggested such experiments, let alone performed them. Fortunately, less lazy researchers have. Knocking out one gene or even several encoding enzymes in the cascade does not stop the blood of mice from clotting. That knockout mice blood doesn't clot as well is irrelevant, since Behe predicted there should be no clotting ability at all. Of course, all that has to be done is look at the blood clotting cascade in whales and dolphins to see that they have what Behe would have considered an incomplete cascade already.

Indeed, all examples held up as for IC are similarly fatally flawed. Behe claims that 'blind searches do not lead to complex systems.' Really? Again, this is a blanket assumption for which he has no evidential basis for making, and Dr. Behe has never made an attempt at experimentally verifying his ideas. For purely random processes this statement is true, but Natural Selection is anything but random. For examples of such complexity arising from blind searches just google 'genetic algorithms'. A word to the wise: If you are going to put forward a radical idea such as this, you'd better have something to back it up with and that something had better be more than half-baked philosophizing.

Interestingly, Behe says 'I think the most compelling evidence for common decent is when you see features in organisms that seem not to have any particular function but look like genetic accidents and if that's the case then a kind of a parsimonious or a reasonable explanation is that these organisms are both descended from some previous organism. This genetic accident happened in the previous organism and both lines descending from that earlier one inherited the change.'

Wait a minute, Dr. Behe - You accept common decent, but deny macroevolution? What the....? Is he trying to tell us that bacteria containing the flagellum, which are closely related to bacteria having the Type III secretory system from which it evolved, both have a common ancestor, yet the flagellum needed to be added to the 'design'? For this to work, the molecular genetic evidence pointing to close relationship to these two types of bacteria must be wrong. Not bloody likely. He's trying to have his cake and eat it, too, by picking data supporting his position and ignoring all other data.

The question must be asked: why does Dr. Behe accept some parts of Natural Selection while discarding others? The answer is simple: he has a major problem explaining the existence of broken genes. I once heard PZ Myers say what he'd like most explained by supporters of ID, why a 'designer' would equip humans and other primates with a broken enzyme catalyzing ascorbic acid synthesis. This is exactly why Behe brings a limited version of Natural Selection into his world. He realizes that ID, as originally formulated, has no answer to this. But if you accept one part you must accept, if you are to remain intellectually honest, Natural Selection in its entirety. Note to Dr. Behe: the Theory of Natural Selection is irreducibly complex.

I've already blogged about the example contained in his new book, Edge of Evolution, where Behe claims that the development of malarial resistance to chloroquine through evolutionary processes is improbable. Behe again arbitrarily says that two mutations are required for any level of chloroquine resistance without explaining why no resistance is conferred by a single mutation in the right place except that it suits his argument. 'But suppose in order to be effective it needed not just one but it needed two and with just one that it didn't help or might even hurt the organism. So it had to get a change not only in the left side of its DNA but somewhere in the middle of its DNA as well. Then it turns out that that is a whole lot more difficult than just getting one [mutation].' Sorry, but as many have pointed out, mutation is not the bottleneck in Evolution. The arbritrary assumption that multiple mutations must take place at the same time is simply baseless. And what exactly is he saying? That a designer is making malarial parasites more resistant to human medical interventions in order to make them better killing machines? I don't think he's thought this through...

But my biggest objection is his analogy of the drunken man to Evolution, which falls flat on its face. (I know, I know - bad pun. Bad!) Behe describes his analogy thus: 'Suppose there were this drunk, this dizzy fellow, who had a blindfold on, and you want to get from some place in the city to the top of some tower in the downtown and suppose he's in the suburb. Well if he had to follow a rule that whenever possible you feel the ground going up you have to take a step up and you can never go back down because going back down means becoming less fit in a Darwinian sense, then if this fellow walks along he will climb up onto roofs of cars or onto porches of houses. Once he's up there he'll get stuck and he's not going to find his way to the tower downtown.' Here he's plagiarizing Dawkins' Climbing Mount Improbable example, the peaks of Dawkins' version correspond to the car roofs and porches in Behe's. Such a view gives the false impression that point B is some kind of objective. In Natural Selection there is no desired end point, just what is working at this point.

Behe twists Dawkins' version to make it appear as if the tower (the highest mountain peak in Dawkins' version) can't be reached by random processes without outside help because it is only one person. The likelihood that one person will reach the tower through a random walk with the rule that you can't take downward steps is indeed extremely low. But Evolution is an ensemble of organisms each taking paths going in any direction without any thought as to where they will end up, not a single one trying to get from A to B. To make this analogy work better, you need many, many drunks (an experiment which seems to be carried out spontaneously during Stampede Week every year). As in Behe's version, you will have many drunks finding car roofs or porches, but there will be those that do indeed get to the tower. In fact, with enough drunks all apexes in the search space will be occupied. His is a horribly inaccurate analogy and I've done my best here to try to correct it.

Are there limits to what can and can not be done by Natural Selection? Absolutely, but it's quite clear that Dr. Behe has not found the Edge of Evolution yet at all.

Yet another nail in the coffin of ID

Seen any of the Terminator movies lately? If so, you may want to wait a while before reading this, but this is cool. Trust me. Even if you spell it 'evilution', you are going to think this is cool. Really cool. Alan Bellows did a writeup on hardware evolution, a brand new area of study, which has direct parallels to biological evolution. The main figure in this article is a Dr. Adrian Thompson at the University of Sussex. The experiment that has so wowed me involved the use of a field-programmed gate array (FPGA) to distinguish between two tones. The FPGA used was small, only 10 x 10 cells in size, and removed access to the system clock (I presume that this ensured that the program could not time the waveforms coming in and accidentally result in a program that just measured the waveform frequencies). Dr. Thompson programmed in a random set of binary data, the initial DNA if you will, and judged the ability of each set of digital DNA. The programs which produced the best ability to differentiate between tones were kept for the next generation, with a bit of random mutation thrown in for good measure.

"For the first hundred generations or so, there were few indications that the circuit-spawn were any improvement over their random-blob ancestors. But soon the chip began to show some encouraging twitches. By generation #220 the FPGA was essentially mimicking the input it received, a reaction which was a far cry from the desired result but evidence of progress nonetheless. The chip's performance improved in minuscule increments as the non-stop electronic orgy produced a parade of increasingly competent offspring. Around generation #650, the chip had developed some sensitivity to the 1kHz waveform, and by generation #1,400 its success rate in identifying either tone had increased to more than 50%.

Finally, after just over 4,000 generations, [the] test system settled upon the best program. When Dr. Thompson played the 1kHz tone, the microchip unfailingly reacted by decreasing its power output to zero volts. When he played the 10kHz tone, the output jumped up to five volts. He pushed the chip even farther by requiring it to react to vocal "stop" and "go" commands, a task it met with a few hundred more generations of evolution. As predicted, the principle of natural selection could successfully produce specialized circuits using a fraction of the resources a human would have required. And no one had the foggiest notion how it worked." And that is what is so cool about this. Until the program was back-engineered, how it did what it did was a complete unknown and totally up to the selection process.

And that was where the surprises were found. A mere 37 of its logic gates were used, compared to hundreds of thousands in a sound processor designed specifically for the task. Even though only a very few gates were used, they were organized in a complex and completely unexpected way. "The plucky chip was utilizing only thirty-seven of its one hundred logic gates, and most of them were arranged in a curious collection of feedback loops. Five individual logic cells were functionally disconnected from the rest– with no pathways that would allow them to influence the output– yet when the researcher disabled any one of them the chip lost its ability to discriminate the tones. Furthermore, the final program did not work reliably when it was loaded onto other FPGAs of the same type." The purpose of the seemingly unconnected logic cells seems to be in supplying magnetic flux, and the program makes use of this in lieu of not having access to the system clock.

"These evolutionary computer systems may almost appear to demonstrate a kind of sentience as they dispense graceful solutions to complex problems. But this apparent intelligence is an illusion caused by the fact that the overwhelming majority of design variations tested by the system– most of them appallingly unfit for the task– are never revealed." This concept is key in understanding why proponents of intelligent design (IDiots) see conscious design everywhere. Natural selection eliminated the 'designs' that didn't work, so we only see the ones that do! So everything around us are the resulting successful designs. It's no wonder why engineers see god everywhere. But it's all an illusion, complexity arising from a simple set of rules. What works moves on, what doesn't is discarded. Random mutations occur ensuring that falsely optimized configurations don't occur. Evolution is such an elegant process!

From Pharyngula, PZ Meyers writes: "That looks a lot like what we see in developmental networks in living organisms — unpredictable results when pieces are "disconnected", or mutated, lots and lots of odd feedback loops everywhere, and sensitivity to specific conditions (although we also see selection for fidelity from generation to generation, more so than occurred in this exercise, I think). This is exactly what evolution does, producing a functional complexity from random input."

I think there are limits on the analogy to biological evolution, but the parallels are immediately obvious. There will always be those out there that say that Dr. Thompson was the designer because he set up the initial conditions. But simulating the initial conditions and creating them (as many IDiots are wont to say of the ) are two very different things, so reading that kind of IDiocy into this is reaching. One thing this experiment makes abundantly clear is that by following the rules set out by natural selection apparent complexity can become manifest in a relatively short amount of time.

Science is so cool.

More comments....

Aaaaawwwwww. It seems I have offended my creationist friend. I did accuse him of being a mental patient, but then I was getting tired of him passing off tautology as argument. As soon as I can actually get into my MySpace blog I'll put the latest in for all to see. Mind you, I did point out several times that it was tautology, that he demonstrated no connection between god and logic anyway, etc., and made no attempt to refute me (other than to say the usual what other explanation is there? crap) so he kinda deserved it. And I gave him an evolutionary explanation (a crude one, admittedly) of where logic came from for good measure. It was getting tiresome anyway.

J. K. Jones said...

"You have not established any connection between the two whatsoever!!! You are simply repeating yourself in the hopes that it might be true! I really see no connection at all! In fact, it is a complete tautology!"

Just because you are not capable of setting aside your prejudices to see the logic of an argument does not mean the argument is not sound. An unchanging ground is required for there to be unchanging laws in a universe that changes constantly. This ground cannot change.

"Such a statement is cause for me to ask if you are on medication for a psychological illness!"

Interesting that you stoop to such childish comments. I reply with: 'Sticks and stones may break my bones, but words will never hurt me.'

""The Christian theistic worldview can account for the laws of logic by stating that they come from God." Again, not explanatory. Just the insufficient 'goddidit'."

Unchanging things have to come from somewhere. There must be an explanation. If we try to explain the unchanging laws of logic or mathematics or morality or the uniformity of nature without finding an unchanging ground for those things. The God I serve does not change in the way He thinks or the way He is. The universe He set up is consistent with His unchanging being and thinking.

"All I see is ad hoc ergo propter hoc and personal incredulity."

I have still not heard a single alternative explanation that we could debate.

I might add that the law of causality also requires an unchanging ground. On top of that, the existence of a logical fallacy requires the laws of logic, and you have not provided an alternative explanation for them.

All I see is someone who cannot get beyond his personal bias long enough to consider an argument. I will leave the last comment to you. It is your blog. Besides, I don't like it when you call me names and arbitrarily insult my intelligence.

June 19, 2007 7:45 PM

Shamelessly Atheist said...

"Just because you are not capable of setting aside your prejudices to see the logic of an argument does not mean the argument is not sound. An unchanging ground is required for there to be unchanging laws in a universe that changes constantly. This ground cannot change.

What prejudice? The whole of your argument is this: God created the laws of logic (no substantiation provided), thus logic proves the existence of a god. To call this a tautology is not prejudice, just a statement of fact. You have not substantiated any connection between a god and logic. I don't even need to give you an alternative explanation for the existence of logic (but for good measure, I do so below) to point out the inadequacy of your statement. This isn't prejudice, just a statement of fact. It is from YOUR prejudice that you ASSUME a connection between god and logic. Like I said, you keep repeating this mantra hoping that the more you say it, the more valid it is. But no matter how many times you repeat it, it's still a tautology.

"All I see is someone who cannot get beyond his personal bias long enough to consider an argument." I haven't seen an argument yet, just tautology. One can not debate a tautology, except to point out that it is indeed a tautology.

"Unchanging things have to come from somewhere. There must be an explanation. If we try to explain the unchanging laws of logic or mathematics or morality [morality is unchanging? BULLSHIT! See below.] or the uniformity of nature without finding an unchanging ground for those things. The God I serve does not change in the way He thinks or the way He is [source of this insight?]. The universe He set up is consistent with His unchanging being and thinking." Baseless assumption after baseless assumption. Even if there is no answer to the uniformity of nature axiom is true (You're right. It does require an explanation. Guess what? Physics provides it. It's called gauge symmetry.), arbitrarily reaching for a supernatural answer as you do is irrational. While it was perfectly rational to do this a couple of thousands of years ago (indeed, it is why religion exists), it is completely unbecoming of anyone living in the 21st century. It amazes me that in every other aspect of the lives of the devout their outlook is modern, but when it comes to questions of life, the universe and everything, they haven't advanced beyond the Bronze Age. Better to say you don't know an answer than to look (and be) foolish by immediately jumping to an unsupported conclusion. Physics has shown us that the universe is actually exactly as we would expect in the absence of a creator. I suggest reading Vic Stenger on the subject.

You really shouldn't have mentioned morality. Morality has been shown to be innate in not only humans, but many other social mammalian species as well (not to the same extent as in H. sapiens, but Evolution predicts this as well). The evolutionary advantage of morality in social animals is obvious: it allows a group to interact in a cooperative manner. It is a set of rules hardwired into the brains of social mammals. Behavioral studies have clearly shown that religion is not at all required to be moral. From religious to atheist, the responses to moral dilemmas are statisically identical. Read Marc Hauser's Moral Minds for an excellent review of the current stated of evolutionary behavioral science. The most interesting thing is that the majority of people can't express the logic behind their responses to moral and ethical situations. Moral calculations are not performed on a conscious level, but are done in regions of the brain not accessible to conscious thought. The value behind this is again obvious. Having to think through every outcome of every decision would be utterly paralyzing.

Contrary to what you believe, you don't get your morality from the Babble, and never did. You don't buy and sell slaves, do you? Commit incest? Kill in the name of God? The morality contained in the Bible is one that is completely consistent with the morality of a brutal time in our history. It does serve one purpose: it shows us that morality is NOT an absolute, but changes with the moral zeitgeist. That there are a few nuggets of good in it is not at all relevant to its value as a moral source. If you have to pick and choose what is good and what is not, you had to already have an internal basis on which to perform your cherry picking.

Logic is just as much a product of the evolution of our species as morality. Logic such as, if three bears go into a cave and two come out, is it safe to enter the cave?, obviously provide value to survival. The way in which humans perform logic analysis points to its purely evolutionary origins.

Evolution is the ultimate designer, shaping form and function through the blind forces of Natural Selection. It is a brute force method for finding optimal configurations. But often (as for 99% of species that have ever lived) it does not find the global optimum, but only the local optimum. If conditions change radically, species can not make the transition from one optimal gene set to a whole new optimal gene set. If there actually was a designer, it isn't a very good one. If you owned an engineering company, would you keep a guy around whose designs failed 99% of the time? This is completely consistent with the blind pushing and pulling on gene propogation combined with the occasional random mutation that we know as Evolution, and completely inconsistent with some nebulous designer. Certainly not a god that showed himself to one small group through a rather disappointing medium copied by purely human hands. Ever wondered why God didn't tell everybody on the planet simultaneously through a truly impressive medium? Instead, he chose parchment. PARCHMENT!? The books you revere are supposed to be the word of god. Why? Because they say so?! C'mon, the National Enquirer is at least printed on newsprint. It even claims to be a bastion of responsible journalism. You believe that, too? Tell it to Bat Boy, not to me. Everywhere scientific inquiry has been applied to religion shows the same thing. Religion is consistent with being man-made and not divine in nature.

I have indeed read David Hume on the problems of uniformity of nature and induction, but I am quite comfortable with them. They are philosophical rather than practical issues, and so far they have not at all been a bother to Science. To say that the problem of the uniformity of nature "seems to have invalidated scientific endeavors" is rather silly considering that we make use of the benefits of Science on a daily basis. Throwing the baby out with the bathwater, as it were. Physics has shown that throughout the history of the universe the laws of nature have not changed, and there is no known mechanism by which they can change. If and when the uniformity of nature axiom fails, then, and only then, will it become a practical issue. (Of course, if they do, it would most likely a complete extinction event.) Till then, Science will continue to successfully refute and supplant the religious superstition currently rampant in the U.S.A. Science demonstrably works, whereas religious explanations have continually been shown to be insufficient, wrong and at times just plain silly.

For instance, prayer in medicine is being advocated by devoutly religious people, including some physicians. But tell me, would you want someone that relies on prayer to heal and not his/her skill as a surgeon? Not one properly performed study on the efficacy of intercessory prayer (even those supported Templeton Foundation money) has shown more than a placebo effect. If prayer is supposed to be a big effect, God seems to be hitting the 'Hold' button a lot lately.

Miracles are another aspect of religion that Science has dispelled. Kinda hard for the Catholic Church to make new saints these days. None of the miracles in the Bible could not have been faked. Remember, there are absolutely no sources of the Jesus myth, so the miracles he is said to have performed never even happened anyway. They were just written in after the fact. There were many prophets around said to perform miracles (I gave you Apolonius of Tyrana as just one example), but once the light of scientific inquiry is shone on them they scurried away like cockroaches in the night. The so-called miracles used to canonize Mother Theresa and Pope John Paul II were pathetic. If you look hard enough, and enough sick people pray to one of them, you will find one person that recovers from an illness. But the rate of recovery of people praying to either of them will not be any different statistically than from a random sampling over the whole population suffering from the same illness. Ever wondered why there hasn't been a real miracle reported in the last oh, let's say, 2000 years? Simple. People back then were superstitious almost to the last person and reasonably so, without the tools with which to combat superstition.

"An unchanging ground is required for there to be unchanging laws in a universe that changes constantly. This ground cannot change." Another tautology. God created the uniformity of nature, therefore the uniformity of nature proves the existence of god.

You're an intelligent guy, but your 'arguments' smack of desperation. You know that you have absolutely no empirical evidence to fall back on in supporting. Thus, you believe that your tautologies are valid, even reasonable, when they are actually irrational. No tautology is rational, nor are any valid. You may not have a problem with the inability of your tautologies to be falsified, but you should. Without falsifiability you are safe from attack, but hampered by the fact that you can not show your position to be true. And the burden of proof is on the one positing the existence of god(s), not the one claiming the null hypothesis.

When you have a real argument let me know, as your tautologies aren't impressing me at all. It was indeed childish of me to stoop to name calling. But as Sam Harris said, "We do not respect stupidity, unless it is religious stupidity." and the time for respecting religious stupidity is over.

June 20, 2007 10:53 AM

A response to my blog on the importance of mechanism in explanations....

I'm having some fun with someone on my blogger.com with respect to comments made on a blog I wrote in May.

J. K. Jones said...

Interesting how you decided that a theist must first be able to explain to you how the univrse came into being before he can claim God's creation of it. The thing of it is, you ignore allot of evidence whne you do that.

All the theist must do is show one thing in the universe which requires a God to create it. Evolution itself is a process that requires a designer. Rational thought is a process which requires a designer as well.

June 13, 2007 1:38 PM

Shamelessly Atheist said...

It is not arbitrary that the burden of evidence is on the one who posits the existence of something. The null hypothesis is that there is no deity. This is logic 101. I have absolutely no idea what evidence I have ignored, but if you start mentioning the bible, save your breath. That document, while of interst to historians, can't even get history correct.

No one has ever provided one shred of evidence for a 'designer'(no matter how voluminously the Disco Institute claims otherwise). I presume that you are trying to say that if Science hasn't explained something yet (which is a far cry from saying that Science can't explain a thing), then it must be attributed to a designer. This is simply a mixture of the god-of-the-gaps and false dichotomy arguments.

The greatest scientific mind ever, Newton, wrote one of the greatest works in Science, the Principia. As he described the laws governing the motion of the planets, Newton, himself a very religious (if in a heretical way) never even mentions a god. It isn't until he gets stumped when trying to calculate the motions of more than two bodies does he finally give in and invoke god because he could not make it stable. Newton didn't know of perturbation theory yet, and while there is no analytical solution describing the motion of three or more bodies, the motion is ammenable to numerical analysis. God-of-the-gaps. And those gaps get smaller every day.

As for Evo, there is no need to invoke a designer. Evo obeys Natural Selection and there is no need invoke a deity at all. This has been shown. What you might be doing is mistaking the origin of life for Evo. These are not the same thing, though many people wrongly lump the two together. The origin of life problem is known as abiogenesis. We know little about it (but more than you think), but just because we do not know something yet does not mean that we should jump to a supernatural conclusion. That would just be a lazy excuse. Why stop there? Why not stop all scientific progress and just say god did it all? This is the very reason that methodological naturalism is the basis of all scientific study. No miracles allowed.

June 13, 2007 10:41 PM

J. K. Jones said...

shamelessly atheist,

Thank you for a thoughtful response.

Some ideas:

Science depends on rationality to proceed. Our rational thinking is based in part on the laws of logic. These laws are universal and unchanging.

God establishes logic because that is the way He thinks. That is the way he set up His universe. God's being and thinking do not change.

A Christian can provide an explanation for the universal laws of logic: an unchanging God upholds them in His being and knowledge. Randomness, convention, and observation of a changing world cannot account for an unchanging standard. Only an unchanging being can.

You must supply a logical alternative explanation for the universality of the laws of logic before we can even disagree on any subject.

Now you have to come up with an alternative hypothesis before the "experiment" begins, although I am not sure what hypothesis testing has to do with this discussion.


Second idea:

Evolution, if true, is a process. That process proceeds toward an end, namely the perfection of life. Random processes do not tend toward an end, or purpose. Only an intelligence can set up a process to do that. Natural selection itself is a part of the process (the feedback loop) that shows intelligent intent.

Evidence for any purpose whatsoever at any point anywhere demonstrates the existence of an intelligence to set that purpose. There is no "gap" here.

Third idea:

How does scientific naturalism establish the fact that "…methodological naturalism is the basis of all scientific study. No miracles allowed?"


If you still want to, we can discuss the Bible latter. But I have found that those discussions tend to degenerate into "my scholar trumps your scholar" very quickly. I do ask that you not neglect the last 100 years of archeologogical and historical research in your studies.

June 14, 2007 5:31 AM

Shamelessly Atheist said...

Don't you see what you just did? You arbitrarily invoke god: "God establishes logic because that is the way He thinks." Where is the empirical evidence behind this statement? Again, this is simply a god-of-the-gaps argument mixed with the argument from personal incredulity. This is how religion came into being. It was a primitive step in trying to understand our place and existence, but since the tools we now have weren't available deities were invented. In future we will have even better tools to answer these questions. We don't know how the universe came into being therefore it was due to a creator. Who created the creator? You can not arbitrarily stop the infinite regression at the creator.

Natural Selection is not at all purposeful. It shapes traits giving the appearance of design. If you select those traits that work better than others for a certain function (i.e., larger beaks on finches for breaking harder seeds), then birds with larger beaks will pass on those characteristics to the next generation. Natural Selection is blind without being random. Evo being random is a common and totally erroneous misconception. Evo does not proceed to some predetermined end at all. If the environment changes (and it always does), then the characteristics necessary for survival are continually in flux. There is no final endpoint, only what works today.

I've already explained why scientific naturalism (the proper term is methodological naturalism) does not allow the invocation of miraculous events. ALL Science stops if miracles are allowed. If you make an exception in one place you have no basis for which it can not be applied everywhere. Science ends because you now have an excuse to not look for the real answers. It is illogical to jump to the baseless conclusion of the supernatural. Gods were created to explain lightning and thunder, but have long since been known to be an insufficient answer. It is no different for invoking deities anywhere else.

So, how do we know that methodological naturalism works? Because it does. The reasoning is rather inductive, but that doesn't bother me. Just like we know that the sun will rise tomorrow because we have seen it rise so many, many times before, we know that naturalism will answer our questions if we keep pushing because Science has explained so much already. We may not ever be able to answer everything, but that doesn't bother scientists. Why? Because we would much rather say that we do not know than be intellectually dishonest and shrug it off as supernatural.

I do not ignore archaeological evidence at all. Take the story of Moses, for example. There is an utter paucity of evidence for the Jews being enslaved by the Egyptians, and 500,000 people don't wander anywhere, let alone the Sinai, without leaving mountains of evidence. Biblical archaeologists have scoured the Sinai clean in attempts to verify the Moses story and found nada. The Noah has no empirical basis and it is simply lunacy to believe it in light of what we now know. Millions and millions of species on a boat? We couldn't even come close to that with modern shipbuilding technology. It is exactly as one would expect from a priori knowledge that these are stories made up by humans. It was simply a bad local flood in a time the world didn't extend much beyond the horizon. What about Jesus? Sorry, there are no contemporary accounts of his existence at all. Even the history of it was wrong. There were many prophets at the time. You were nothing if you couldn't perform miracles. Apolonius of Tyrana was said to do the same things Jesus did, and he was just one of many. That the Jesus story was the only one that survives in popularity is not very impressive. I could go on and on and on. Religion simply doesn't bear close scrutiny and makes every effort to make sure no one does look too closely.

June 14, 2007 10:44 AM

J. K. Jones said...

"God establishes logic because that is the way He thinks." Where is the empirical evidence behind this statement?"

Laws of logic cannot be established through empirical evidence. They are abstract concepts. They don't exist out there somewhere where we can see them.

God is transcendent; that is, He is beyond the material universe and is its creator. God has originated the laws of logic because they are a reflection of His nature. Therefore, the laws of logic are absolute (or unchanging). The are unchanging because there is an unchanging God.
It sounds as if you are trying to force me to use the scientific method to explain the laws of logic. Logic is used to evaluate the evidence we see with our senses. It is, in one sense, thought about observations of the world. Using the scientific method to establish logic is a circular argument.
There are no gaps here because scientific observation can never prove an abstract law. It's a here and now thing, not a way back when thing.

"Who created the creator? You can not arbitrarily stop the infinite regression at the creator."

You cannot have an infinite regression of finite causes, either. The line of causes would never have been moved through to get to the things that exist now. The regress must stop with something, or someone, which has always existed.

"Natural Selection is blind without being random. Evo being random is a common and totally erroneous misconception. Evo does not proceed to some predetermined end at all. If the environment changes (and it always does), then the characteristics necessary for survival are continually in flux. There is no final endpoint, only what works today."

Thanks for educating me on the concept. Then the purpose of evolution is to improve life so it will survive in today's environment. Remember that the environment is part of the system to.

I still do not understand how "methodological naturalism" can establish its own truth claim. How does the empirical observation of the world we live in justify the claim that only scientific observation of the world we live in yields information? Saying that it works "Because it does." is a cop-out.

I'll leave the Bible and archeology stuff alone for now, but there are answers and there is evidence. I have been looking closely at my own religious beliefs for several years now, and they "bear close scrutiny."

June 15, 2007 2:23 PM

Shamelessly Atheist said...

So you agree, then, that there is no empirical evidence for a god(s). I would then consider the discussion closed, but I would doubt that you would be satisfied with this.

"You cannot have an infinite regression of finite causes, either." I'm not sure how this was relevant, but I believe you are referring to the fatally-flawed First Cause argument. The problem with this argument is that there are a number of processes which do not require any cause. These tend to lie within the quantum realm, such as radioactive decay and virtual particle formation/annhiliation. Current theoretical models place the formation of the universe also in the realm of quantum mechanics.

Why does everyone think that everything has to have a purpose? Evo has no purpose. It is BLIND. It has no agenda of its own. In fact, the universe is completely oblivious to what humans do, believe, etc. The vast majority of the universe is completely hostile to human life. It has no consciousness (regardless of what Deepak Chopra thinks), no purpose, no agenda. If we puny humans can't get our heads around that, the universe doesn't care. Who are we to be so arrogant as to think such a thing?

"Saying that it [methodological naturalism] works "Because it does." is a cop-out." Hardly. I'll admit that there is an element of faith in the idea that all phenomena can be explained through natural laws. But do you then include other forms of knowledge like the so-called 'inner knowledge'? There is nothing which says that this isn't a simple word substitution for 'belief'. David Hume made it very clear that we can not rely on our perceptions since these are continually being fooled. Optical illusions are a prime example of this sort of thing.

David Hume said it best: "If we take in our hand any volume; of divinity or school metaphysics, for instance; let us ask, "Does it contain any abstract reasoning concerning quantity or number?" No. "Does it contain any experimental reasoning concerning matter of fact and existence?" No. Commit it then to the flames: for it can contain nothing but sophistry and illusion." In other words, anything based only on our feelings and 'inner knowledge' without experiment and empirical data to back it up is junk.

People that trust in their beliefs without empirical evidence to guide them end up believing in weird things, like near-death experiences. We actually know that these odd experiences are due to neuronal depolarization due to lack of oxygen. The exact same near-death experiences can be reproduced in centrifuges. Fighter pilots see this in training all the time.

Without empirical evidence, you can't talk intelligeably about anything, including god(s), simply because there is no data to work from. What I always find amusing when theists say that we can not know God's plan for us immediately speak volumes about said plan.

"...the laws of logic are absolute (or unchanging). The are unchanging because there is an unchanging God." Wow, now that statement is missing about a thousand intermediary steps. Prove it, or at least have some supporting data. It smacks of 'I can't think of why logic works, therefore there is a god.' That is horrible logic. Logic is a human invention based on how the universe works. The ultimate logic is mathematics. In this universe, 1+1=2. This may not be true in other universes, but it works for us.

If you think methodological naturalism can't establish itself, how do you know that there are indeed laws of logic? Same problem. In Science we use what works to explain phenomena. In fact, it's the ONLY thing that works. And it keeps on working, and working,... Science dies in the presence of metaphysics, because then any crackpot idea based on a feeling one has after eating cheese for breakfast goes. Saying 'goddidit' is just invoking intelligent design because we are stumped. But as I showed clearly in the blog, it is no explanation whatsoever. It provides no mechanism for observed phenomena.

This is a direct challenge: I would love you to explain to me how invoking a designer is at all scientific. Any hypothesis must have these attributes:

(i) has data in support
(ii) explains new data as it comes in (we'll skip this one for now)
(iii) makes testable predictions
(iv) is falsifiable

Missing any one of these attributes and it ceases to be Science. I'll tell you now that I have only the utmost disdain for non-empirical methods...

June 15, 2007 3:50 PM

J. K. Jones said...

"David Hume said it best: "If we take in our hand any volume; of divinity or school metaphysics, for instance; let us ask, "Does it contain any abstract reasoning concerning quantity or number?" No. "Does it contain any experimental reasoning concerning matter of fact and existence?" No. Commit it then to the flames: for it can contain nothing but sophistry and illusion." In other words, anything based only on our feelings and 'inner knowledge' without experiment and empirical data to back it up is junk."

Faith is based on reason, not "inner knowledge." I have sound evidence from the world as it now exists for God's existence: the existence of undeniable uniform and absolute abstract laws like the laws of logic and mathematics.

Again, the claim that "only empirical evidence can establish truth" is itself an abstract truth that cannot be established through empirical evidence.

Have you ever studied Hume's skepticism regarding the uniformity of nature? He seems to have invalidated scientific endeavors. He said something about us not being able to say with confidence that the world will behave in the future the same way it did in the past. That destroys inductive reasoning, the basis for science.

Science requires the uniformity of nature, or that nature behaves in the future the way it did in the past. Hume says we cannot count on that.

"What I always find amusing when theists say that we can not know God's plan for us immediately speak volumes about said plan."

I find that amusing to. Like Mark Twain before me, it's not the parts of God's plan that I don't know that bother me. It's the parts I do know. The part about living a perfect life devoid of sin. The part about me not doing that. The part about having to humble myself and trust in Christ's death on the cross to pay the penalty for my sins. Christianity invalidates any false pride in my own morality and good works.

"The ultimate logic is mathematics."

I don't care which uniform and absolute set of laws we take first: logic or mathematics. They are both unchanging, invariant and abstract (not something we can find with the five senses). We could talk about the uniformity of nature in the same way.

These abstract laws are not the result of observable behavior of object or actions. We do not observe the laws of logic occurring in matter. Therefore, no law of logic can be observed by watching nothing. We assume that logic's laws work in order to evaluate scientific evidence.

The Christian theistic worldview can account for the laws of logic by stating that they come from God. God is transcendent; that is, He is beyond the material universe being its creator. God has originated the laws of logic because they are a reflection of His nature and thinking. Therefore, the laws of logic are absolute. They are absolute because there is an absolute God who upholds them.

"…how do you know that there are indeed laws of logic?"

Take one for instance: the law of non-contradiction. It says that something can not be both A and Non-A at the same time, in the same relationship, and in the same sense. You cannot deny this law. If you say "A can be both A and Non-A…" I could then interpret you as saying "A cannot be both A and Non-A…" The laws of logic are undeniable because to question them is to invoke them.

I am not here saying anything about a faith that is unreasonable or a 'blind leap.'

I do not accept the idea that a truth claim must be falsifiable for it to be reasonable. The laws of logic are not falsifiable in the sense of requiring empirical data to validate or invalidate them. Neither are the laws of mathematics or the uniformity of nature for that matter. All of these things must be assumed to be true to have scientific or empirical knowledge. We presuppose that their principles are necessarily true. We assume, for example, that nature will behave in the future the way it does in the past.
They are all established by an absolute God who designed His universe to exhibit these traits.

June 18, 2007 6:31 AM

Shamelessly Atheist said...

"Faith is based on reason, not "inner knowledge." I have sound evidence from the world as it now exists for God's existence: the existence of undeniable uniform and absolute abstract laws like the laws of logic and mathematics."

Bullshit! You have not established any connection between the two whatsoever!!! You are simply repeating yourself in the hopes that it might be true! I really see no connection at all! In fact, it is a complete tautology!

Such a statement is cause for me to ask if you are on medication for a psychological illness!

"The Christian theistic worldview can account for the laws of logic by stating that they come from God." Again, not explanatory. Just the insufficient 'goddidit'.

"I am not here saying anything about a faith that is unreasonable or a 'blind leap.'" Yes, you are, for the above stated reasons...

All I see is ad hoc ergo propter hoc and personal incredulity.

June 18, 2007 8:59 AM

God vs Evo - Part III

So how does an engineer come to believe that life was designed, discarding a heck of a lot of data to the contrary, as well as a perfectly good explanation? It didn't take a lot of thinking. The first is obvious. Having grown up in a religious setting makes for a prediliction of seeing design in life. We often borrow ideas from nature and incorporate them into things we actually do design. The mind is prepared by both a religious upbringing and a career in engineering to see design. But nature does what works, discarding things that don't. This creates an illusion of design.

Remember, 99% of all species that have ever lived on this planet are long gone. We see a progression of complexity everywhere we look. The eye is more complex in new species than in phyla which have been around longer. The brain of humans is more complex than that of a chimpanzee, but not dissimilar. There are so many examples that I could give, but other authors have said it better elsewhere. Common descent is the only explanation for the similarities and the dissimilarities that we see.

Anyhow, back to the battle. I left off with Don attempting to tell me that atheists want minority rule....

It is instructive to look at a more secular society in comparison. From here in The Great White North, we look southward and see politicians tripping over each other in their eagerness to demonstrate that they are more religious than their opponents (it's embarrassing to watch…); we see biblical references in what should be secular institutions like judicial buildings even though neither your legal system or ours has anything to do with them and the law must be for everyone, not just Believers; we see official favoritism towards Christian groups even though the First Amendment was placed in your own constitution to prevent that very thing. That's just for a start.

In Canada, no one running for public office either expresses their religiosity or questions that of others; we do not place obviously divisive symbols representing only one group (and thereby giving that group preferential treatment) in our public institutions. I was asked to take an oath last year. In Canada, there are different oaths depending on whether you are theist or atheist. Both are equally legally binding. This kind of accommodation hurts no one and at the same time does not show any favoritism. It works incredibly well and completely circumvents the current hiccups in the American system due to theocratic 'reforms'. I was not a vocal atheist at all until my eyes were opened by people like Ann Coulter, Bill O'Reilly and their intolerant ilk. We don't have them up here, yet there are many theist politicians in Canada. It just doesn't matter to us unless their religiosity starts to become policy. It's not that we don't care about beliefs, it's just that we accept that everyone is an individual and we go out of our way to accommodate widely varying beliefs. As a result, we have almost completely avoided the problems that occur when religion is mixed with politics. We have seen what happens when societies become theocratic. Life under the Taliban was truly repressive, and if you don't think that America can end up that way you are kidding yourself.

I was surprised that Don didn't bring up Michael Behe's concept of irreducible complexity, though he does list his book as reading material at the end. The only thing as discredited as the concept of irreducible complexity (demolished even before the book was published) was his atrocious and laughable testimony at the Kitzmiller trial. Behe can't even be bothered to keep up with the relevant literature, so how can he be taken seriously? Contrary to Don's belief, there is no conspiracy in Science to keep ID out of the journals. From Science classes, yes, but that's because ID contains no Science. It's vacuous. The trick to getting published is to present positive evidence for something, not negative evidence against something else. ID has no positive evidence in its favor and Judge Jones recognized this in the Kitzmiller trial. The only place where Evo is in crisis is in the court of public opinion and the Disco Institute has done a remarkable, if harmful, job of it. The US is the laughing stock of the world, ranking second only to Turkey in rejecting Evo.

In essence, and as usual, the sum total of evidence presented for design was zilch, unless you count "I am an engineer. I know design when I see it. This is design." This sums up the ID position in toto. The rest just seems to be twisted attacks on Evo, which is to say, not evidence at all.

And since he spoke of Newton, perhaps the greatest mind in history, Newton found the inclusion of God unnecessary in his Principia till he hit a snag. He couldn't get the planetary system to stabilize in his math, so what did he do? You guessed it. He invokes God. Perturbation theory solved the problem later on, of course. I mention this because it shows that even the greatest minds jump to a supernatural conclusion when they find that they can't explain something. God has always been the God-of-the-gaps. Your friend himself retreats into this trap himself several times. For instance, he says "If evolutionists know that life evolved from non-life why don't they create life in the laboratory." (He never did answer my question as to why a designer would incorporate a broken enzyme into the design. There are a lot of other reasons, all in a similar vein, to reject the design hypothesis- the eye (wired backwards), the ureter (makes a rather unnecessarily circuitous route), etc. As an engineer, I'm surprised that he has missed all this. I mean, what kind of designer throws away 99% of his designs after he builds them? "if it walks like a duck, quacks like a duck….", you fire the duck's ass for incompetence.)

As to the complexity of the brain, I don't know enough about devo to answer his criticism properly. But then, neither does he to have made it in the first place. (I've asked a devo specialist for insight into this...) But I do know that the brain does self-assemble under biochemical control, which places it under the purview of Evo (actually, Evo/Devo). A great deal is known about brain development, and none of the explanations involve magic. My limited understanding that chemical signaling is important, which means that the timing of when genes are turned on and off is critical in terms of the final outcome. A gene for consciousness, you ask? There isn't one, of course. Don seems to maintain this strawman view of Evo – one gene, one trait. There are a couple of reasons why mathematics is a bad way of dealing with Evo. First, Evo simply doesn't lend itself well to mathematics, though it is used in simulating it with computer modeling. Second, there aren't many (if any) mathematicians out there that are also well-versed in the nuances of Evo. Evo is not for the faint of heart (or mind), and William Dumbski [sic] especially seems utterly incapable of understanding it. Spend less time trying to prove that brain development is magic and more time looking at how it does in fact develop. And Don wonders why I think mathematicians without training in Biology (like Dumbski [sic]) should stick to mathematics.

"Science is built on truth not consensus," Don said. Sort of, but I'm not sure what truth means. Is truth the observation? It's certainly not theories. Truth is an absolute. Scientific theories are provisional hypotheses which: explain the current data; explain data obtained after positing the hypothesis; makes testable predictions; and is falsifiable. Theories model reality (truth). In discussing the current thinking about a particular theory, it is often useful (as in the case of Evo) to poll the experts. Each individual expert, however, judges the validity of the theory according to the characteristics that I have just listed. Truth is the ideal goal, but I don't think that any scientific theory has accomplished this. Pretty much everything he wrote was just a rehash of failed apologetics mixed in with Disco Institute PR releases (which is all they have ever produced on ID).

Don brings up the old 'evil atheist' list. But the implied insult to all atheists is that old canard of the evil atheist list, and I took it personally. Very personally. Is he saying that I am prone to mass murder? That in being an atheist, I am evil? Stalin, Pol Pot, Hitler... Wait - Hitler? Sorry, while ideologues all with personal ambition (to the point where they were really promoting religions without a deity), Hitler was a THEIST. He was born and raised Catholic (and tellingly never excommunicated) and said often that in his final solution he was doing God's work. I would not insult any Believer with a list of theists that committed atrocities in the name of religion, even though the body count would be far higher my list, starting with numerous characters in the Bible, to de Torquemada, to Jim Jones, to David Karesh, to Paul Hill. (Ooops. That's a list, isn't it?) I don't like to speak in biblical terminology, but if there is such a thing as evil, Jerry Falwell (a man who promoted hatred and fear in his followers) would be my candidate as its personification. George Bush Sr. knowingly allowed 500,000-1,000,000 Iraqis (the estimate provided to the White House by the NSA) to die due to ineffective sanctions post-first Gulf War. All he had to do was give the Shiites and Kurds ammo and Hussein (a man Bush himself helped to power) would have been toppled with far less loss of life. Not ideal, but far better than what actually occurred. Most of those sanction victims were children. That puts him in amongst the top killers of all time, but history is written by the victors. After all that killing by proxy, I don't remember George acknowledging his atheism. In fact he has been quoted as saying he doesn't think atheist Americans should be considered citizens. How Christian of him.

I live a very moral life, though my morals and ethics may be different from yours and your friend's, I will put them up against anyone else's for comparison any time. I would much prefer to speak of those atheists that have done something with their lives, like Mark Twain, Abraham Lincoln (probably a deist, but certainly not a Christian), Thomas Paine (a deist, but with significant atheist leanings), Oscar Wilde, Albert Camus, Isaac Asimov and many, many others, as I would of theists that have performed similar works. Religion is no guarantee of morality. The Bible itself condones slavery (amongst other unsavory behaviors), something that today we find reprehensible. To make that list and recite it to me, your friend made my case for me against religion. I am dismayed, despondent and insulted beyond measure by the response. The Evolution of our species (and others, it has been found) has resulted in an innate set of moral rules. The so-called Golden Rule is just a codification of this. Mere babies will behave in accordance to this rule, far younger than they could have been taught it, or acknowledge the existence of God. Science has at every turn peeled back the layers of religious belief till there is essentially nothing left but denial.

In the final part, Don shows his true baseless prejudice against atheists (and pissed me off) when he quotes Julian Huxley....

My ongoing conversation with the religious at The Things That Matter Most...

Well, anyone that is still with me after reading that monstrous, convoluted blog entry of yesterday is truly hardcore. For those who have not read the prior blog entry on this, it is necessary to at least refer to it to fully understand this and the next several entries. I'm going to give people a bit of a break and separate my response out into several parts. I'd like to say that these things are labors of love, but I don't think the word 'love' is appropriate. Certainly, they're not my usual cup of tea, since I like to pick a topic, write succinctly and clearly on that without going off on tangents, and not bore/confuse you poor readers to death.

I don't know that I will ever send this off to Don Ortloff (via Lael Arrington), but I will post it here. The quote mining of Don's I ignored, as I did the anecdotal emotionalistic claptrap at the end designed to try to convert me. To quote Bugs Bunny, 'He don't know me vewy well, do he?' It begins.....

Don:

plays the same invalid numbers game that Dembski plays. William Dumbski [sic] has been thoroughly debunked elsewhere and in the interests of brevity I won't get into it here. All one has to do is google it. Suffice it to say that these number games are self-interested convoluted methods of promoting the argument from personal incredulity that show no more than that DNA sequences could not arise through random chance. Fancy that. ToE says the same thing. The massive fallicies in his arguments have been pointed out to William Dumbski [sic], yet he continues to say things like 'we can not explain cellular machinery without invoking a purposeful design' and then usually brings forth Behe's example of the bacterial flagellum when it has been shown clearly in the literature how in fact the bacterial flagellum could evolve. This makes Dumbski a LIAR. He wants you to believe that a non-purposeful evolutionary process is the same thing as saying it is random. Bullshit. Natural Selection is anything BUT random.;

tries to tell me that Tacitus and Josephus were contemporary sources on Jesus. It is in doubt as to whether Tacitus even was the author of the missive on Jesus, and neither Tacitus nor Josephus had even been born before the supposed Ascention! I reiterate: there are no contemporary accounts of the Jesus/Horus myth! As for the existence of Caesar and why his existence is (now) accepted without question, scholars had long ago established from numerous sources (not all literary) that Caesar was a genuine personage. The reason no on questions his existence is that his existence was established long ago. At least we have Caesar's own writings, which is much more than we have for Jesus. Unlike for Julius Caesar's life, the data surrounding Jesus' birth, life and death is completely uncorroborated even though records from the period are available.;

hypocritically accepts hearsay data of the absurd account of Noah and the flood, and then asks for 'real' evidence for Evo (which he doesn't accept anyway). People say that they have seen reminants of the Ark (you mean that geological formation that people keep mistaking for the Ark?) and finding a bit of wood of approximately the right age. Yes, there was wood, even in the time of Noah. Of course, the whole myth is just a retelling of Ziusudra and the flooding of the Euphrates in ca. 2900 BCE for which we actually have evidence of the event. The same can not be said for poor Noah, nor for the myth of Moses and the Exodus, nor for....;

tries to tell me that the 2nd law of thermodynamics can be applied to preclude the generation of order in an open system (He's trying to snow a Chemist with this?! Boy, was he barking up the wrong tree.);

that asymmetric synthesis is impossible without direction when all that is required is a surface for one optical isomer to be preferred in a reaction. The synthesis of one optical isomer of dl-pairs, such as l-amino acids, over their . l- and not their mirror image d-amino acids are exclusively the building blocks of enzymes, yet have identical physical properties. (asymmetric synthesis is big money in the pharmaceutical industry, which according to him isn't possible);

that Evolution includes the origin of life in its theory, when abiogenesis is a completely different problem. The only relationship between the two is temporal – abiogenesis had to occur before Evo could start its work. We've come a long way since the Stanley-Urey experiment. This is primary evidence that Don has never read anything on Evo outside of Christian 'Science' lit;

that behavior has no biochemical basis (in answer to his question of what part of the genome governs emotions like love, a number of biochemicals like oxytocin, the genes that encode their synthesizing enzymes and the genes which control their activation come to mind immediately) and therefore cannot be under evolutionary control (I would like to know how he then explains the observed genetic changes in the Russian silver fox experiment of Dmitri Belyaev if genetics play no role in behavior, where silver foxes were bred for either tameness or viciousness). Your friend seems to think that one gene-one enzyme is how DNA works. It does not. Genes interact, sometimes in unpredictable was (definitely the case in the Belyaev experiment, unintentionally resulting in changes to coat color and tail stiffness). Emotions such as love are just as likely to develop as fear. Co-operative behavior is just as effective in species which use social coherence as a survival strategy as the fight-or-flight response, even in tooth-and-claw natural selection (there is no such thing as Darwinism). None of this takes away from the actual feeling of love itself or makes it any less wonderful. Again evidence that Don has never read anything on Evo outside of the Disco Institute's official reading list (which means all he knows of Evo is the usual strawman the Diso Insitute disingenuously touts);

Part II tomorrow....

New argument for God's existence?

This past week Ray Comfort and Kirk Cameron debated with the Rational Response Squad on the existence of God. Comfort promised us a proof of God, so while many of us in the atheist community were dubious about whether these two twits had even the brain power to come up with something new, we held our breath and actually hoped we wouldn't see one of the tired, old, pathetic apologetics we've be subjected to for the past thousand years. Verdict? We risked hypoxia for nothing. Not really a surprise when these two clowns are involved.

The argument? Ray Comfort held up a picture of a painting of the Mona Lisa and told us that it is obvious that the object must have been made by a painter, a designer if you will. By analogy, then, the universe must have had a creator. This creator they call 'God'. Sound familiar? It's hardly original. William Paley used this argument more than two hundred years ago.

On the surface, this argument seems powerful and compelling. Something that has the complexity contained in a painting must have been designed. But this argument's strength is in fact its fatal flaw. Once the question 'how do we know the painting was designed?' is asked, the argument is dead. We know that a painting was produced through a willful and conscious act of an agent (the painter) because we understand how a painting is made, even if we hadn't seen the painter paint this particular painting. Indeed, we do not even need to know who the painter was. This is an example of making a conclusion based on an understanding of the mechanism by which a painting can be made. This is good Science and this part of Paley's argument from design is so far legitimate.

The flip side of the argument is that like the painting, the universe and its contents is so complex that it must also have had a designer. The problem with this analogy is that 'God did it' does not suffice as a mechanism by which anything can be explained. In point of fact, not only does this response 'beg the question' (I would say 'questions'), but never answered the question in the first place. Genesis tells us that God said 'Let there be light, and there was light'. In essence, 'God did it.' If I say to my coffee maker ,'Let there be coffee', I think its easily predicted that I must go without caffeine. A terrible fate indeed. Generation of coffee requires that I use hot water to extract flavorful compounds and caffeine from coffee beans. In other words, a mechanism must exist for creating a cup of coffee from a handful of beans. Genesis is just another example of bad Science, an attempt without supporting data to explain the universe's existence in the absence of a plausible mechanism. This is a very different animal from the creation of the painting.

Mechanism is an extremely important concept in Science. Saying the universe is here because God created it tells us nothing. We gain no knowledge from it, and it is therefor valueless. Tell me HOW God created the universe and then I'll have a listen. Evolution is a fact. We see a progression of speciation in the fossil record for which the only known plausible mechanism is natural selection. Show me a fossil rabbit in the Paleozoic and then natural selection would fail as a potential mechanism for speciation. But we never see such out-of-order lineages. Gene mutations in current species are predicted by Evolutionary Theory. For instance, have you ever wondered why dogs and cats do not need to eat fruit in order to maintain their vitamin C levels? Primates have a mutation in the gene encoding L-gluconolactone oxidase (a PZ Meyers favorite) which catalyzes the reaction producing ascorbic acid (vitamin C). This is also true for fruit-eating bats. When fruit-eating bats split off from an ancestor common to fruit- and non-fruit-eating bats a mutation in this gene occurred, making this enzyme ineffective in this fruit-eating lineage. Indeed, the use of molecular genetics as a molecular clock is in very good agreement with the fossil record, greatly strengthening the argument. The universe is old. We know this from the measurements of red shifts in supernovae. Our home planet is quite old as well. We know from various methods of radiometric dating that the Earth is ca. 4.5 billion years old. The fact that numerous different methods point to the same age makes this estimate very strong.

The argument from design really shows its inadequacy when the knowledge of mechanism is removed. Let's take a scene from the movie The Gods Must Be Crazy, a movie I highly recommend. In this scene, a Coke bottle is discarded from an airplane flying over the African savanna and is picked up by a Bushman (followed by a series of incidents which force the poor sop to conclude that the gods are nuts, hence the movie's title). Having never seen a bottle before, and never having known how a bottle is made, the Bushman makes the perfectly human (and just as perfectly incorrect) conclusion that the bottle was made by the gods.

Was the Bushman's conclusion made on the basis that the bottle is so complex? No. The Bushman jumped to the conclusion without a plausible mechanism. Complexity is just a nebulous buzzword used by the IDiots. When you can quantitate complexity and also determine how much complexity is too much for a conscious agent to NOT have created the universe, then we'll talk some more. But this idea that the chances of a cell spontaneously forming are about the same as a tornado moving through a junkyard and spontaneously creating a Boeing 747 does not cut it as an argument, especially when Evolutionary Theory agrees.

We humans are predisposed to jumping to conclusions in the absence of data or a plausible mechanism. Michael Shermer has written about this extensively in his book Why People Believe Weird Things. Invoking the supernatural as an explanation is an example of bad Science. The scientifically-correct conclusion the Bushman should have made is that he simply can not know the source of the Coke bottle or how it was made without more information. While this is an unsatisfactory answer to any human being (I am not different), jumping to the conclusion that the supernatural is responsible for the Coke bottle's existence, while understandable, is illogical and unscientific.

This is exactly the problem with Paley's argument. On the one hand, we know how a painting can be made from the application of pigments to a canvas in a concerted fashion by a conscious agent. A plausible mechanism is available (good Science). In Paley's time, no plausible mechanism for the creation of the universe was available to draw any conclusion - indeed, we still do not know how it came to be -yet he concluded that it must have had a creator (bad Science). The scientifically-correct conclusion is that there is no conclusion. No scientist, myself included, is satisfied by such an unsatisfying answer (ok, so that's a tautology - sue me). But the difference is that we atheists don't find retreating to the supernatural any more satisfying.

Of course, the final joke of the debate was that Ray Comfort was not holding up a painting as he asserted, but a reproduction of the Mona Lisa. The inaccuracy of this fits exceptionally well with his, or rather Paley's, 'argument'. Neither jumping to conclusions without supporting data nor superstition, alone or in concert, can ever be considered as good Science.