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)

The Biology of Sexual Orientation - Cristian C A Bodo

Reposted from the American Sexuality magazine online.

The Biology of Sexual Orientation

Insight from animal research about what turns us on

By Cristian C A Bodo

What determines sexual orientation? What makes a person gay, bisexual, or straight? These sort of questions hold an undeniable interest to the general public and the answers are still hotly debated both by the experts in the field and by society at large. There are some powerful reasons for this universal appeal: First, the vast majority of us have experienced in the course of our lives some sort of sexual attraction toward other human beings, and this attraction in turn exerts a powerful influence in our mood, our behavior, our social interactions, and on the image that we have of ourselves. Since this plays such a key role in our lives, it is only natural that we would be interested in knowing at some point about its origins, and why we are oriented only toward people with certain characteristics and not others.

The examination of sexual orientation also holds relevance to specific social policies. Whether sexual orientation is the result of a conscious choice by the individual, as opposed to just another trait that comes "built-in" in our system, helps determine if it should be categorized as a "moral problem" or not. This seems to matter a lot in shaping out attitudes toward sexual minorities. Specifically (and for better or worse), the public appears to be more sympathetic to variations from the norm, in this case strict heterosexuality, if they are convinced that the individual has no "say" on this departure since it is the product of biological determination. On the other hand, sexual minorities have traditionally regarded this argument with suspicion. They fear that scientific research may open the door to treating these variations as little more than a disease and that efforts will be made to reduce or eliminate incidences of homosexuality in human populations.

Still, as it often happens with contentious issues that have such an impact for everyday life, society has turned to scientific research in order to get some answers. Despite the many occasions in which it has been proved otherwise, science still holds in the public conciousness the image of an unbiased actor whose answers are based solely in the pure application of a rational methodology and are therefore beyond the usual "contaminations" introduced by those who have specific interests in directing the public opinion toward their side of the field.

The question of sexual orientation has received special attention from biologists from early on. In part, this is due to the relevance that this trait is supposed to have for the survival of animal species with two (or more) separate sexes: If reproduction depends on successful mating with a member of another sex, then being attracted and actively attempting to interact with them would seem to be important to ensure that the genes of one generation be well represented in the next.

Plenty of experimental work has been done using lab animals to try to figure out how this is established, and how they develop an attraction for potential mates belonging to a sex other than their own. Most of it has been carried out in rodents (rats, mice, hamsters) for the simple reason that they breed well and adapt easily to a laboratory environment. Their proverbial capacity to deliver plenty of litters in a short time also comes handy at the time of doing an experiment.

The evidence derived from lab animals points directly to hormones derived from the gonads (testes in males, ovaries in females), specifically testosterone, in the determination of sexual orientation. When male pups are castrated at birth, they no longer seek the company of females after they have gone through puberty. Conversely, when females are injected with testosterone early in life, they later show an attraction toward other females, just like a male.

This is often referred to as the "organizational" effect of hormones, meaning that hormones trigger changes in the brain circuit, so that the brain develops in a particular way making animals predisposed to seek the company of one sex over another after reaching sexual maturity. In addition, the levels of hormones that they have in adulthood are very important to maintain this preference: If the gonads are removed, the preference quickly disappears, no matter how strong it may have been before the surgery. So the evidence is strong for a "built-in" mechanism in the determination of sexual orientation in rodents. Whether they will be attracted to females or to males when they grow up seems to be largely determined by the presence of functional testes or ovaries early in life (or even before they are actually delivered by the mother). The million-dollar question, the one that continues to generate heated debates both within and outside the scientific community, is whether this can be extrapolated at all to humans. And the answer is far from being trivial, since there are indeed powerful reasons that call for caution when doing so.

Sexual behavior in rodents is strictly associated with reproductive function, to the point that females will normally accept to mate with a male only during a particular stage of the estrous cycle: immediately after ovulation. Attempts by the male to initiate copulation during any other stage of the cycle are generally met with rejection, and this can turn into downright aggression. It is easy to see why this should be so. By limiting sexual activity to the period in which the female is actually fertile, the waste of energy that mating not resulting in pregnancy represents is actually avoided. Not surprisingly, gonadal hormones control the coordination between these two events (ovulation and sexual receptivity). Cycling ovaries release estradiol and progesterone to the bloodstream, which triggers ovulation and sexual receptivity.

In humans, on the other hand, the situation is radically different. Despite several attemps that have been made over the years to measure variations in sexual desire in women during the cycle, there is virtually no evidence to support such a claim. In humans, and other selected mammalian species, the willingness to engage in sexual activities seems to be dissociated from the hormonal status, and therefore not limited to be a mere prerequisite for succesful reproduction. On the contrary, we are all familiar with the multiple roles that sex plays in human societies, ranging from the expression of affection to the validation of social status. Even in non-human primates we can see some clear evidence of this emancipation of sex from its primitive role: Pygmy chimpanzees (or bonobos) are famous for using sexual intercourse to regulate many aspects of their social interactions, including greeting each other, resolving conflicts between members of the same clan, and exchanging food and other commodities.

Does this diminished role of gonadal steroids in the regulation of sexual activities also translate to the determination of sexual orientation in humans? With perhaps a single exception, researchers have in general failed to find a link between this characteristic and exposure to gonadal hormones at any point during the life of the individual. The exception is a study that showed women affected by congenital adrenal hyperplasia (CAH), a syndrome that caused their adrenal glands to excrete an excesive amount of sex steroids during their development, exhibited a higher proportion of individuals reporting same-sex sexual orientation compared to the general population. Notice, however, that this is not the same as saying that all the women exposed to high hormonal levels as a consequence of their syndrome became homosexual, which suggests that if hormones are playing a role here, they have to be doing it in combination with other factors. On the other hand, there is not a single study to this date that has conclusively proved that gay men are exposed to subnormal levels of testosterone or other sex hormones during development.

So, the evidence for gonadal hormones as the determining factor for sexual orientation in humans seems to be much less abundant than does the evidence in animal models. Perhaps, in part, this is because in the former case studying the phenomenon under strict experimental conditions is impossible, and thus researchers have to rely almost exclusively in the so-called "experiments of nature," clinical syndromes such as CAH in which it is particularly difficult to control for other variables—such as psychosexual history, genetic and social background—that may affect the outcome.

Another reasonable consideration is that with the evolution of higher cognitive functions, our sexuality became a much more complex phenomenon, with multiple purposes beyond mere reproduction and also with multiple variables affecting its different aspects, and this includes of course sexual orientation. And yet, it is difficult to shake off the feeling that some deeply ingrained biological root exists that determines who we feel sexually attracted to. When asked, most people declare having no recollection of making a conscious choice about this issue at any point in their lives. Instead, there is a strong feeling of having been "made" in certain way, which implies an underlying biological cause that overrules any attempts to modify it by conscious decision. (This has been and often still is the cause of a heavy psychological burden for gay/lesbian individuals raised in an environment that does not tolerate their sexual orientation and blames them for it.) But regardless of whether improved experimental methodology and more advanced technology would allow us one day to shed some light on the elusive biological factors that determine sexual orientation in humans, it is important to ask ourselves if we are interested in finding an answer to it, and thus if it should continue to be the object of scientific enquiry. As mentioned at the beginning, sexual minorities have repeatedly expressed concerns about this, since they fear that it may actually increase discrimination practices against them.

It is easy to sympathize with this point of view, especially considering the many instances in which supposedly neutral scientific knowledge was used in the past to justify racist policies or to deny women their civil rights. But at the same time it is perfectly reasonable to wonder if such an attitude is not putting the blame in the wrong place. Instead of making researchers scapegoats, we should ask why society at large would use the tools they create to enforce discriminative policies.

There is a wide amount of variation in human traits, ranging from some that have an obvious external manifestation (eye, hair, or skin color) to others that are virtually impossible to recognize without resorting to specific test tools (blood type), and they are known in many cases to have an evident genetic component. Even though human societies seem to have the unfortunate tendency to use these variations to discriminate, we have made remarkable progress in exposing this tendency as irrational and as the cause of much suffering, so that what was once universally accepted and justified is today relegated to the fringes. There is no reason to believe that this would not also be achieved in the case of our attitudes toward sexual orientation, even if an agreement on its biological causes is eventually reached as a consequence of further scientific research on the subject. By embracing too quickly the other option, seeking to prevent scientists from looking for the causes because of fear of what we may do with such knowledge, we may indeed find ourselves sharing our views with very strange bedfellows.

Cristian C A Bodo was born in Buenos Aires, Argentina. He received his Ph.D. in neuroscience from the University of Virginia in August 2007. The topic of his dissertation research was the role of gonadal steroids in the sexual differentiation of the mouse brain.

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.

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 - Last Installment

Many of us that have looked at religious or anti-religious blog comments will have seen this inanity: "If there were no god nothing would stop me from killing and raping" or some similar idiocy. I have news for people that believe this crap. Morality is innate. This has been well-demonstrated scientifically. If you want to review the literature on the subject, I highly recommend reading Marc Hauser's Moral Minds.

It not only totally confounds me, but insults me to no end this idiotic, stupid and dispicable belief that people chose to believe Evo to be the path that life took must be immoral. Why is this belief prevalent? Kent Hovind espoused this crap and look where he is. Don't bend over for the soap, Kent. Believers think this to be the case because they believe that atheists must be denying god even though for some reason we know god exists. Evo is part of our denial. This silly and prejudiced belief is born of arrogance. How can anybody not believe god exists when I 'know' he does? This so-called 'inner knowledge' is synonumous with belief, and is therefore not knowledge at all. Knowledge requires evidence, for which there is (again) none. The internet show The Things That Matter Most did a whole show entitled Evidence for God Within Our Souls and Desires without ever first providing evidence for the very existence of the thing they are using to provide evidence for God!

Talk about the pot calling the kettle black! Creationists deny the Science behind Evo at every turn! I've shown clearly that creationism is born of ignorance. In the 21st century, this is inexcusable. The new form of ignorance is so-called 'intelligent design', an idea completely devoid of substance. There is no Science here, folks. Who designed life? How was life designed? How was the design implemented? Without answers to these questions, you are essentially left with goddidit. Empty and vacuous.

Don shows he is no different, and I was absolutely insensed by his quoting Julian Huxley. Don has, to his credit, apologized (I'm not sure he knows exactly what for, though), but this is irrelevant. He believes this travesty, and so has raised my ire... We begin yet again with the last part in this series.

"The world's leading evolutionist, the late Sir Julian Huxley, grandson of Thomas Henry Huxley (Darwin's Bulldog) and brother of Aldous Huxley, once said on the Merv Griffin show that scientists would have not been so ready to accept Darwin's theory of evolution except for the fact that the idea of God was not compatible with their sex mores." Now Don has really pissed me off. What he implied is that those that accept Evolution are really just looking for an excuse to remove God from their lives and deny God's existence, even though they know somewhere in their minds that God exists.

Let me tell you something, Don,. I don't just deny God's existence, I have absolutely no thought as to God's existence until some theist tries to convince me otherwise. In essence, anyone that believes as 'Sir' Julian Huxley, that atheists use Evo as an excuse to be 'wicked', is projecting their prejudice and bigotry onto their inability to understand atheism. Kent Hovind said as much in a debate with Prof. Pagliucci that I blogged about some time ago. I find it ironic (and not without some self-satisfaction, I'm embarrassed to admit. Well, no, but I have to say that…) that I am where I am, and he is where he is now. I have actually had someone ask me on my blog, what I did that I don't feel that I can be forgiven for? My reply is 'Nothing. What did you do that you feel YOU need to be forgiven for?' Religiosity of a society has been shown to have a direct link to crime, spousal and child abuse. Yet, I would not stoop to call religious people wife-beating, child molesting criminals. I would not even say that religion is a cause for these undesirable activities. That would be an improper conclusion. 'Sir' Julian Huxley can (figuratively) go to hell.

I'm not looking to be saved, nor am I looking to for myself. I know who and what I am. I like my life. You say that Christians are supposed to 'witness' (what were they witness to?) and not coerce, but the two look very much the same. America seems well on its way to making that dream a reality. I have seen the faces of evil, and they look a lot like Jim Baker, Oral Roberts, Jimmy Swaggart and the late Jerry Falwell, amongst a host of others. People that have created corporations selling fear of what will happen in an afterlife they have no idea even exists. Hope does not beget reality.

I must admit, your engineer friend did change my mind about one thing: Sam Harris is right. I now realize that the PC attitude I had towards religion is only an invitation to be trampled by Believers. To quote Christopher Hitchens, 'Religion becomes philosphy as astrology becomes astronomy.' It is my fervent hope that this happens.

Your friend asked how I will handle death. As Mark Twain is attributed as saying, "I do not fear death, in view of the fact that I had been dead for billions and billions of years before I was born, and had not suffered the slightest inconvenience from it." Amen. Atheism makes one realize that the one life we have is precious and by extension we understand that everyone's life is precious. I'm not so sure religion promotes this, particularly those with the promise of an afterlife, as I have seen ample evidence to the contrary. I'll keep my atheism, thank you.

I just don't see a point in any further response. But I will keep listening to your show [The Things That Matter Most]. I am very pleased that you do not limit yourself to Believers as many would do, and many of your guests (believers or not) have been quite interesting. I'm looking forward to the interview with Vic Stenger.

Randy Tyson

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....

God vs. Evo Part II

I just realized something last night. I really should have asked these people if I could put the communications I have had with Lael and Don up on my blog. It never occurred to me till now to do that, and for that I do apologize, but seeing as it's a bit of a fait accompli....

One thing you will clearly notice with creationists in general is the selective change in standards of evidence used for and against anything related to religion and its war on Science. For instance, yesterday my comments about the complete and utter lack of evidence for the biblical Jesus. There are no contemporary sources accounting Jesus' life (Josephus wasn't even born yet and there are major problems with using Tacitus, since it is likely that not only did he NOT write anything about Jesus, that the writing was done much later and someone attempted to attribute the authorship to him), no corroboration of the 'historical' account (there was no census taken at the time of Jesus' birth, except one that was NOT done by Pontius Pilate, and that one some time prior to even the earliest possible birth date, no Massacre of the Innocents is recorded anywhere but the Bible, no accounts outside of biblical codices of even his existence). With Caesar, we have the man's own words, the dedications to him and an unbroken history of political rulership which includes him. We have none of this with Jesus.

I mentioned yesterday that Don keeps demanding hard scientific evidence to refute the at-first-glance impressive odds against life-by-natural causes, while thinking that anecdotal evidence of people saying they saw something that might be Noah's Ark is the motherload of proof! What's needed in any discussion like this is an evidentiary standard that encompasses both positions. A good start would be a framework that has already shown itself to work, so let's try the legal framework. Jesus: No substantiation or corroborating evidence, no eyewitness accounts, no physical evidence. In short nothing. Noah, Moses and David fall short as well. Evo, on the other hand, has comparative morphology, paleontology and molecular genetic evidence all corroborating each other under one framework theory. Kind of tough to dispute it, but Don tries. He mentions the finding of a fossil fish that pushes back the earliest date of this form of complex life and claims that by altering our timeline as we must do in this situation makes Evo unfalsifiable. Sorry, but that's bullshit. I did know of this recent finding. Was I worried? No, because even though it did indeed change the timeline, but IT DID NOT FORCE AN OUT-OF-ORDER SEQUENCE. If you find a fossil rabbit in the Cambrian, then we've got a problem and ToE is falsified. Not only is Science not dogma, it continually works towards divesting itself of dogma.

Don mentions Simon Greenleaf's conclusion after viewing all the evidence that the Ascention actually occurred is hardly impressive in the light that he came from a very religious family (that all the family members had biblical names was a bit of a clue) and his standard of evidence was likely to have lowered in favor of inclusion rather than exclusion of questionable sources. Kinda like Don...

On to Part II....

(Continuing from "Don attempts to tell me...")

that Christians were the founders of Science. Baloney! Ask Galileo (persecuted for scientific conclusions not held by the Church), Descartes (forced into fleeing to the Netherlands by religious authority), Hypatia (murdered by a Christian mob incited by "Saint" Bernard) and others what religion thought of their scientific advances. Early scientists professed their Christianity, therefore Christianity was responsible for the invention of modern Science?!? This is spurious logic. We don't know how many of them were actually atheists. Those that professed their disbelief had a nasty tendency to be murdered by religious authority. These men were thinkers in spite of religion, NOT because of it, and it was Christianity that tried to suppress their work and do them bodily harm. Hypatia (from what little we know of her she was a remarkable woman) was flayed alive with abalone shells by a Christian mob! Christianity has an uninterrupted history of suppressing knowledge. For instance, the church even attempted to suppress the invention of the printing press! Far be it for the church to allow the common man to read the scriptures! They might start thinking about it for themselves! For once they were right. The Bible has turned more people to atheism than anything else. Besides, it was the ancient Greeks, not Christians, which started the modern process of Science. Islam had at one time a much better record than Christianity for fostering modern scientific thought. The word 'algebra' and most star names are of Arabic origin, and we use Arabic numerals.;

that there are real prophecies in the bible even though every last one is either self-fulfilling or fulfilled within the biblical text. Sam Harris has likened the latter are much like prophecies made in The Fellowship of the Ring coming to fruition in The Return of the King! C'mon, every generation since the beginning of Christianity thought that the prophecies were being fulfilled and that they were in the End Times! They aren't at all specific and require 'interpretation', just like Nostradamus'. Let's put this claim that all these prophecies have come to fruition to the test. Remember, I only need to show one failure. How about Ezekiel's Tyre prophecy (Ezek. 26: 1-11; 29:17-20)? Tyre was supposed to have been destroyed. A quick look at a map will show where Tyre still stands. He also predicts that Babylon would conquer Egypt. I don't think that one will ever be fulfilled for some reason... As a prophet, Ezekiel, well, sucked. Utterly. And forget the Book of Daniel prophecies, since scholars agree that it was written in ca. 165 BCE and not 6th cent. BCE that it claims, and thus simply wrote prophecy through the eyes of then recent history. Looked good while the fraud lasted, though. The list just goes on and on and on. A full (and very long) list of failed prophecies is available at The Skeptic's Bible. I'd like to see one, just one so-called prophecy that wasn't self-fulfilling, unambiguous, doesn't require 'interpretation' and wasn't made after the event actually took place. Just one.

implying that Einstein was correct when he said God does not play dice when time has shown us that Bohr was correct and God does indeed gamble. I'm not sure where Don is going with this quote, other than continuing his disingenuous quote mining. Einstein's 'god' has absolutely no relation to an Abrahamic god, or any personal god. He was quite clear on that subject. In 1935 Einstein, Rosen and Podolsky proposed an experiment called the 'EPR paradox' in a vain attempt to refute Quantum Mechanics, the results of which they thought were impossible. It's unfortunate that Einstein never lived to see the results of the actual experiment, for which Einstein's 'impossible' outcome was indeed observed. I like to think that he would have dropped his objections to QM having seen the results.;

that because we have so few transitional fossils that Evo is discredited (without accounting for the actual many transitional forms that have been found. Can anyone say bird? horse? whale? etc.?). I'm not a big fan of Stephen Gould (the more I learn about him the less I like him), but he may have been correct about punctuated equilibrium (the debate goes on). However, this was so obviously a quote mine. Gould may very well have said "We fancy ourselves as the only true students of life's history, yet to preserve our favored account of evolution by natural selection we view our data as so bad that we never see the very process we profess to study.", yet he remained a scientist staunchly committed to the study Evolution right through to his death. I frown greatly upon quote mining, and Don does this all over the place.;

that there is some sort of crisis in biology over Evo (You have GOT to be kidding me. I'm in the field and have never heard one peep about it till now...). I think I saw that book in a store last summer and on the jacket the promo started with 'There is a quiet controversy…', at which I started laughing [you might remember that incident in McNally-Robinson, Boomer]. It's so quiet it's silent.;

that "Christ commanded Christians to be witnesses not coercive." WHAT!?!?!? Coercion doesn't have to involve putting someone to torture. It means attempting to subvert them to your belief in any way, INCLUDING 'WITNESSING'! There is a double standard here. When Believers 'witness' it is not only acceptable, but many think it is commanded by their god. When atheists try to reason with Believers about the illogical nature of their (blind) faith, whoa, Nelly! That's evil! The only thing that atheists have ever wanted was to have a level playing field. Even most of the militant ones. Why do you think they went militant? If theists respected nontheists (or believers in religions other than their own) they would see how their views of how things should work impinge on them. Putting the Ten Commandments in a secular building is favoritism towards a group, in this case the Christians (the Ten Commandments were indeed NOT the basis for the legal system, but rather has Hammurabi to thank for its basis.) Let's face it. It is the Christian right that is doing all the trampling, NOT atheists.

"Atheists don't want minority rights, they want minority rule." Bullshit. The way I see it, the Christian right wants a theocracy, and all others (including, but not limited to, atheists) are simply fighting for their survival. Debbie Schlussel believes that freedom of religion does not include freedom from religion, something I doubt the Founding Fathers intended the First Ammendment to mean. Ann Coulter- well, no one gives a hoot what that guy thinks. Doesn't anybody see the danger inherent in this kind of intolerance? Such a slippery slope leads to the logical conclusion of returning to the days where nonbelievers, or believers in other religions, were oppressed. What Don mistakes for an attempt at 'minority rule' is simply the inevitable (and well-deserved) backlash of those that the religious right has wronged. The religious right has had it coming for some time now.

I talk a bit about our significantly more secular (for now) society, whether or not Science is about Truth and comment on the 'impossible' complexity of the brain in Part III.

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....

Faith and Science

In my last blog on the MySpace version, I had the following comment:

"None of this can ever be proven. So what must you have in your theorys? FAITH. You really have no evidence of transitonal fossils, Have not found the missing link between human and ape....."

My rebuttal was scathing, and rightfully so. First, Science does not deal in proof. Never has, never will. Science is about explaining observations, coming up with a provisional explanation which explains the data. As to this person's assertion that there are no transitional fossils, that's baloney. Go to any museum of natural history and you will see (literally) tons of them. There are many lineages which have demonstrated the progression to new forms. The development of the horse, dinosaurs to birds, the whale from land to sea mammal, and many others have been clearly delineated. Indeed, Evolutionary Theory predicted that such intermediary forms existed and where they would be found in the fossil record. This is the ultimate test of any theory and in this the Theory of Natural Selection has been astoundingly successful. The human evolutionary lineage is also remarkably fleshed out, despite this person's belief. It is very difficult to find such fossils, though we have and continue to add to our knowledge when a new fossil is found.

This commentor also ignores (or is perhaps unaware of) the fact that while the fossil record is of great interest in the verification of Evolution, it is not all that important. Darwin did not have fossils to work from when he wrote his great opus, the 'Origin of Species'. He was using comparative morphology. Just as important has been the development of molecular genetic techniques to look at and even time branching in the phylogenetic tree. Using the molecular clock, for instance, molecular genetics has shown that champanzees and man have a common ancestry which split some six million years ago. All of this data fits together elegantly. When you have different techniques from completely different areas fitting together like that you know you have a very robust theory.
Could the Theory of Natural Selection be wrong? Yep. What is the likelihood of it being wrong? About the same as a tornado going through a junkyard and spontaneously assembling a 747. ToE is correct far beyond any doubt, let alone reasonable doubt. Any protestations by those that take the a literal interpretation of the Bible are simply the weak, desperate cries of those drowning in a sea of the untruths they seem incapable of divesting themselves of.

But I did say one thing in response that was incorrect: that there is no faith in Science. As Sam Harris has pointed out, there is faith at some level in Science. But this kind of faith can not be equated with religious faith. Let's take a look at a couple of examples to illustrate this point. Let's say that I want something from a department store and I need it by this evening, but I have no time to go out and get it. So, I ask a reliable friend to take some of my hard earned cash and buy it for me. I certainly would not ask a complete stranger to do this, so why do I ask my friend? Simple. This friend has a track record of doing similar things for me. This is faith. I have faith that my friend will accomplish the task that he/she has agreed to do.

Now, let's take a look at the second example. Let's say the manual for my SVT Focus says that my car can fly. Truly fly long distances, not just when going over hilly terrain. But it also says that it will only do this when there is no one in the car, and no one is looking. Any reasonable person would be skeptical about this, wouldn't they? But if you take a literal interpretation of the manual, you would say that it does. Why? Because it says so right in the manual, of course! The correctly skeptical person would require evidence that the manual is correct, but a literal interpretationist does not. Is this literal interpretation faith? Absolutely not. It is BLIND FAITH, a completely different animal. It is belief without substance, and is therefore totally unreliable. Can blind faith ever be correct? Sure it can. By accident. But look at the number of faiths in the world today, which falls in the thousands. Let's say that one is correct. Even if you are a believer you have only a small chance of being right. Those odds drop vastly farther when dead religions are included in the calculation.

There is a vast difference in the type of faith that is in Science from that which Believers hold. In fact, we have confidence in Theories (note the use of 'T' here) because they explain observations, make testable predictions, and are falsifiable. Faith is more about the methodologies used in Science, not in the actual theories themselves. Blind faith can be correct only by accident, and is NEVER right.