"I do agree with your thing about teaching Biblical creation as science in school like as science is limited by the fact that all origins beleifs were about a single event long in the past and thus cannot be repeated."

It's bizarre that people really think like this. Just because events happened in the distant past doesn't mean that they are immune to scientific study. In fact, many natural events in the past are actually far MORE robust as far as physical evidence than recent events on a human scale. In terms of life on earth, it's vast diversity and appearance, it's consistent patterns of genetic heredity, and so forth all open up ample opportunities to study the past in great detail.

"At the end of the day all faiths (evolution included) are limited by one thing they are faiths and thus scientific evidence can never conclusively prove them correct (though it can somtimes prove where they are disasterously wrong)."

You've conflated too many things here. Yes, science never claims to conclusively prove anything correct: but that is an epistemological commitment to a neverending checking of knowledge claims against evidence, and a continual openess to new evidence and perspectives. But that isn't the same thing as tossing up ones hands and declaring that nothing can be known or that everything is just a matter of faith. Science delivers facts and knowledge far more credible and certain than any other method of inquiry into the natural world. If you are comfortable calling the existence of ancient Athens, Greece as fact, then there is no reason, why you should not be able to admit that the known age of the earth or the common descent of life is a fact of, indeed, even greater certainty.

"Because of this people will have to make their own decisions on which faith they wish to belive."

Here is an even more telling misunderstanding of science. Personal faith is, indeed, all about what one personally wishes to believe. But that is not how science operates. Science is a broadly social activity wherein all admitted evidence has to be open to everyone, not just the personal inner mind of a particular individual. The broad facts of science are not personal interpretations but the outcomes of tests, both labwork and theoretical, for which the process and results are transparent, their implications placed in the open. That is a radically different process than faith, and to conflate the two as if they were the same is a cheap attempt to run away from the conclusions of science by declaring that all knowledge is of equal unreliability no matter what its relation to evidence or sound argument. It's a poor, bitter person who, only upon losing a game of chess, declares that the game stupid and pointless and the outcome doesn't matter.

"I feel therefore that ethier origins should be left out of the cirriculum (so it can focus on more observational science) "

What is "observational" science, in your opinion? Do you really think that geologists never observe or examine the evidence with which they construct a picture of the early earth or the movement of continents?

rite man
thanx for the reply on my space like. Cool hope you enjoy ur stay at Northern Ireland and do all ya want like. I do agree with your thing about teaching Biblical creation as science in school like as science is limited by the fact that all origins beleifs were about a single event long in the past and thus cannot be repeated.

Altough I do belive the biblical perspective because the biblical record is consistent with the sientific, historical, archelogical and anthralapological evidence. I also belive the Biblical record because of its consistencey dispite being written over 1600 years and having over 40 different authours in some 19 different walks of life and remaining consistent . Also the heroes of the faith such as david and noah are critisied and sometimes the enemies of Israel are complimented Darius the mede and Ataxerxes surely not a book a man could write.

At the end of the day all faiths (evolution included) are limited by one thing they are faiths and thus scientific evidence can never conclusively prove them correct (though it can somtimes prove where they are disasterously wrong). Because of this people will have to make their own decisions on which faith they wish to belive. I feel therefore that ethier origins should be left out of the cirriculum (so it can focus on more observational science) or to give people the balance allow an informed descion and not just brainwashingand teach them intelligent desighn alongside macro evolution.

Keep up the Good work Ryan
God Bless
Nathan

Ryan,
I appreciate your research and studies of origins. I think that you may make a big difference in the scientific community. I am just beginning in the biology degree myself and will have to print out and read your interesting articles in detail. I caution you though, not to spend too much time in debating on the creation/evolution debate and carry on with your most important studies. You may come up with something irrefutable and who knows, win a pulzer prize or something.
I had been lost in arguement for sometime while trying to bring some people up to par on the matter but found it best to stay at the top of the pyramid(if you catch my drift). I just hope you continue you research on the matter and I'll be following along like a little puppy. And I hope these religious freaks don't distract you or slow you down. Keep up the pace and good luck. Find the answers.

An excellent post, Kagehi, but I think the core of it, the proof-of-concept of evolution, is something Ryan doesn’t deny. I agree though that simulations such as these also provide an example of evolved “irreducible complexity.”

Ryan, I have great respect for your young enthusiasm, your eagerness to discuss biology and your love for the science. Believe me, I’ve been there, as I suspect many of your commentators have. So I hope you’ll give me some consideration when I warn you that although this is a wonderful asset, it can also be blinding. Students in your position most often lack perspective, I certainly did. You statement that you’ve studied this since you were fifteen, with implications that this means you “know your stuff” demonstrates this lack. It’s wonderful that you’re a student of biology with a strong interest, but you have a long way to go. Your statement that this time was spent “dealing with the origins debate” suggests that your focus during this time was misplaced.

I would like to make a suggestion, and I hope you’ll give it some thought. You’re a student at a university. Find a good professor, one you can get along with, of a form of evolutionary biology, such as evo-devo. Ask to discuss this subject with him or her. Set aside a large amount time for this, it could easily turn into regular meetings. If you’re having difficulty convincing them to make the time for it, show them this blog, and if necessary find one who cares a bit more about teaching. It wold help an awful lot if you also signed up for their class!

I suggest this because clearly, you’re intelligent, you have a strong and enthusiastic interest in biology and evolution, and you show significant independent initiative in your study of it. Yet you’re not learning. It is not only that you fail to see the problems with ID, that you fail to understand the refutations of the IDists’ claims. I think you fail to understand the mechanisms of evolution properly. For example, above you equate natural selection with evolution. That is very false, and you need to understand why. You seem to be unable to separate abiogenesis from evolution–again, you need to understand why they are not the same. You claim sickle-cell anemia is not a beneficial mutation on the basis that “I would rather take the malaria any day before the sickle-cell anemia.” Excuse ME, Ryan, but that betrays a fundamental misunderstanding of the nature of both diseases and the dynamics of these genes and their expressed phenotypes when they are at work in the environment that gave rise to them.

If you approach a good evolutionary biology professor and ask them: “I don’t really get evolution. Could you help teach me?” you can get a lot of help. Again, especially if you are also taking one of their classes, and if you ask nicely. Don’t HAVE a good evo professor at your school? Well...California has a lot of very good universities. Bound to be one lying around somewhere. ;) And if all else fails, there’s the web. There are a number of them who might respond favorably via email, which has the advantage of being doable at their (and your) leisure.

I would leave you with one other warning. Again, from what I see of your interest, your enthusiasm and your initiative you would probably make a good Ph.D. student. That would also afford you an excellent opportunity to study biology at much greater depth, and answer many of your questions. But I see two possible reasons why you are not learning evolution properly. One, that your education is insufficient, hence my suggestion you track down a professor and, if you haven’t, take some evo-specific classes. Two, that you are filtering your input. I know that you feel you are an open-minded person, but remember what I said about perspective. As you continue with your biology studies in whatever form they take, I cannot emphasize strongly enough that you must constantly ask yourself: “Am I approaching this with a pre-conceived notion? Am I trying to fit the data to an idea I already have?” This is a distilled version of the question religious creationists need to ask themselves: “Am I a creationist because I’m religious, or because the evidence says so?”

Your basic argument hinges on the impossibility of complex and seemingly irreducible systems forming through chance. There are two serious errors in this assumption. The first is assuming that what does X now always did X. Chance is at least a likely to employ a screw driver to open a can of soup as a person. It might take a tornado to do it and nature certainty wasn't planning to eat the contents, but this hardly means some being or force 'had' to be around to specifically command the tornado to plunge a screwdriver through the side of a can. Ok, maybe that is a silly example, but the point is that once a mutation exists, it can through other mutations change to produce entirely different functions and sometimes the exact way it got from W to X isn't real clear. The second argument against it is that your disbelief at it being possible is just that, disbelief, and not an argument in and of itself. I have one word that refutes it: Avida

The Avida project was developed to test the fundimental underlying principles of Evolution. It has done so in spades. One of the things it produced, through random mutation, guided by survival bias, was highly complex and often bizarre solutions to the basic math problems being used to determine if it survived and how well. Yep, evolution is guided by the same. You improve and do better or you die off. That is hardly random, even if the actual mutations themselves do occur randomly. This is a 'major' error creationists make in claiming that random evolution is the same as random mutation. Its not, any more that a pachinko machine is 'random', so long as physical forces from the pins in the machine and gravity dictate where the balls go. But its not guided in any 'thinking' sense either, save maybe by the initial and fairly pointless initial dropping of the ball. Point is, Avida has disproved the validity of your disbelief. Not only is it possible for random changes, within the bounds of some physical system that dictates survival, to produce complex things, it does so in a way that produces entirely irreducible systems that break the moment you remove a single instruction from the artifical DNA. And no human hand, save for the initial creation of the conditions, dictates 'what' code/solution the lifeform discovers to survive. If anything, Avida would seem to imply that once you had even the most basic form of life, even basic organic chemicals and a means to interact to produce it for that matter, any 'being' that started the process would lose ***all*** control over the final result. This hardly bodes well for either space aliens or a God. Once a thing evolves at all, you cannot predict or control 'how' it does so.

The Avida project can be found here:

http://dllab.caltech.edu/avida/

Oh, and thousands of creationists have downloaded it, without being able to prove there are flaws with the simulation. I am sure the argument would be, "yes but its just a simulation". Yeah, but one doesn't have to set off an atomic bomb to simulate an atomic explosion, based on the 'basic' math dictating how it works. The only way that a simulation of evolution can be falsified is to prove that the actual mutations themselves are being artifically introduced at each stage and *not* merely being guided by simulated conditions. In other words, for that to be invalid, one must invalidate any simulation, even one that perfectly simulated the entire earth. Why? Because gravity, sunlight, the amount of food in the environment, the day/night cycle and 'everything' that has significant direct impact on life on this planet constitute conditions that 'force' life to conform. Avida uses a far simpler system, which would logically imply a) that it might have been 'too simple' to produce what it did, or b) having produced it, it implies that life could form under almost 'any' conditions, given some 'basic' starting point, like organic molecules. The first is obviously false, the later... doesn't leave much room for someone to 'guide' it, space aliens or otherwise.

Just wanted to add one more thing. Here is a quote from Plunge "it's a mystery to me now, so ALIENS must have done it!". That was my second theory and it seems easier on the brain so I'm going to agree with Plunge it has to be an advanced race of alien life forms.

Chris

First off great site.

I have been plagued with these same questions here lately. I don't want to rule out one belief without giving the other a fare chance. The only conclusion I have been able to come up with is that one exist because of the other. But it seems to be a double edged sword. So is science merely a study of the creator's creations? Is it to great a theory for comprehension?

One question...What is it in an organism that tells that organism that it needs to mutate to survive in the first place?

I know there are things like birthdefects and such but like a previous comment stated that most likely the organisms that were not thought as a good genetic mate would most likely not reproduce and die out. But what if it didn't need a mate to reproduce...see there's the double edged sword again. Some people may say giraffes grew long necks so they would be able to reach high branches for food. What if the giraffe already had a long neck and it eats from tall trees because it prefers to eat standing up instead of laying down?

I guess I'm just rambling...sorry.

Again great site,
Chris

Geoff,
Sorry for the misunderstanding in what you were getting at. I thought you were referring to Gould's original paper which I have read. I did not realize that this was a website. The truth is I have very little time to read every web site on the net about this topic and so I have missed alot of them. Many of the websites, especially from creationist organizations, have very poor science so I rarely read them anymore. I stick more to peer review scientific articles (to answer CK's question). But because you recommended it to me I will pay a vist to the site and see what it has to say.

"You stated that Behe retorted his argument. Not true. "

Of course it's true. Behe's original argument was very straightforward and powerful: he could identify particular chemical systems which he claimed were IC and by definition this meant that they could not have had functional intermediaries. This is a very strong claim, and had it been so, it would have been a powerful argument against natural selection as a mechanism for the construction of things like blood clotting.

Unfortunately, the argument ran into a few serious problems. The first was that you can't prove an empirical claim merely by definition: i.e. you can't demonstrate that there are no possible functional intermediaries just by asserting that something looks complex and interoperated enough to be IC. The second was that for virtually every example he gave turned out not only to have functional sub-parts or simpler arrangements, but that when you start looking into lines of common descent, you find "frozen" evidence of these transitions as well as the usual branching homologies. In the case of some systems where research has been done, biologists have even worked out very probable evolutionary steps and then compared them against modern species to test their assumptions about what proteins were available to be modified and how.

Now, of course, Behe hasn't admitted what he's done, but what he definately has done is to stop making the strong claim that basicaly was at the core of "Darwin's Black Box": that he could show us IC structures and that they by definition could not have evolved gradually. The mousetrap analougy, essentially, is dead. Instead, he's retreated to a far far weaker argument that scientists can't (always!) prove to his personal satisfaction the EXACT pathways by which simpler machines became more complex, or that he finds the possibility that mutation hit upon these particular pathways improbable. That's basically the argument from incredulity all over again (it's a mystery to me now, so ALIENS must have done it!), and has none of the revolutionary potential or interest that IC originally had. Whenever it becomes too obvious that a particular system did, in fact, evolve, Behe simply claims that it wasn't IC after all and retreats back into some other not well understood mystery.

Not to mention that Behe's argument was basically disingenuous to begin with. Most of the chemical machines he discussed had only been recently examined for the first time, and most of them are STILL not fully understood as functional systems. It's decidely premature to start claiming that if we don't have a ready answer for how some system we barely even understand yet evolved then it's impossible to explain. It's hard enough to try and track down possible paths of gene lineage via molecular evidence without even knowing what you are looking for in terms of the end point of functionality. For all the neat supposedly clean engineering diagrams Behe and you present concerning the flagellum, the real picture is far far messier and less well understood.

"Check out his latest publication and I think you will be quite convinced. "

He's moved the goalposts repeatedly. His latest simply does so again. "Oh yeah, well explain this... IMMEDIATELY or else I win!" isn't an argument, especially if you don't find the complete vaccuum of "ID" to be a useful default alternative. "Poof!" isn't an explanation for complexity and even if it was, it explains a problem by creating an even bigger problem.

". Secondly you questioned why modern cells had to spring into existence all at once. Let me ask you, exactly which major system of the cell would you remove first? "

You are thinking backwards, which is part of your problem. Systems in biology almost never simply pop in and out of being. In your model of things, one simply chops off a key component necessary to the functioning of a cell in it's particular modern environment, it dies, and you conclude that there is no way there could be a simpler cell. But no one thinks that, if you reverse that model, you have a picture of what either abiogenesis or evolution must be claiming happens. Instead, more primitive systems, usually with DIFFERENT functionalities to begin with, see various parts modified and shifted until they hit upon some previously unanticipated advantage and are refined from there. Proteins with a particular function are often borrowed, copied, loaned, slightly modified in ways that give rise to new functionality (which is aided by the fact that proteins are remarkably flexible in their ability to have multiple different effects on entirely different processes all at once).

"I urge you to re-read the post on abiogenesis and consider the simple fact that all of the cells major systems to fulfill the seven keys to life have to be in place for even the first life to arise."

Your problem is that you are hung up on Platonic categories like "life." There IS no hard and fast line that divides life from unlife. Are viruses life? Are plasmoids? How about Speigelman's monster, a self-replicator that requires only an enzyme to come into being (not even any seed RNA to begin with!) and can both replicate and evolve even though it has less than a hundred bases and no other major life features to speak of? All of these things are modern examples of things adapted to function in particular environments: the fact that these environments in modern times happen to be living cells is beside the point. Nothing prevents similar things from thriving in particular primitive earth conditions.

What the passage you are looking at suggests is that there are 7 key functions that all modern living things have that allow us to bestow upon them the TITLE of "life." But this sort of awards ceremony is decidely irrelevant for discussions of what the simplest self-replicator might have been like on its way towards what we understand as life today. We're talking there about things that come long before the awards ceremony is held, and no one who discusses the various possibilities of abiogenesis thinks that the awards ceremony is the START of the story. The only reason they even aim towards things similar to modern cells is that we know in hindsight that that was the end direction that was taken and we are trying to figure out how they got that way. But the story is far longer and more complicated.

"“Modern” cells are not very different than proposed primitive cells in their basic design."

This is disingenuous. Yes, primitive cells are certainly similar to modern cells, and no wonder given that they are ancestors of modern cells. But even primitive cells are a stop way way down the road from what most biochemists discuss when they think of the first self-replicators.

"Think about the fact that amino acids (proteins) have to be constructed through use of an enzyme, which amazingly enough, is also a protein!"

Proteins aren't amino acids, they are made of amino acids, many of which can, in fact, be created without proteins. Enzymes _encourage_ particular chemical reactions (and more complex enzymes particular sequences), but it's not like chemistry is impossible without them, or that proteinite enzymes are the only natural catalysts that encourage particular reactions. Again, you are trying to claim that a stone arch, which requires every piece to be in place before it can stand, had to have come into being fully pre-constructed. But there are many ways to build a stone arch stone by stone.

" Furthermore, DNA replication is required for reproduction."

Even from reading your previous posts, it's obvious that you already know that this isn't true. So why would you say something like this?

"Prove to me how replication and transcription evolved and you will make major strides in convincing me that we might have a naturalistic origin. (You won’t find one by the way. I have been looking for years.) "

You're 21! You've almost certainly spent more time looking for a girlfriend than you have studying this stuff. Going to a few PR events with ID proponents does not a biologist make you.

"Also, I am glad you mentioned the Kreb Cycle and Blood Clotting evolution. "

Right. Someone who just became old enough to drink is going to handily do away with 30 years of research by someone like Doolittle... in a tiny post on a blog! When Behe has been flailing away at it for years without any luck. Good luck trying to explain away Enirque Melendez-Hevia's team's work on the Krebs cycle too. If you didn't even know of these people before posting (and hence asked for references on their work), are we really to believe that you are suddenly going to read up on them, become within days an expert in their particular subspecialties (something that took them decades), and dismiss all their conclusions on the basis of your newfound expertise?

Yes, Brahe, I was - and either the original point sailed clear over Ryan's head, or he confirmed my suspicion about his disingenuity. You decide.

Dude,

You need to steep yourself in evo biology, not just scratch the surface. I think it is cool that you like to think about these things, but you can't think about them in a vacuum, you need to really read what is out there, and I mean the hard core stuff, not just "it seems so complicated, it's can't all be evolution". I think you really do not grasp the power of the evolutionary process. Nor does this process diminish life as we know it, merely only some people's ideas of how they want life to be.

I believe that Geoff Coupe was referring to the Panda's Thumb blog at http://www.pandasthumb.org/.