A Great List of Biblical Fallacies

To see the list click here. Which ones are the most difficult? Why?

48 comments:

A. Thinker said...

Fallacy is not the right word for what's posted there. Contradiction, yes, fallacy, no. I'm sure you know that.

As for my favorite actual biblical fallacy, I think it's when poor Job asks god, "Why me?!" and god responds by getting his panties all in a bunch and screaming at him, "You dare question ME!? Inconceivable!" (Even though god somehow knows what Job is thinking, and why, he still has to puff out his chest and act like a jerk!)

Overall, that list is not that great. I see a lot of things that were interpreted in ways that make it blatant that the authors of the blog don't know the standard arguments for the buy-bull.

John W. Loftus said...

Thinker, here is my own take on these kinds of things

A. Thinker said...

I know. I read all your posts, even the ones touting your own book. :) Good stuff.

P.S. What does it take to be invited to post at this blog? Being a former pastor/what have you, breaking through the chains of delusion, then finding it? I'm not asking to be a poster here, I'm just genuinely curious and don't believe I've read it anywhere yet.

A. Thinker said...

Oh, forgot to mention, I liked your post about the inconsistencies way better than the "great" list, and not just because you used the correct word (inconsistencies vs fallacies). You clearly knew what you were talking about/how people interpret the buy-bull. I appreciate that, and all of your insightful posts.

John W. Loftus said...

Thinker see this.

Streetapologist said...

A Great List of Atheistic Fallacies

or rather inconsistencies....

1. Darwinian evolution
2. Laws of logic
3. Ethics
4. Altruism
5. Predication
6. Meaning

And my favorite inconsistency

#7.Spending this much effort to refute the God who (according to DC) doesn't exist.

Bravo.

A. Thinker said...

I don't get it. The first six of those are perfectly consistent, not only with each other but with reality. That's really saying something for atheism, isn't it?

And, of course, your seventh is us expressing the logical extension of the above six to people like you who can't see past their noses.

So, basically, I don't see any inconsistencies or fallacies at all. Was it meant as a joke, and I just completely missed it?

Streetapologist said...

Can't see past my own nose, okay.

Who's in need of an explanation? What sort of thinker are you?

Joseph said...

There would be no need to refute God if people like you weren't dogmatically propagating the idea.

Shygetz said...

Who's in need of an explanation? What sort of thinker are you?

Um, a.thinker is right. The evidence indicates that 1 and 2 are true beyond a reasonable doubt. 3 and 4 are explained very well by evolution and ethology/sociobiology, and so are neither fallacies nor contradictions.

I don't understand what you mean when you say "predication" is a fallacy/inconsistency of atheism. Please elaborate.

Number 6 is neither a fallacy nor a contradiction for atheism; however, arguing from meaning is a direct fallacy for theists (a textbook Argument from Consequences). Regardless, atheists find plenty of meaning within their lives, your view of the validity of this meaning aside.

Number 7 is funny; we argue for humans to use an evidence-based method of looking at the world instead of relying upon the schizophrenic invisible sky man and his zombie alter ego (and their ghostly side persona, can't forget that), and you wonder why? When you are sick, do you go to a doctor, or do you say that medicine stuff is a bunch of hooey and go to a faith healer?

If you answered "doctor", then you know why we object as we do, although you may not admit it to yourself. If you answered "faith healer", then I wish you the best of luck, and encourage those of a similar mind-set who are of sufficient age and maturity to make such a decision to follow in your footsteps.

However, please don't take your children with you. It's not their fault you're nuts; take them to a real doctor.

A. Thinker said...

Thanks shy. I appreciate the sentiment and of course agree completely.

I assume, but am not sure, that by predication, he/she meant being able to derive a proposition through predicates. I find it interesting that he/she finds the laws of logic to be fallacies/inconsistencies. Now what in the world do you suppose that means?!

Streetapologist said...

Gee I am overwhelmed by your superior intellect. But somehow the genius atheist(s) have completely missed the point.


Um, a.thinker is right. The evidence indicates that 1 and 2 are true beyond a reasonable doubt. 3 and 4 are explained very well by evolution and ethology/sociobiology, and so are neither fallacies nor contradictions

Assuming that you accept (1) which according to the above you do; then
(2)needs some sort of rational justification.

(1) entails that notion that human origins are entirely due to chance process, IOWs nothing precludes (2) from becoming false tomorrow. Flux simply doesn't explain universal _immaterial_laws_of_logic.

(4)simply cannot be explained by (1)if one accepts everything entailed in the theory including but not limited to survival of the fittest.

Please note the title of my comment was borrowed from the post, I didn't assert that any of these were fallacies, you *assumed* this however this was parody.As my comments indicate my list includes "things" that are inconsistent in the antitheistic worldview.

Laws of logic aren't fallacious, rather as pointed out above antitheists can't account for them. By accounting I mean "provide rational justification" for (x) in a chance universe.

knerd said...

The most obvious and often overlooked contradiction in Christian theology is that Jesus was both God AND Man.

Talk about hedging your bets!

zilch said...

(1) entails that notion that human origins are entirely due to chance process, IOWs nothing precludes (2) from becoming false tomorrow. Flux simply doesn't explain universal _immaterial_laws_of_logic.

You need to read up on chance in evolution, streetapologist. A good place to start is here. Briefly, and ignoring for the moment some complications: mutation, a chance process, creates variation, which is acted upon by natural selection, which is anything but a chance process.

The idea that evolution is a chance process is widespread among fundamentalists, and there's no excuse for it: not only is it taught (I hope!) in high school at the latest, but oodles of websites are dedicated to it.

I don't get what evolution has to do with the laws of logic, either. Explain, please.

streetapologist:
(4)simply cannot be explained by (1)if one accepts everything entailed in the theory including but not limited to survival of the fittest.

Again, you are un- or misinformed. Altruism can be explained in two (overlapping) ways: genetically based altruism, which is of obvious utility to social animals, and cultural altruism, which is based upon the perception that cooperation is necessary to build societies. The genetic basis of altruism is still poorly understood and hotly debated. Check out this link.

zilch said...

Whoops, I was a bit unclear above. When I said "The idea that evolution is a chance process is widespread among fundamentalists, and there's no excuse for it: not only is it taught (I hope!) in high school at the latest..." I meant of course "...not only is natural selection taught (I hope!) in high school at the latest..."

WoundedEgo said...

Bill Ross, here... new to DC. Great blog!

When I was a boy, trying my hand at carpentry, I tried to connect two boards with brads. The brads were about an inch long and very thin. They went through the first board and about a half inch into the second board. I pounded in about 25 nails, but they just did not hold the boards.

That list is kind of like that. Quantity does not make up for quality.

I think of a court of law. They don't accept lots of coincidences. That does not remove a reasonable doubt. They need real evidence - damning evidence.

When I was a believer, a list like this might motivate me to do some research, but for the most part, if the first one was weak, I would probably not even look at the second one, assuming it was no stronger.

But as I studied the Bible for myself and really understood it, a handful of very fundamental problems arose that caused a sea change in my thinking, and ultimately led me to realize it was not something I could reasonably consider true any longer.

I recently put these "Shockers" as I call them into a book, called "Bible Shockers!" It is a Bible study more than anything else. But as one grasps what the text is actually saying, I think any reasonable person will have to conclude that it is hardly a book for an educated person to embrace as a reasonable outlook on life.

I invite you to visit my site, http://bibleshockers.com

Bill Ross
"What I lack in youth, I make up for in immaturity!"

Streetapologist said...

Zilch said:
The idea that evolution is a chance process is widespread among fundamentalists, and there's no excuse for it: not only is it taught (I hope!) in high school at the latest, but oodles of websites are dedicated to it.

First, I am not a fundamentalist, so this assertion commits the guilt by association fallacy.

Second, Gould argues in the source
you provided that the sense of chance used by evolutionary
theory is the same as contingency. I would use the word "chance" in the same sense as Gould, in a contingent universe immaterial invariants e.g. laws of logic need rational justification. This point has been glossed over and no justification has been offered.

in, you are un- or misinformed. Altruism can be explained in two (overlapping) ways: genetically based altruism, which is of obvious utility to social animals, and cultural altruism, which is based upon the perception that cooperation is necessary to build societies.

Well then, please do enlighten me by answering but one question:

How does altruism comport with "survival of the fittest"?

If altruism is simply a manipulation of a conspecific then it seems that Christianity once again comes out on top. As many atheists here would assert, Christian parenting is simply manipulation. On what basis then would the atheist have to assert the contrary? That manipulation is undesirable? If altruism isn't at bottom manipulation then once again the burden falls to the athesit to explain altruism.

Prup (aka Jim Benton) said...

Street apologist:
Your two main points are important ones, one which has been dealt with repeatedly here.

Let me try to answer them, starting with the second: 'How does altruism comport with "survival of the fittest"?'

The reason it does is that 'fittest' does not mean strongest, fiercest, or even bravest. It means -- yes, it IS a tautology -- best able to survive in a particular ecological niche. The fittest may be the best able to run away, or the best able to hide, or the best able to breed, or the best able to make use of the specific food available in that niche.

It is also obvious that 'adaptability' is an evolutionary advantage -- because one key to evolution is that niches change. The species that can best respond to those changes is more likely to survive.

Those changes can be caused by climate change -- even before man's actions the climate was cyclical -- by exhaustion of a specific food in a specific place -- or its own evolutionary adaptation -- by an accident -- like a species of finch being blown off course and winding up on a neighboring island where the available seeds are different (see the story of Darwin's finches) or by pure random genetic mutation.

Now humanity has evolved four specific traits that has helped make it the most adaptable species. (Whether they are, in fact, distinct traits, or if the evolution of one automatically includes the other is an open question. I am treating them as separate to make a point. I also have no quarrel with any argument that they are simply a 'matter of degree' that other animals have them to a lesser extent.)

The first is the communication of abstract ideas. Not just 'language' which many species have, but a language that includes abstractions, generalities, and ideas of time and the future.

The second is the ability to convey specific experiences from one human to the next, again over time -- and to generalize from them. Many species can say "Go there, find food." Humanity seems to be the only species that can say "No food there today. Go there in three months. Find food." (This is sometimes called 'time-binding.')

The third is the ability to cooperate on long-term goals -- including to plan and react to changing circumstances.

And the final one -- and, ironically, the most difficult one for many religious people to grasp -- is ethics. (And please note that I contend that our ethical sense continues to evolve, and incredibly quickly because or ability to communicate over time and distance and our ability to share experiences with more and more diverse people is increasing exponentially -- writing, printing press, telephone, radio and television, and the internet each represent a major step forward in our ability to 'time-bind.')

Religious people -- probably because they have been fed, since birth, on the damnable lie that 'man's heart is wicked' -- have difficulty in realizing that ethics are a survival trait, that it is simply smater to act ethically than not to. (True, for the earlier stages it can be argued 'act ethically to the tribe, and unethically to those outside it' but that's where the continual evolution comes in. And religions, of course, were invented by relatively primitive peoples.)

Ethical action improves cooperation. It also keeps from distracting the group from working on long-term projects because they have to devote people and time to protecting themselves against thieves, murderers, etc.

Honesty aids cooperation and communication, which is why it is one of the earliest ethical standards. (If you can't trust a report, you can't act with as much confidence and assurance to respond to that report.)

The idea that, without the demands of a God, man would descend oto a Hobbesian 'war of all against all' is, I'm sorry, simply absurd. Man's most important characertistic is that he exists in a society -- from family to tribe to nation to humanity as a whole -- always has, and has evolved -- to a greater or lesser degree -- to operate within that society.

(A human may, once grown, 'set off on his own' and even leave all society behind. And it is good, possibly necessary, that some humans do just that, if they somehow add their experiences to the 'common pool.'

But if he is not first exposed to such society, he truly becomes feral, no different from an animal.

(One final remark here -- I hope to deal with your other point later, after a physical therapy appointment and before the Mets. There is NO inherent connection between evolution and atheism. Most theists, except for a small number of Americans, fully accept evolution and their theism, seeing evolution as the mechanism their God instituted to bring about his 'plan.' I happen to be both an evolutionist and an atheist, but I've repeatedly insisted that these are two different attitudes, and that i was an evolutionist five years before I became an atheist.)

Prup (aka Jim Benton) said...

A quick correction to my last point. I said 'most theists.' Muslims are an exception, since they -- unlike Christians in general or Jews -- are bound by the 'prime directive' of their religion to accept their 'holy text' (The Qur'an) as being directly dictated by God and infallible and unchangeable. There ARE Muslims who accept evolution, but the proportion is MUCH smaller than among Christians.

zilch said...

Hmmm. Streetapologist, we seem to be on two different planets.

First, I am not a fundamentalist, so this assertion commits the guilt by association fallacy.

Should I have said "fundamentalists and others? I wasn't trying to cast aspersions on anyone; just stating a fact. It's immaterial to the point whether you're a fundamentalist or not.

Second, Gould argues in the source you provided that the sense of chance used by evolutionary
theory is the same as contingency.


Yes, and so? I would agree with Gould, but he's not talking about natural selection here. You claimed that Darwinian evolution "entails that notion that human origins are entirely due to chance process", and I pointed out that chance is only part of evolution: natural selection is most definitely not chance, so your statement is false.

I would use the word "chance" in the same sense as Gould, in a contingent universe immaterial invariants e.g. laws of logic need rational justification. This point has been glossed over and no justification has been offered.

I didn't gloss over this point; I asked you what evolution has to do with laws of logic. And regardless of whether the universe is "contingent" or not, I would say that the rational justification for the laws of logic is that they work. If you need more justification, please tell me what kind.

How does altruism comport with "survival of the fittest"?

This is a good question. Under most circumstances it doesn't, because the survival of my genes (speaking from the point of view of most organisms) is not benefitted, and might well be adversely affected, by my helping others. There are, however, two kinds of circumstances where my genes are benefitted by helping others. The first is when the others are kin, the closer the better. Parents helping their offspring, and worker bees helping the queen, are examples of this. Of course this is not usually considered "altruism".

The second kind, helping non-kin, can only arise in social groups where the whole group benefits if they cooperate, and where the organisms can recognize one another and remember who helps and who doesn't. This is necessary to prevent cheaters (non-altruistic organisms) from living off the do-gooders, and requires a minimum amount of intelligence.

In practice, wherever there's altruism, there is cheating also, but if the system works properly the cheating is held down to a tolerable level, so everyone still benefits. There is increasing evidence that altruistic behavior, and cheating when possible, are both inborn to some extent, at least in higher social animals such as chimps and humans.

If altruism is simply a manipulation of a conspecific then it seems that Christianity once again comes out on top.

Here I don't understand you at all. I thought we were talking about genetic altruism. Are you saying that Christianity is genetic? Cultural altruism, such as expressed in religious strictures or social contracts, although overlapping genetic altruism, is not the same thing. We can decide to do all kinds of things that our genes don't tell us to do, and indeed go against our genetic tendencies: look at celibate monks, for example.

As many atheists here would assert, Christian parenting is simply manipulation.

Okay, you've lost me completely. What in the everlovin' brown-eyed world are you talking about?

zilch said...

Whoops, prup's post and mine crossed in cyberspace. I would say that they complement one another, but that prup did a more thorough job of explaining how altruism can develop culturally.

Shygetz said...

streetapologist's prose reminds me of the Sokal hoax.

I would like to build upon something previously brought up regarding altruism. As previously mentioned, kin altruism is easy to explain; it increases the chance of passing on related genetic material, and altruistic tendencies increase as kinship increases.

Non-kin altruism is also noted in the animal world, and is probably related to empathy (which is a measurable response in many animals). It is an important part of socialization, which in many niches greatly improves the reproduction of society members. It works, it can be passed down through genetic inheritance (some animals have altruism without having culture), so evolution uses it. No contradiction there.

As has been previously pointed out, the laws of logic work. No further justification is needed from an evolutionary standpoint; believing in the laws of logic is not counter-selective, and is almost certainly selective, so it is unsurprising that the human mind and/or cultural memes would have evolved to utilize them.

If altruism is simply a manipulation of a conspecific then it seems that Christianity once again comes out on top.

If you are stating that Christianity as a cultural meme has been successful in sustaining its own existence, I would not argue with you there. So has Bhuddism, Islam, and Hinduism. So has racism, sexism, and various other bigotries. Similarly, influenza has been an extraordinarily successful human parasite. The fact that it is successful does NOT mean it is useful to humans, much less that it is true. It just means that the idea is efficient at perpetuating itself. It can do so by benefiting its host (mutualism), which is the case of the laws of logic (and possibly was the case with original folk religion); by benefiting iself without significantly harming its host (commensalism), which is probably the case with many "faiths" that do not require any cost, such as deism; or by benefiting itself to the detriment of its host (parasitism), which I would argue is the case for faiths that require significant material sacrifice from its adherents. Evolution and memetics both have room for all three kinds of interactions, so Christianity's success should not be viewed as a sign of Christianity's benefit to humans.

I strongly suggest Dr. Dennet's Breaking the Spell: Religion as Natural Phenomena for an excellent look at the topic of organized religion as a cultural extension of naturally ocurring folk religions.

On what basis then would the atheist have to assert the contrary? That manipulation is undesirable?

When it comes to culture, atheists argue about the truth of an idea, not about its effectiveness in replicating itself. I do not know any atheist that argues that Christianity DOESN'T persist without evidence; we argue that Christianity SHOULDN'T persist without evidence.

Streetapologist said...

I thoroughly enjoy the fact that it takes no less than three of you to attempt to refute me.

Should I have said "fundamentalists and others? I wasn't trying to cast aspersions on anyone; just stating a fact. It's immaterial to the point whether you're a fundamentalist or not.

I am doubtful that the characterization above was simply an observation.

Yes, and so? I would agree with ,Gould, but he's not talking about natural selection here. You claimed that Darwinian evolution "entails that notion that human origins are entirely due to chance process", and I pointed out that chance is only part of evolution: natural selection is most definitely not chance, so your statement is false.

In an ultimate sense life came about by chance. Read the article you referenced and see what Gould has to say about "rewinding" the tape of evolution. It is fallacious to assert that because natural selection isn't (supposedly)based on chance that in the same sense evolution as a whole is not therefore based on chance.

I didn't gloss over this point; I asked you what evolution has to do with laws of logic. And regardless of whether the universe is "contingent" or not, I would say that the rational justification for the laws of logic is that they work. If you need more justification, please tell me what kind.

That is a fine pragmatic answer. If the only justification is that they work, they are no longer universal and are simply conventions. How then would we know that the law of contradiction tomorrow won't be replaced by something that works better?


As for altruism, it simply doesn't comport with the selfish gene theorist. My point about Christianity refers to SGT who assert that altruism at bottom is simply a form of manipulation to get some desired effect.

If SGT are correct than atheist have no valid reason to decry Christians for "manipulating" their children as they are simply doing what SGT predicts they will.

If on the other hand altruism is not as the SGT say, then atheism is presented with an insoluble dilemma. Altruism (and altruisitic behavoir e.g. hospitals, churches and charities) aren't just undesirable they would have to be inherently evil. Why? Because it mitigates against the survival of the fittest (best able to adapt, live, prosper) genes.

Joseph said...

"I thoroughly enjoy the fact that it takes no less than three of you to attempt to refute me."

Having delusions of grandeur?

zilch said...

Okie dokie. Streetapologist says:

I thoroughly enjoy the fact that it takes no less than three of you to attempt to refute me.

What joseph said. But hey, take enjoyment where you can get it is my motto.

In an ultimate sense life came about by chance.

Oh? Seems pretty unlikely, doesn't it? Of course, this is a reason that many people invoke magic for life's origins: they imagine that a cosmic accident that assembles a living cell to be as unlikely as Fred Hoyle's hurricane assembling an airplane in a junkyard. And of course they're right: such an accident is so unlikely that you would have to propose a very large Universe, or amount of time, or number of Universes, to make it plausible.

However, there is another explanation, and it doesn't require magic. Order can emerge spontaneously, given the right conditions. Shygetz can certainly explain this better than I, but briefly speaking: given order, and energy, higher order can increase locally. This is why Miller and Urey were able to generate amino acids back in 1953 starting with water, methane, ammonia, and hydrogen. The addition of energy in the form of a spark made the increase in order possible. More recent work has demonstrated the emergence of vesicles (tiny spheres with walls of lipids, similar to living cells) and many other kinds of organic compounds.

Now, we're still a long way from creating life, and it may well be that we will never know exactly how it appeared on Earth. However, recent experiments (I found Robert M. Hazen's Genesis: The Scientific Quest for Life's Origins to be a good overview) have shown that the same combination of chance (the Earth is possibly a very lucky planet for the evolution of higher forms of life- see Rare Earth, by Peter Ward and Donald Brownlee) and the tendency for the local emergence of higher order built upon lower, in a process akin to natural selection (which is not a chance process, as I have said) make our presence here, solely based on natural processes, eminently plausible.

No gods necessary, and indeed invoking magic in the form of a God is no explanation at all; it just adds another, even more highly ordered being, that must in turn be explained. Of course, most believers balk at explaining the origin of God, and simply invoke some kind of magic: "He was here all along, He's the Uncaused Cause, He's divinely simple" etc. This kind of explanation might suffice for those who tell their kids that yes, the magician is really doing magic when he pulls that rabbit out of that hat, but it is not sufficient for us reality-based thinkers.

If the only justification is that they [the laws of logic] work, they are no longer universal and are simply conventions. How then would we know that the law of contradiction tomorrow won't be replaced by something that works better?

We can't know absolutely that it won't be. However, we can't know absolutely that we aren't brains in vats. Based on the track record of the laws of logic, however, I'm willing to bet a large sum of money that they won't be tossed tomorrow.

If SGT are correct than atheist have no valid reason to decry Christians for "manipulating" their children as they are simply doing what SGT predicts they will.

This is a version of the is/ought fallacy. David Hume said it best, so if no one objects, I will quote him:

"In every system of morality, which I have hitherto met with, I have always remark'd, that the author proceeds for some time in the ordinary ways of reasoning, and establishes the being of a God, or makes observations concerning human affairs; when all of a sudden I am surpriz'd to find, that instead of the usual copulations of propositions, is, and is not, I meet with no proposition that is not connected with an ought, or an ought not. This change is imperceptible; but is however, of the last consequence. For as this ought, or ought not, expresses some new relation or affirmation, 'tis necessary that it shou'd be observ'd and explain'd; and at the same time that a reason should be given; for what seems altogether inconceivable, how this new relation can be a deduction from others, which are entirely different from it."

In other words, just because something is a certain way, for instance the fact that our selfish genes create propensities to behave selfishly, doesn't mean that we ought to give way to them. We humans have not only evolved certain desires, but we've evolved the ability to extend and modify these desires through reasoning. If "is" (say, sexual desire or hunger) were always "ought" (what we acted upon without mediation), we would not have the cultures we do.

Thus, atheists (and everyone else) can have valid reasons (the desire to live in peace, in joy, in love, in exultation of our Universe) to pursue, or not pursue, paths that may conflict with our more primitive penchants.

Now, I believe that any set of morals or laws that one lives by, natural or supernatural, is "irrational" in the sense that it cannot be justified all the way down by logic or the laws of the Universe. But that doesn't make it meaningless or unecessary. If we want the benefits of society and culture, we have to cobble together some structure, as well as we can, that we can live by and with.

That's what morals, laws, and religions do. The problem I and many other atheists have with religions is partly with particular rules they have (for instance, saying that disobedient children should be stoned- of course, a lot of them are...) but also with their introduction of a carrot-and-stick wielding Sky Daddy to enforce the rules. We should outgrow this Santa Claus/ Boogie Man.

Shygetz said...

As for altruism, it simply doesn't comport with the selfish gene theorist.

Kin altruism does. If you are right, and altruism goes so hard against our selfish genes that it must imply a closeness to God, then that makes ants the most godly of creatures. Ants gladly give up their lives and their selfish genes to protect the queen, so that the queen can make more brothers and sisters, most of whom will also die without reproducing to support a queen.

Of course, you are wrong. The laboratory of nature has proven you wrong, and mathematical models support the interpretation of the data; kin selection actually can act to amplify genetic projection into the future, where an individual compromises its survival to greatly increase its kin's ability to project its genes into future generations.

Non-kin altruism can involve a competing selective mechanism, covered by memetics. This competing selective mechanism operated in competition with genes for resources, much in the way an organism would. Evolution doesn't claim to be the ONLY force in the world, you know...

In an ultimate sense life came about by chance.

If, AND ONLY IF, by life you mean the first replicator. After that, it was the non-random factor of selection.

The idea of a replicator coming about by chance is not so obscene, given the early experiments into the spontaneous generation of biological organics, and given the incredible lengths of time involved.

In the rest of your post, you make the ABSOLUTELY INEXCUSABLE error of mistaking "what is" for "what should be". Unlike creationists, scientists' explanation for how things work is not the same thing as their morals. Natural selection as an ethical framework is abhorrent.

Unlike zilch, I do not think that all laws and morals are irrational. I believe that many laws and morals aid in the genetic fitness of people who subscribe to them by allowing them to maintain a stable social structure. At one point and time, religion served that purpose. However, religion is now no longer required for a stable society; various moral and political philosophies have taken its place that do not have the drawbacks that religion has (does not require material sacrifices, does not require irrational conclusions about the material universe, etc.)

Brother Crow said...

A PERFECT EXAMPLE OF WHY POINTING OUT BIBLICAL FALLACIES OR INCONSISTENCIES OR OTHER BULL---- BIBLE STUFF...CHRISTIANS DON'T CARE!!! They say the Bible is the Word of God, the very foundation of "revealed truth" (as opposed to unrevealed truth - whatever)...and they twist it, ignore it, come up with excuses for why they don't obey it (excuses which often depend on the very scientific methodology they deny when confronted with it as a proof of the bible's fallacies and inconsistencies).

As I said before, to Christians, the bible is like Harry Potter's wand...a "book of magic" (and not just the words, but the very book itself). It reveals "hidden knowledge and power" to those who have "a pure heart" or "truly desire the truth"...it is gnostic, of course. And the only ones who have the right (besides God - whoever) to determine whether or not a person is of pure heart or truly desire to know the truth are the ones who have the "hidden, secret knowledge" - and then of course they only acknowledge the legitimacy of others if they agree with them.

That is why all these fallacies and inconsistencies are fun for us atheists and agnostics and other people who actually use the brains they have...but for the Christian, they are for the most part meaningless...unless they already have one foot out of the closet.

B H said...

Just throwing this out, because the wonderful term seems to be being misused in a few cases: part of the point of The Selfish Gene is that its genes that are selfish, not organisms. An altruistic gene across a population of social animals only has to survive twice to be passed on.

Lee Randolph said...

Shygetz,
a hearty amen on your last post, brother!

Here is some quick and dirty data supporting you

zilch said...

streetapologist: In an ultimate sense life came about by chance.

shygetz: If, AND ONLY IF, by life you mean the first replicator. After that, it was the non-random factor of selection.

Here we are getting into the murky area of exactly what chance is. Assuming for the moment that the Universe is nondeterministic, then one could argue that any local decrease in entropy is not "chance". That would mean that the myriad spontaneous outbursts of increased order in the Universe are not "chance", which seems a bit generous.

But where does "chance" give way to "not chance", then? I would say that this is another continuum, with life definitely on the "not (primarily) chance" end, crystal formation being somewhere in between, and, say, the appearance of organic molecules in molecular clouds in space being pretty much "chance". But I don't see where you can draw a line. It's quite possible, as Hazen points out in his Genesis, that metabolism preceded replication, and the development of metabolism doesn't seem too "chancy".

shygetz said: Unlike zilch, I do not think that all laws and morals are irrational. I believe that many laws and morals aid in the genetic fitness of people who subscribe to them by allowing them to maintain a stable social structure.

I agree, and perhaps "irrational" is the wrong word. There are certainly better and worse laws and morals, and the better ones can be grounded in our knowledge of our desires, which are not the result of chance, and are largely held in common. I should have said "not absolute".

akakiwibear said...

The range of topics in this thread is large, so if I may return to the evolution topic. I have no questions about evolution, understand and accept it. While I often make comments to stir up the pot this is not such a posting, but a genuine question.

I would be pleased if someone could explain to me how the code (the combination of A, G, C and T) that is captured by the DNA molecule, plus the encoding mechanism and the decoding mechanism all of which are essential for reproduction and evolution and each with no other discernable purpose evolved/developed and from what source.

It strikes me that a code, the ability to encode and decode are most unlikely simply appear together when each has no other purpose, so they must have had an origin or source. Certainly from an information theory (which I do understand) perspective I see this as a major question and know of no similar system that just happened. Not sure if there are any evolutionary biologists reading this, but thought I would ask for an explanation anyway.

Joseph said...

Supplemental to akakiwibear's question, and in the same spiritu of honest wondering, I have a question of my own: isn't the concept of a "code" something that we've imposed upon our study of DNA as a way of simply explaining what we see? Don't know if I'm making sense or not.

Lee Randolph said...

Hi akakiwibear,
what have you done on your own to answer that question? There are a couple of theories that come to mind. I'm wondering, without telling you, if you are familiar with them or are just throwing that out there as an argument from ignorance to say that since there is no definitive answer it must be god.

zilch said...

joseph- no, calling genes "codes" is accurate, if by "code" we mean "instructions to be read and followed".

akawikibear- I'll second lee. Why don't you google "abiogenesis" and "origin of life" and see what you come up with. A good starting place is Wikipedia.

But to answer your question briefly: no one thinks that a replicator complete with DNA-encoded genes and transcription mechanisms appeared by chance. Obviously, such cells or protocells must have evolved from something simpler. How this happened is not known and may never be known in detail. But there is lots of research going on, and it looks as though we might someday have at least a rough outline of how life evolved. Check it out yourself- it's a fascinating field.

Shygetz said...

It strikes me that a code, the ability to encode and decode are most unlikely simply appear together when each has no other purpose, so they must have had an origin or source.

The DNA code does have another purpose; to replicate itself. That is, in fact, it's primary purpose; everything else in incidental. It's ability to serve as a code for protein translation is solely a secondary function that serves the primary function of reproduction. And the DNA code works through the simple means of interaction followed by catalysis. The only reason it works as a "code" at all is because of the specificity of the interaction, which is a parameter that is known to be readily acted upon by evolution, and the pool of interacting substances that form the specific interactions.

I could imagine many different scenarios that could lead to the gradual (always gradual) formation of a DNA code. Most of them would involve communities of independant replicators acting in a mutualistic fashion to increase each other's reproduction. Say, for example, that replicator A and replicator B interacted. The interaction structure catalyzed a conjugation of a methionine (a sulfur-containing amino acid) to one of the replicators. This methionine had the effect of acting as a reactive species scavenger, protecting the replicators from damage from cosmic rays. The interaction would be based on a complimentary code between the replicators, which could be acted upon by evolution to make the interaction tigher, weaker, modulated by the environment, etc. The catalysis (which is caused by the 3D shape of the interacting pair) could also be acted upon by evolution parallel to the interaction itself, to make the catalysis faster, change the catalyzed reaction, etc. Then, replicator A undergoes a reaction with another replicator A, forming two tandem replicator A's, each with a binding site for a replicator. These two binding sites can now evolve seperately, and each can bind with a different replicator. So say that a complex with one A and two B's reproduces ok, but a complex with one A and two B's, each with a methionine attached, survives and replicated better. You will get evolution to improve the addition of methionine to B. Now, say that you find out that a complex of one A, one methionine-attached B, and one B with an arginine survives even better than the two-methionine version, as the one methionine offers enough protection, and the positively charged arginine attracts the negatively charge chemicals you need for reproduction better. Now, you have a code, where the template of replicator A encodes binding to a sequence of methionine-argining in two different replicator B's, all by gradual step-wise evolution.

zilch said...

Thank you shygetz!

akakiwibear said...

Hi Shygetz – that’s a lot to digest thanks for the effort! You know your stuff.

Lee, no, not a wild throw, but the outcome of an unfinished discussion that happened around me over a few beers. I had not done much research at the time of posting and was hoping for a quick conclusive atheist repost.

Zilch – thanks for confirming the “not known” – that was what I picked up over the beers.

To all of you, following my comment I went off and did some research.
Interesting outcome, to summarise (I have the links below) Perry Marshall seems to be the main player here and in spite of much looking I found no real rebuttal of his case. I will try and summarise here for those who don’t want to bother with the full story.

DNA is a code = instruction to be followed.
For the code to work it (all the information needed to “build” a human, a cat or a bacteria) has to be encoded transmitted and decoded. You need all three things to be simultaneously present. The DNA is only the communication medium.

Start with DNA molecule then transcription into mRNA = encoding. This process has no other purpose other than to encode (i.e. the encoding is not a by product of another life process nor is the encoding a primary process that occurs for its own sake). The code structure is very specific, get it wrong and the “build” is flawed or fails. The code structure is based on the A,G,C & T pairings.

The mRNA is then decoded as described by shy using another very specific process. The code being unique/specific and the encoding/decoding process are all essential to the transmission of the information.

Perry argues that there are no naturally occurring codes – he is an ID person with, for once a really sound case – and that the requirement of simultaneous existence of the code + encoder + decoder renders it beyond chance, and equally important is that the three elements of the code system – and in particular the code itself - have no other function and are part of no other life process (they are a prerequisite for reproduction) they could not have evolved (a) having nothing to evolve from and (b) being a statistical nonsense.

OK that's what Perry said, now some other stuff. Interesting the smallest number of protein coding genes known is 182 built on a base of 159,662 base pairs in the carsonella ruddii. This is less than required for the cell to fully function and it borrows its host cell DNA to enable reproduction.

So for the first independent working cell we would need a functioning code system based on more than 182 protein coding pairs to have occurred by chance in nature with no evidence that it has ever happened again.
http://www.newscientist.com
/channel/life/genetics
/dn10259-bacteria-boast
-the-tiniest-genomes-to-date.html

As I see it, the “argument from ignorance” rebuttal is not valid here. The argument from ignorance essentially says that in the absence of ANY rational explanation ‘God did it’. I agree that is a weak position.

But, the argument from ignorance rebuttal is always defeated by the existence of a rational explanation. In this case a specific rational explanation is advanced, in fact is demanded by the case, and that is that a causal intelligence is necessary to produce a code system

I agree nothing in Perry’s argument proves that God is the intelligence, but it does demonstrate an essential requirement for a causal intelligence.

It is not important that we know much about the causal intelligence to acknowledge that Perry’ case for one is rational and convincing. I think Perry’s conclusion that it is God is perhaps an example of “a rose if called by …”

One could argue that Perry’s assertion that all code systems require an active causal intelligence to come about is a hypothesis that requires only one example of a naturally occurring code to be defeated and since none have been produced, the hypothesis stands.

The links:
Perry Marshall’s update of Paley’s design argument which also addresses Hume’s criticism Exec summary http://www.cosmicfingerprints.com
/ifyoucanreadthis.htm
Marshall and 30+ sceptics debate http://www.cosmicfingerprints.com
/iidb.htm
The counter arguments summarized http://www.cosmicfingerprints.com
/dnanotcode.htm

Shygetz said...

To all of you, following my comment I went off and did some research.

No, you didn't. Research requires examining scientific literature. You went to a crank's website (which I will shortly demonstrate). Big difference, and don't demean true researchers by equating yourself with them. If you want to do true research on abiogenesis, I would be happy to point you to peer-reviewed science, or even pop accounts that rely upon peer-reviewed science.

Start with DNA molecule then transcription into mRNA = encoding. This process has no other purpose other than to encode (i.e. the encoding is not a by product of another life process nor is the encoding a primary process that occurs for its own sake).

This is untrue. The transcription process has nothing to do with encoding; it essentially copies the DNA into a different but highly related format. Transcription and mRNA stability is important for regulation (it is the best understood and perhaps the most important way to determine which genes are turned on or off at any time). It is important for amplification (if you need a lot of protein, you can copy one DNA gene into thousands of mRNAs, and then translate each mRNA into hundreds of proteins). It is also essential to allow proteins to be translated during DNA replication; if you had to read the DNA at the same time you were trying to copy it, you could have big trouble.

The code structure is very specific, get it wrong and the “build” is flawed or fails. The code structure is based on the A,G,C & T pairings.

Also untrue. The code is degenerate. There are many errors you can make with no functional difference in the protein. Similarly, proteins can often suffer many mutations without grossly affecting function. Finally, since you make lots of mRNAs, if you make a few bad ones and tons of good ones, the good protein will far outnumber the bad (and the cell has ways of getting rid of many kinds of incorrect proteins to keep them from gumming up the works).

The mRNA is then decoded as described by shy using another very specific process. The code being unique/specific and the encoding/decoding process are all essential to the transmission of the information.

You are playing fast and loose with the term "information" which means something very specific. I predict that you are just about to make a big mistake...

Perry argues that there are no naturally occurring codes – he is an ID person with, for once a really sound case – and that the requirement of simultaneous existence of the code + encoder + decoder renders it beyond chance, and equally important is that the three elements of the code system – and in particular the code itself - have no other function and are part of no other life process (they are a prerequisite for reproduction) they could not have evolved (a) having nothing to evolve from and (b) being a statistical nonsense.

DNA is the replicator--it has no need for another function. The mRNA is the regulator and amplifier through which the DNA interacts with its environment, and has MANY other purposes than "coding" (which, as I mentioned before, it really doesn't do). Protein is, in most cases, the effector. The diversity of its amino acids allow it to have a more complex 3D structure, carry out much more complex chemistry and catalysis, and similarly. None of them exist solely for the purpose of perpetuating a "code".

Similarly, "codes" defined the way you are trying to define it do occur in nature, even outside of biology. For example, mineral crystals are known to be able to perpetuate its structure (which contains information) by interacting with a supersaturated solution of non-crystalized mineral, causing this mineral to crystalize, thus transfering its information to the mineral through a structural code by purely natural processes.

So for the first independent working cell we would need a functioning code system based on more than 182 protein coding pairs to have occurred by chance in nature with no evidence that it has ever happened again.

HUGE error #1: the earliest replicator CERTAINLy wasn't a cell. Therefore, the first cell did NOT come about by chance; it came about by natural selection (a purely NON-RANDOM event) working on the populations of replicators. Therefore, your random chance argument is irrelevant--evolution SPECIFICALLY states that it could NOT happen by random chance, but REQUIRES natural selection.

As far as the smallest replicators we know of, the answer is a single gene. They are called transposons, there are many of them, and they encode a single protein called a transposase that helps it to move around in the cell to aid its replication in host organisms.

I have already given a specific example of how the early coding replicators COULD have occurred naturally. Design is not required.

In this case a specific rational explanation is advanced, in fact is demanded by the case, and that is that a causal intelligence is necessary to produce a code system.

False. Mineral crystals do not require intelligence to perpetuate their information via a structural code, which stands as a concrete natural counterexample to Perry's hypothesis.

It is not important that we know much about the causal intelligence to acknowledge that Perry’ case for one is rational and convincing.

No, it is merely important to be ignorant about the natural world. Fortunately, ignorance is an eminently treatable disease, and I'm offering you the cure. Will you take it?

One could argue that Perry’s assertion that all code systems require an active causal intelligence to come about is a hypothesis that requires only one example of a naturally occurring code to be defeated and since none have been produced, the hypothesis stands.

Yet I named a naturally occurring code--mineral crystals. Consider the "hypothesis" refuted.

From now on, do yourself a favor; look to biochemists for biochemistry, and look to engineers such as Perry Marshall for engineering. Next time you decide to rely upon the authority of an engineer for biological chemistry, I will demand that you drive to work in a car I design.

zilch said...

shygetz- once again, a great job. Do you write a lot in your work? You certainly have a knack for clear explanation.

An aside- it seems to me that a disproportionate number of evolution-deniers are engineers, and not biologists. Might there be a wee bit of bias here? Engineers spend their time designing things, and sometimes reverse-engineering things, so it should perhaps not be surprising that they look for an intelligent Designer or an Engineer behind the exquisite complexity of life's design too.

Of course, in a way, life does have an intelligent designer, but one spread across vast distances of time and space: natural selection. Its intelligence is not gathered together in one Being, but consists of the uncountable increases in order, one tiny step here and one there, which are preserved because they did what worked to pass themselves on: got energy from food or sunlight, escaped being food themselves, survived heat and cold, found mates...

This is what makes natural selection not random; a designer, but not itself designed: while the variation thrown up by mutation is random (ignoring for the moment that mutation works upon a hierarchically evolved system), natural selection makes choices that any engineer would approve of: that which works better is more likely to survive.

The difference between an engineer designing something, and natural selection designing something, is that the engineer designs from the top down, and natural selection from the bottom up.

The engineer can look at what works, and use logic, foresight, and knowledge of physics to design things, all at one go (although in practice engineers depend upon previous designs too).

Natural selection has no logic, or foresight, or knowledge of physics. All natural selection does is select: those variations that work better for whatever reason at getting their genes into the next generation, are the ones that get to play in the next round: one tiny incremental improvement at a time.

But tiny incremental improvements can lead to big changes, given world enough and time, and we've had world enough and time: billions of years, and untold quadrillions and brontillions and stegasaurillions of living things. What Nature lacks in the way of foresight, she more than makes up for in extravagant numbers of trials.

Shygetz said...

zilch: I am a faculty member specializing in biological chemistry and protein structure at a major research university. I do write a lot, although usually not for a lay audience. Thanks for the compliments.

akakiwibear said...

Shy, thanks for the full reply - I do not consider myself a creationist so it was interesting to see what looked like a good argument refuted.

I am not sure your example of a crystal is analogous with a code system which requires multiple elements, the code, transmission, en/decription.

The DNA code clearly has these elements, but the crystal does not. The crystal contains information in its molecular structure - it is essentially information about itself, and it is not transmitted through a different medium and then decoded to reconstitute the original information. Compare that to the encoding of a new individual (male + female = new individual' code) it is then transmitted and decoded and the new individual "built". It seems to me the hypothesis still stands with no example of a naturally occurring code. BTW did you read Marshall's replies to the criticism of his case?

Also I am not sure I have enough bio knowledge to appreciate your point about the first replication not being at cellular level - did life not start at cellular level, a bacteria or something?

You comment about the signal degrading during transmission is correct and a characteristic of code system subject to noise which uses error detection/correction to restore some lost info or if it can't then the error is incorporated into the info. You comment confirms that DNA works like a code system.

zilch said...

I won't presume to answer for shygetz, akawikibear, but I have to make a couple of points here. First of all, I went to Perry's site and read his argument, then I read some of the last pages of the debate (not all of them- there are over nine hundred comments, and I do have work to do as well!).

My conclusions: one, Perry is rather full of himself. Doesn't mean he's not right, but his smugness is annoying. Two, his argument is sunk right out the door, imho. He basically says "DNA is a code, all other examples of code that we know of are designed by minds, thus DNA is designed by a mind". The problem that immediately comes to my mind is that other codes (by his definition) exist that are not designed by intelligent beings- for instance, the pheremones that some orchids use to attract male bees which say, in effect, "come mate with me- I'm a female bee!" Shygetz already mentioned crystals as another example.

But the principle problem is that induction does not prove anything, and is always subject to correction based on more evidence. Perry's is basically the argument from ignorance: "I can't imagine any way DNA could have evolved, so it must be magic".

Here's an example of how induction can fail. Any scientist living forty years ago, if asked, would have told you the following: Some animals (mostly insects, such as termites, bees, and ants) are eusocial, that is they live in colonies with only one reproducing female. All known examples of eusociality are arthropods. Thus, any eusocial animal you find is an arthropod.

But in the mid-seventies it was discovered that naked mole rats, which are not arthropods, are eusocial. Thus, in the absence of exhaustive information and perfect theories (and our information is never exhaustive, our theories never perfect), we can never say with certainty whether we are correct or not.

Perry, however, asserts that his argument is a "proof" for the existence of God. Now, I can't prove that God does not exist, but historically speaking, science has a track record for coming up with explanations for the world that, while not perfect, are a damn sight better than the religious explanations. The same is true in this case.

Perry's invocation of information theory to "disprove" evolution is also uninformed. He claims that if random changes to a text degrade the message, that proves that mutation cannot create information, and thus evolution must be directed by a mind. But the comparison is faulty, for several reasons.

One- in a text, each word is correctly spelled in itself or not. The same is not true of a genome: there are no "right" or "wrong" genes, just genes that do different things. And while it is true that most random changes to a genome are not improvements, a few are; and they provide the raw materials for natural selection.

Two- whereas a text message has a certain prefixed meaning, so any change is likely to degrade that meaning, the same is not true of a genome: any given genome produces (when all goes well) an organism, which succeeds or not. If a mutation in the genome produces a different organism, this organism will succeed or not based on how well it does (natural selection), not on how faithful a copy of its parent it is.

Three- nature has lots of time and lots of organisms to work with. While it's hard to imagine evolving one text to another by changing one letter at a time, and thus airily dismiss the possibility as Perry does, it can be done and it has been done. All that is necessary is time, patience, and selection.

Shygetz said...

I am not sure your example of a crystal is analogous with a code system which requires multiple elements, the code, transmission, en/decription.

It is not meant to be an analogy; Marshall stated that no code that transmits information can exist without design, and crystals are definitely information (as carried in the relative spatial coordinates of the atoms) transmitted by code (in this case, non-covalent bonding interactions) and decrypted into information (in this case, organization of random assortments of molecules into more ordered crystals).

The DNA code clearly has these elements, but the crystal does not. The crystal contains information in its molecular structure - it is essentially information about itself, and it is not transmitted through a different medium and then decoded to reconstitute the original information.

Umm...what do you think carries information in DNA, if not its molecular structure? How do you think DNA transmits the information, if not through chemical bonding? A protein does NOT contain the "same information" as DNA; information means something very specific, and you just messed it up.

Let's look closely at the crystal and compare it with DNA/RNA (since, as I pointed out previously, RNA is almost identical to DNA, and is NOT a decryption process--it is a regulatory amplification step, and the protein generation is the "decryption" process).

Information:
DNA/RNA--spatial orientation of bases
crystal--spatial orientation of atoms/molecules

Code:
DNA/RNA--non-covalent bond network between mRNA (the near-copy of DNA template) and tRNA that carries the amino acid
crystal--non-covalent bond network between the crystal and the non-crystal atoms/molecules

Decryption:
DNA/RNA--bonds between neighboring amino acids bound on the mRNA template
crystal--bonds between neighboring atoms/molecules bound on the crystal template

Even though they are differences, crystals CLEARLY refute Marshall's central "hypothesis" that codes to transmit information cannot occur naturally. Indeed, there is a school of abiogenesis that thinks that inorganic crystals were the first replicators, and evolution worked upon them to give us what we have today.

Do you want to change your central "hypothesis" to say that codes that transmit information from one medium to another does not occur without intelligence? Fine. You can seed crystallization in one substance using a crystal made of a different substance (look up "heterogeneous crystal nucleation", but be prepared for some serious reading). So, you've transmitted information from the origianl crystal structure through chemical bonds to completely different chemicals, which then form a completely different crystal structure.

Also I am not sure I have enough bio knowledge to appreciate your point about the first replication not being at cellular level - did life not start at cellular level, a bacteria or something?

Depends completely on your definition of "life". However, the first thing that was affected by evolution was NOT at the cellular level, and that is all evolution cares about; whatever you or I decide to call "life" is irrelevant to evolution and abiogenesis. Evolution affects anything that:
1) replicates itself
2) features variation in replicates at some rate, and
3) is subject to natural selection

Living things are a subset of replicators, and are therefore subject to evolution. The boundary between early replicators and what one would define as life is very fuzzy.

You comment about the signal degrading during transmission is correct and a characteristic of code system subject to noise which uses error detection/correction to restore some lost info or if it can't then the error is incorporated into the info. You comment confirms that DNA works like a code system.

No, I did NOT say the signal degrades during transmission; I said the DNA code is degenerate. That means that there are multiple DNA codons that are translated into the same amino acid. Therefore, you can have multiple changes in the DNA code that do not represent changes in the protein sequence; they are called silent mutations, and they are quite common. This fact is contrary to what you said (I assume when paraphrasing Mr. Marshall):
The code structure is very specific, get it wrong and the “build” is flawed or fails.
The DNA code can tolerate many errors while still making the same "build".

The signal does degrade during transmission, just like the signal from an existing crystal is not transmitted perfectly to the non-crystallized atoms/molecules in solution, resulting in flaws in the new crystal; do you now cede that this fact means crystallization works like a code system?

BTW did you read Marshall's replies to the criticism of his case?

I tried to when I read your post originally. The link demanded a name and e-mail address. As I did not want to be buried by spam, I supplied a false name and e-mail address, hoping to be sent to the proper website. Instead, Mr. Marshall's site sent an automated e-mail to the fictional address. If Mr. Marshall seriously has something of interest to say, he can publish it in the peer-reviewed literature. Failing that, he can at least do what most self-respecting cranks do and publish it on the web for unfettered access. I will not give the man my e-mail account to bombard so I can read his (at least thus far) thoroughly false and unoriginal meanderings on a subject he clearly does not understand.

On a similar note, do you go to engineers for medical treatment? For legal advice? Then why on earth do you trust one's knowledge of subjects as intricate, detailed, and well-studied as evolution, biophysics, and information theory?

I think I will make a post on this phenomenon, as it is not unique to you and (in my opinion) should be addressed.

Shygetz said...

Turns out the reason I couldn't get to Marshall's linked response to criticisms wasn't because it wasn't there, but because my browser was truncating the address, which sent me to Marshall's default page. My apologies.

Marhsall's "responses" are FILLED with serious errors. Marhsall defines "code" as:

I define "Coded information" as a system of symbols used by an encoding and decoding mechanism, which transmits a message that is independent of the communication medium.

Unfortunately, the "message" is NOT independent of the communication medium; it is ENTIRELY RELIANT upon the medium. Indeed, it could be said that the message IS the medium.

Proteins work as they are. It doesn't matter if they are built by a cell through RNA translation, or if I make them manually with chemistry in a tube; they still work (within certain limits that have to do with folding kinetics, and nothing to do with a "message").

The book Information Theory, Evolution and the Origin of Life is written by Hubert Yockey, the foremost living specialist in bioinformatics.

Dr. Yockey is NOT the foremost living specialist in bioinformatics (although he is well-respected).

Marshall then relies upon a legend at a public museum to define very technical terms. This is poor science; you go to peer-reviewed literature, not museum legends written for lay audiences when defining scientific terms.

If there are pebbles below a rapids, there are pebbles below a rapids. There is no coded information associated with them - unless you measure their size, in which case you have created information to describe the pebbles, based on your chosen symbols and units of measurement. Same with orientation of sand dunes, layers of hailstone. Those objects represent only themselves; there is no encoding and decoding mechanism within these material objects, such as there is in DNA.

This is where he really goes over the side. A counter-example was provided of pebbles at the base of a waterfall; you will find that the pebbles will be assorted roughly by size, and this assortment is information. Marshall states that the assortment is not by information; the pebbles are pebbles. You MAKE information when you "measure their size."

If this is true, then DNA nucleotides are DNA nucleotides. We MAKE information when we determine their identity. It's crap. The water interacts with the pebbles, using gravity and hydrodynamics to transmit information to the pebbles, causing them to assort in a predetermined pattern based on their physical properties.

mRNA interacts with the amino acid-loaded tRNA, using chemical bonding to transmit inforamtion to the tRNA and cause it to assort the amino acids in a predetermined pattern based on their physical properties. They are both transmitting information in code. Marshall just doesn't like it, so he INVENTS a difference.

The information in DNA is independent of the communication medium insofar as every strand of DNA in your body represents a complete plan for your body; even though the DNA strand itself is only a sequence of symbols made up of chemicals (A, G, C, T).

Untrue, as any first-year cell bio student can tell you. The DNA does NOT contain a complete plan for my body. If I take a cell in my body, it will not grow into a new me. Why? Because it lacks the environmental stimuli to do so. These environmental stimuli are REQUIRED to make the body during the developmental process, and a lack of these stimuli are among the most common causes of miscarriage. The genes can make the parts, but they still require the environment to make the whole).

We could store a CAD drawing of a hard drive on the same model of hard drive, but the medium and the message are two distinctly different things. Such symbolic relationships only exist within the realm of living things; they do not occur naturally.

Well, if he means that the idea of code exists only naturally, I'll go one farther; it exists only in conscious animals. However, the physical processes by which one medium influences another medium in a predetermined way IS natural, and THAT is a code. If you wish to create symbology behind these interactions (like people do), that's fine. But the interactions themselves are physical and independent of intelligence.

Likewise, a strand of Aunt Mildred's DNA uniquely specifies that she is a woman, that she has RH Negative Blood Type, two arms, two legs etc.

A single unit cell of a crystal packing uniquely specifies the bond angles of the crystal, its space packing group, bond lengths, etc.

Yockey also describes the encoding of DNA to mRNA in the reference above (see the figures from Shannon's book and Yockey's book).

Transcription of DNA to mRNA is NOT encoding (at least, not in a useful sense). The two use almost identical chemicals; it is closer to replication, just using a slightly different medium. It is very analogous to homogenous crystal seeding; one template creates a nearly identical template. Indeed, some replicators carry their genetic information in RNA instead of DNA (HIV being a popular example).

You have described the encoding / decoding process in DNA exactly as Yockey has; he maps it to the Shannon communication model. This happens without the intervention of intelligence, just like your computer getting automatic virus updates. But water flows and hailstones and sand dunes do not encode and decode information in this way. Only intelligently designed systems map 1:1 to Shannon's model.

Nope. Let me map crystal formation into a Shannon model.

Information source--seed crystal
Message--spatial orientation of atoms
Transmitter--non-covalent bonding interactions
Channel--spatial orientation of atoms "message" in non-covalent bonding "code"
Noise--non-productive kinetic traps; heterogenous occlusions
Channel--spatial orientation of atoms "message" plus trap/occlusion "noise"
Receiver--unsorted atoms/molecules interacting with crystal surface
Message--spatial orientation of atoms plus noise
Destination--previously unsorted molecules now sorted with predetermined spatial orientation of atoms

Fits nicely, and directly refutes his "hypothesis".

The question that naturalism can't answer is where the code came from.

First of all, that's not a question; it's an assertion. Second, naturalism can and has proffered answers as to how the pattern arose--evolution. It's actually made a lot of predictions about the nature of the code which turned out to be true, so it is a predictive theory, not just a post hoc interpretation.

The proper formal terminology is “The pattern of base pairs in DNA are a code.”

And yet the pattern of rocks at the base of a waterfall is not? Why? Because Marshall has not ascribed meaning to them.

Marshall seems to be begging the question--a code is a pattern to which an intelligen being has ascribed meaning. Since an intelligent being must ascribe meaning to a pattern for it to be a code, then intelligent beings are required for codes to exist. I ascribe meaning to DNA patterns (even though I do not understand DNA at all), therefore DNA patterns are a code. I refuse to ascribe meaning to any other patterns in nature, so no naturally occurring codes exist.

He exemplifies this nicely when he says:
Snowflakes and tornados and sand dunes and water molecules do not contain coded information because there is no system of symbols, no encoding / decoding mechanism, no transmission of a message (plan, idea or instructions) that is independent of the communication medium. In other words, these things represent nothing other than themselves.

Yet if you look at DNA, you will not see a collection of T, C, G, and A. You will see cyclic compounds binding to other cyclic compounds, composed of carbon, hydrogen, nitrogen, and phosphorous. Humans made the symbols, and they are only meaningful as symbols. We could just as easily invent symbols for different sizes and shapes of pebbles and have Marshall's code for waterfalls.

Fortunately, Marshall isn't the only intelligent being in the universe. I ascribe meaning to the pattern of rocks at the base of a waterfall--it is a message regarding their hydrodynamic properties, written in the code of assortment. Therefore, that pattern is a code.

Marshall then goes on to insist that the plan for a human being written in DNA code is independent of the DNA that makes up the human. That's not right...that's not even wrong. Ignoring the fact that DNA and RNA itself often plays a direct role in cellular function independent of protein synthesis, the DNA itself (the physical entity) is absolutely required for the organism. You couldn't replace the DNA with a recording tape and still have a functioning organism, no matter how good your record is.

Why? Because organisms have evolved to work with physical DNA, AND ONLY physical DNA. The medium IS the message. DNA encodes instructions for making more DNA; that is all, and nothing more.

The decoding of the human genome is the interpretation of DNA's base pairs, mapping them to specific biological functions.

I wish Marshall would decide what the decoding was. Now he claims it is function. In that case, all chemical reactions are codes, as they result in products that have different functions from the original, and they are predetermined by the physical conditions. This is just getting sillier and more incoherent.

A water molecule does not contain coded information because it represents nothing other than itself. Through chaos, water can form steam or clouds or condensation or snowflakes, depending entirely on the conditions. But unlike DNA, water molecules contain no code or instructions which specify in advance what any of these larger forms will take.

But crystals do. So Marshall directly implies that, since crystals contain advance instructions on what form the later product will take, it is a code.

This criticizer has it right:
You have not shown that DNA qualifies as a code under definition 3. Your mere assertion won't cut it. The chemical interactions in DNA are not a message in any conventional sense. No communication has taken place. Nothing there is in any way symbolic. Our descriptions may be symbolic but the chemistry is not.

To rebut this, Marshall quotes an article that says that biologists have made some insights into genetics using information theory. This is true. We have also made insights into humans by studying rats; this doesn't mean humans ARE rats, it just means that there are useful parallels. While one could say that information DOES exist in the genome, to say that communication is occuring is to anthropomorphize the process inexcusably. While there are some parallels that may inspire fruitful study, it is NOT communication in the sense Marshall implies.

If, as you have already inferred, DNA uniquely determines any phenotype characteristic at all, then it does qualify as a code.

Phenotype is a term of convenience, not a physical property. It is DEFINED as a subjective analysis, and as such, is not criteria for a strict definition of "code".

A sequence of symbols only has to uniquely determine one thing in order to qualify as a code.

And he changes the definition of code yet again. It doesn't have to determine function, just any one thing. So, pebble assortment (which dictates the precise hydrodynamic flow of water in a stream) is a code.

Gravity, by itself uniquely specifies nothing in advance

Sure it does; it specifies in advance the properties of an object under given conditions, just like DNA.

Marshall is silly, inconsistent, and wrong. He is out of his depth in a subject in which he has only shallow textbook knowledge. I (and you, by the way) have better things to do.

zilch said...

shygetz- I'm sure you do have better things to do than to fisk Marshall, but I for one am glad you did. Thanks- I'm learning loads of interesting stuff.

akakiwibear said...

Hey Shygetz - your effort for the lengthy reply is much appreciated!!!!

I am working through it!! Does Marshall still take comments, I am sure you could keep him awake long into the night.

BTW, I assume your comment On a similar note, do you go to engineers for medical treatment? For legal advice? Then why on earth do you trust one's knowledge of subjects as intricate, detailed, and well-studied as evolution, biophysics, and information theory? applies to trusting biologists opinions on theology?

Sorry, but I just could not resist that last comment - I know it applies equally to myself as it does to Dawkins or to many others

Cheers

Shygetz said...

applies to trusting biologists opinions on theology?

Can one really be a scientific expert in a fictional field?

Does Marshall still take comments, I am sure you could keep him awake long into the night.

I don't know if he takes comments; however, it really doesn't matter. He would lose no sleep. I saw how he dealt with the valid criticisms he got there; he brings up invalid points, misrepresents the science, and plays word games. He is either willfully lying (which in this case I doubt), or so firm in his dogmatic belief that he is correct that he dismisses contrary arguments before carefully considering them (which I suspect), both of which are antithetical to the progress of science. I will satisfy myself in pointing out the holes in his logic to interested people.

As a non-scientist, the only question you should ask is this: If your work is so air-tight and revolutionary, why not submit an article to a top-tier peer-reviewed journal? Tons of stuff gets published that is directly contrary to the current paradigm, and if his reasoning is sound it should be able to withstand learned criticism and impartial editing. Just look at relativity, quantum mechanics, the bacteria that cause ulcers, viruses that cause cancer, etc. All of these went directly against strongly entrenched scientific opinion, but the authors' had evidence and well-reasoned arguments, which is ALL that science values. Eventually, these ideas won out based on the strength of evidence and argument, DESPITE current scientific opinion.

If he finds one journal is unfairly biased against him, submit to another. Scientists have to do it all the time, and it's a valid way to get your work published. But, if he tried a dozen journals and they all find it to be weak, perhaps its not bias, it's just bad science. Publishing in peer-reviewed journals is free (well, submitting is free--a few journals charge for publishing but most don't), and it's the only way to really gain traction in the scientific community. If you have a sound scientific idea with evidence to support it, there is NO excuse not to publish it in peer-reviewed literature.

Publishing scientific ideas to the popular media without peer review is the sole domain of cranks and quacks. Get your science from scientists, and by all means, get your theology from theologians. But when they disagree about something important and REAL (like how best to treat your cancer), I bet I know which group you'll trust more.

Seeker said...

I want to thank all of you for your posts, and in particular "Shygetz" for his detailed explanations. I hope you happen across this "thank you" note...despite it coming nearly a year after your posts.

I came across Perry Marshall 4 or 5 years ago. I was a Christian with doubts when we crossed paths. Perry Marshall introduced me to his arguments and we traded several long emails. Ultimately, what Perry was saying did not sound true to me. But I don't have a background in Information Theory or genetics or biochemistry to argue from a position of authority. I felt that DNA shows itself to be a naturally developing structure. I never saw a need for "intelligence" required to explain it. But I couldn't argue the definition of code with Perry or the ins and outs of information theory. I'm grateful to finally find someone who has directly addressed Perry's argument with facts and appropriate knowledge.