What would the creationist movement do without their amazing ability to copy and paste absolutely anything from anywhere and give it a whole new context (as if by magic!) and without the few of them who actually can write and think to some degree and enjoy large sums of money from the whole deal?

I thought using unsourced information without any modification was a case of plagiarism?

GenesForLife wrote:
A scientific theory, in case you did not get the memo, is an explanatory framework of scientifically verifiable facts, driven by empirical data, why do I get the impression this is a fuckwitted attempt at the fallacy of equivocation with the layman's meaning of "speculation"?

how can facts, that supposedly happened millions of years ago, be verified by empirical data ?

Crimes without eyewitnesses and or video evidence are unseen, unobservable and in the unrepeatable past, so even if they do leave behind other evidence such as DNA, that says nothing about the truth, ey?

why do you think, so many people have been convicted falsly, just based on evidential data from the past ?

The fact is that the mechanisms of evolution and the natural processes postulated as part of the Theory of evolution are amenable to empirical testing, regardless of how much fuckwittery you continue to show it won't change, and the postulated processes are based on real world physical data that persist in ways ranging from the fossil record to the genomes of extant organisms, you fail pathetically at this asinine "were you there" canard.

how exactly do you feel the fossil record and genomes of exant organisms supports the theory of evolution ?

Since humans cannot be trusted, and you didn't see yourself being born, can we safely assume that you weren't born because you didn't see yourself being born? Your existence today is the persistent physical evidence of your birth, and this doesn't make the "theory" of your birth any less valid.

how exactly does your example relate to the theory of evolution ?

Wow, that is some amount of projection, what amount of empirical evidence do you have to describe Cali's posts as wishful thinking while your mythology apparently isn't? That is some level of hypocrisy, innit?

all the evidence i have, i show it here.

Except Cali is backed up by evidence, what have you? Mythology?

i have the exact same historical record as Cali has. Maibe macroevolution is mythology ?

All Abrahamic faiths are predicated upon starting off from a gene pool of two people and said mythology involves a global flood which the Egyptians and Chinese never encountered

http://www.morgenster.org/signs.htm

The fact that the oldest stories of the Bible can be found in Chines signs is an evidence that Chinese as well as Jews (= the modern name for the people of Israel) have common ancestors, who have lived these stories and have told them to their descendants. This proves that these stories are historical events in stead of inventions of the Jews.

The Chinese language contains about 600 basic symbols, which are basic words. Other words can be formed by combining these basic symbols to more complicated pictures. Sometimes a symbol is added to a word in order to present the pronunciation of that word. In this article we consider words without that pronunciation symbols.

http://www.creationism.org/csshs/v06n2p04.htm

An examination of Chinese tradition, and the legends of the equally ancient Far Eastern Miao tribes, suggests that China was colonised after a flood like that described in the Bible.

The flood was as important in the ancient mythologies of the peoples of China, as it is to Scripture. Many primitive peoples described it as a catastrophe of Biblical dimensions. The Miao Legend states that a single human couple escaped the deluge in a wooden drum, and then gave birth to the first members of post flood humanity.1 The Shu King, China's first "history", states:

destructive in their overflow are the waters of the inundation. In their vast extent they embrace the hills and overtop the great heights, threatening the heavens with their floods

If it is the Quran, "he is produced from a gushing fluid, which emanates from between the ribs and the loins" comes to mind, stuff which makes elementary errors in basic biology doesn't have anything going for it when explaining existence et cetera come to mind, got any friggin evidence to suggest otherwise?

i don't support the quran, so your mentioning it is not of interest to me.

The whole nature of "this is the truth" and the believe it or else dotted throughout, including threat of eternal torment, does that quite well, y'see.

we are well asked to study the bible, and not to believe it without thinking.

I'll let someone deal with the finetuning canard that I suspect will be erected

why don't you deal by your own to clarify it just for yourself ? why is it not of interest for you ?

by the way, care to link us to proper peer-reviewed evidence in scientific journals pointing towards a creator?

you know well scientific journals hold on to the base of modern science, which relies on the philosophy of naturalism. Nothing shall be explained metaphysically.

Secondly, a deistic creator doesn't automatically mean you can shove in your brand of magic man into the argument.

actually, i can. the cosmological argument fits excellently to the God of the bible, and not another one.

Since when did argument become tantamount to empirical evidence, got any, have you?

neither do you have any which supports macro-evolution. do you have any ?

abiogenesis cannot be explained. Human consciousness,ability of speech, and moral knowledge cannot be explained through science. And so many phenomenas remain unexplainable trough exclusion of the supernatural.

And the evidence for your blind assertion is what? If I'm guessing correctly, obfuscatory sweet fuck all.

your bias becomes truly obvious. feel free then to present rational and convincing explanations for the cited issues, above.

Is that blog a peer-reviewed paper?

does your world view only rely on peer reviewed papers ? if so, why ?

Since evolution is an ongoing process observable currently, this is yet another canard.

Show me macro-evolution then

Ellipses are used in threes, firstly, secondly, pointing out nonsense isn't tantamount to being arrogant, projection much?

the way its pointed out, is arrogant.

cience isn't an argumentum ad populum, old chap, learn this lesson quickly, and if they accuse scientists of "interpreting" things differently based on personal bias, it is indeed defamatory.

Cali came up with this ....

Any evidence of any scientific progress ever achieved by not using materialism at all?

sure. Christianity played a important role of scientific progress :

http://www.bede.org.uk/sciencehistory.htm#conclusion

Christianity had an important impact on every step of the road to modern science. Let me now summarise exactly what they were:

The preservation of literacy in the Dark Ages

Because it is a literary religion based on sacred texts and informed by the writings of the early church fathers, Christianity was exclusively responsible for the preservation of literacy and learning after the fall of the Western Empire. This meant not only that the Latin classics were preserved but also that their were sufficient men of learning to take Greek thought forward when it was rediscovered.

The doctrine of the lawfulness of of nature

As they believed in a law abiding creator God, even before the rediscovery of Greek thought, twelfth century Christians felt they could investigate the natural world for secondary causes rather than put everything down to fate (like the ancients) or the will of Allah (like Moslems). Although we see a respect for the powers of reason by Arab scholars they did not seem to make the step of looking for universal laws of nature.

The need to examine the real world rather than rely on pure reason

Christians insisted that God could have created the world any way he like and so Aristotle's insistence that the world was the way it was because it had to be was successfully challenged. This meant that his ideas started to be tested and abandoned if they did not measure up.

The belief that science was a sacred duty

This is not so much covered in this essay, but features again and again in scientific writing. The early modern scientists were inspired by their faith to make their discoveries and saw studying the creation of God as a form of worship. This led to a respect for nature and the attempt to find simple, economical solutions to problems. Hence Copernicus felt he could propose a heliocentric model for no better reason that it seemed more elegant.

Not all these factors were unique to Christianity but they all came together in Western Europe to give the world its only case of scientific take off which has since seen its ideas spread to the rest of the world. An learned examination of why other civilisations failed to make the leap forward can be found here.

For the anti Christians desperate not to give credit for their own faith of scientism to the religion they hate, two questions must be answered. First, if the dominant world view of medieval Europe was as hostile to reason as they would like to suppose, why was it here rather than anywhere else that science arose? And secondly, given that nearly every one of the founders and pre founders of science were unusually devout (although not always entirely orthodox) even by the standards of their own time, why did they make the scientific breakthroughs rather than their less religiously minded contemporaries? I wonder if I will receive any answers.

Fail, you don't understand the differences between hypothesis, verified fact, laws and theories well, do you?
You are using the nature of hypotheses to argue against the whole of science, mendacious indeed...

its wellknown, modern science relies on the philosophy of naturalism. what is mendacious about that ?

bollocks, since evolution acts on extant creatures and is observable, and has been observed, this is combined with persistent physical and molecular evidence hallmarking the postulated processes in the past, may it be the fossil record or the phylogenetic trail.

how do you explain it, that some of our ancestors were far more sophisticated, than it was thought ? the phylogenetic trail should suggest. complexity is increasing. recent studies show the opposit......

More blind assertions, and isn't this a repeat? Only that I've had to wade through so much of your nonsense I might've forgotten.

http://en.wikipedia.org/wiki/Karl_Popper

Karl Popper famously stated "Darwinism is not a testable scientific theory, but a metaphysical research program."

how true...

But they themselves can never, by showing said scientific validity, and despite your assertions of thousands of scientists being creationists, cannot get their "interpretations" into proper scientific journals? Quelle surprise!

yes, they cannot. you should know by your own, why they can't.

http://elshamah.heavenforum.com/philoso ... w-t335.htm

"Naturalistic science" points to naturalism, whether philosophical or methodological, both of which are essentially the same. Neither of which will allow the supernatural as a cause for anything in this world, even if logical. Natural causes must account for everything. So if scientific findings shows limits in natural causes, it doesn't matter because natural causes must have done everything. This shows that it is not the science that is important, but the reigning philosophy of naturalism. By definition, it will exclude any other possible explanation, whether presuppositional or logical or even rational, including the possibility of the supernatural, so it is true that naturalistic "science", or rather the naturalistic interpretation of scientific evidence will always miss a supernatural explanation. Whatever the supernatural is, the naturalistic mind will not accept it. That's why it is true that research today is not about finding real answers, but only confirming a naturalistic philosophy

here's a int - peer review rejects mere "interpretations" unless there is empirical data provided in support and warrants direct deduction, and Cretinists have none

peer review rejects answers, which are not based on naturalism.

The evidence points to evolution and not to special cretardation, fucking deal with it.

how beautyful your bias is in evidence.....

How does being any of that automatically mean that whatever they write down is true?

i've not said that. I just corrected cali's canard, the bible writers were just uneducated sheperds....
and even if they were : what evidence is there, they are automatically worthless to testify what they experienced , just based on their uneducated secular activity?

Creation scientist is an oxymoron, since creationism makes no testable predictions.

Non of the historical sciences do.

Try the fossil record

please show how the fossil record evidences macro-evolution.

then several cases of speciation

speciation is NOT macro-evolution. learn this.

including Diane Dodd and Drosophila pseudoobscuraHeliconus heurippa and Hyla versicolor

that is speciacion, not macro-evolution.

and , off the top of my head, macroevolution is evolution at the species level, cause it is at the species level at best all organisms exist, microevolution occurs within populations of species.

your above examples of fruit flies etc. fail to present empirical evidence of macro-evolution.... wanna try again ??

Ignorant bullshit, read the literature and come back, and trying to indulge in goalpost shifting by redefining macroevolution doesn't count, here's a hint, check wikipedia first for the definition of macroevolution.

I've done so. epic fail so far to provide hard empirical evidence of evolution on species level.

What objective standard do you use to assert fine tuning? is there an unfine tuned or a fine untuned universe which you no of to show the difference "design" makes?

you may have a study of the odds of a fine untuned universe, and then we talk. Your effort of credulity must be really overwhelming.... the finetuning of the universe is the strongest evidence for theism.

False dichotomy, chance and design aren't the only options, in fact, even with stochastic processes , there are variables involved which still follow basic, unaided natural processes.

which one ? please present them

The ability of the components necessary for life to be formed under prebiotic conditions, formulated based on the persistent physical evidence such conditions leave behind, is something that is currently under research, and Dr.Szostak's work is quite significant in this regard, among the work of many others, again, abiogenesis research is a field that still demands scientific rigour in testing postulates empirically, something that creotards don't get, don't understand, and never make an effort to do so when screaming "Goddidit, the babble says it"

you can struggle as much as you want. Abiogenesis is a lost case for atheists :

http://www.epm.org/resources/2010/Mar/1 ... t-exist-w/

To sum up the evolutionary dilemma: Even if the physical impossibility of forming and gathering the necessary physical building blocks of a cell were overcome, it would still require information. And it would still require a ‘language.” And it would need to immediately form a copying mechanism. Looking at it from a different angle, you need a cell to create a DNA molecule. But you need DNA to create a cell. What is required to create DNA and cells is information arising from intelligence. Which brings us back to the Biblical model. to sum up the evolutionary dilemma: even if the physical impossibility of forming and gathering the necessary physical building blocks of a cell were overcome, it would still require information. and it would still require a ‘language.” and it would need to immediately form a copying mechanism. looking at it from a different angle, you need a cell to create a DNA molecule. But you need DNA to create a cell. what is required to create DNA and cells is information arising from intelligence. which brings us back to the biblical model.

With respect to evolution, populations of real living organisms have been observed evolving in real time.

That is called micro-evolution. No creationist will defy this fact. Thats the only part of the theory of evolution, which can be called a fact.

Bullshit assertion, read the fucking literature first.[/quote]

i've done so. prove me wrong.

What scientists actually postulate, and they postulate this with respect to every observable phenomenon in the universe, is that well defined and testable mechanisms are responsible. Mechanisms that are amenable to empirical test and understanding, and in many cases, amenable to the development of a quantitative theory. Two such quantitative theories, namely general relativity and quantum electrodynamics, are in accord with observational reality to fifteen decimal places. As an aside, when someone can point to an instance of mythology producing something this useful, the critical thinkers will sit up and take notice, and not before.

I have not seen you here, postulating a other mechanism, than chance, to explain the existence of the universe, its fine-tuning to life, and abiogenesis. Wanna try again ? i give you a hint. It might be physical need ? you can try this one....

1) Quantum inflation

quantum inflation is a epic fail to explain the origin of our universe.

http://elshamah.heavenforum.com/astrono ... ns-t65.htm

"The recent use of such vacuum fluctuations is highly misleading. For virtual particles do not literally come into existence spontaneously out of nothing. Rather the energy locked up in a vacuum fluctuates spontaneously in such a way as to convert into evanescent particles that return almost immediately to the vacuum. As John Barrow and Frank Tipler comment, ". . . the modern picture of the quantum vacuum differs radically from the classical and everyday meaning of a vacuum-- nothing. . . . The quantum vacuum (or vacuua, as there can exist many) states . . . are defined simply as local, or global, energy minima (V'(O)= O, V"(O)>O)" ([1986], p. 440). The microstructure of the quantum vacuum is a sea of continually forming and dissolving particles which borrow energy from the vacuum for their brief existence. A quantum vacuum is thus far from nothing, and vacuum fluctuations do not constitute an exception to the principle that whatever begins to exist has a cause."

"In the case of quantum events, there are any number of physically necessary conditions that must obtain for such an event to occur, and yet these conditions are not jointly sufficient for the occurrence of the event. (They are jointly sufficient in the sense that they are all the conditions one needs for the event's occurrence, but they are not sufficient in the sense that they guarantee the occurrence of the event.) The appearance of a particle in a quantum vacuum may thus be said to be spontaneous, but cannot be properly said to be absolutely uncaused, since it has many physically necessary conditions. To be uncaused in the relevant sense of an absolute beginning, an existent must lack any non-logical necessary or sufficient conditions whatsoever."

"As Barrow and Tipler comment, "It is, of course, somewhat inappropriate to call the origin of a bubble Universe in a fluctuation of the vacuum 'creation ex nihilo,' for the quantum mechanical vacuum state has a rich structure which resides in a previously existing substratum of space-time, either Minkowski or de Sitter space-time. Clearly, a true 'creation ex nihilo' would be the spontaneous generation of everything--space-time, the quantum mechanical vacuum, matter--at some time in the past."([1986], p. 441)."

2) Life is fine-tuned to the universe by evolution

when we come to the hard questions, the light weight answers of atheists become VERY obvious, and their unreasonable faith construct becomes obvious as well.

we have simply BETTER explanations on hand for our universe, and that is evident for any honest rational thinker.

The universe is finely tuned to permit life on our planet. Over 120 fine tune constants are know up to know, and as more time pasts, more are discovered. This might be due to chance, to physical need, or to design. Chance is a very bad explanation. Some advocate a Multiverse. But to have just one life permitting universe, you need 1 to 10^500 attempts to get it done. Thats a 1 with 500 zeros. If we put it in comparison, that in our universe, there exist around 10^80 atoms, this shows how improbable it is, that a Multiverse could explain finetuning. Beside this, the Multiverse argument does not explain away God. A mechanism needs to be in place to trigger these multiverses. It could not be by physical need, since if so, why are there many planets, which are not life permitting, but our is ? So its best explained by design. Our earth/solar/moon system is a very strong evidence. Our solar system is embedded at the right position in our galaxy, neither too close, nor too far from the center of the galaxy. Its also the only location, which alouds us to explore the universe, In a other location, and we would not see more than stellar clouds. The earth has the right distance from the sun, and so has the moon from the earth. The size of the moon, and the earth, is the right one. Our planet has the needed minerals, and water. It has the right atmosphere, and a ozon protecting mantle. Jupiter attracts all asteroids , avoiding these to fall to the earth, and make life impossible. The earths magnetic field protects us from the deadly rays of the sun. The velocity of rotation of the earth is just right. And so is the axial tilt of the earth. Beside this, volcano activities, earth quakes, the size of the crust of the earth, and more over 70 different paramenters must be just right. To believe, all these are just right by chance, needs a big leap of faith. This is indeed maibe the strongest argument for theism.

3) Chemical reactions, none of the three are chance, get that? They're driven by well defined natural processes.

to produce life, you need carbon molecules.

http://elshamah.heavenforum.com/astrono ... e-t191.htm

Lee Smolin (a world-class physicist and a leader in quantum gravity) estimates that if the physical constants of the universe were chosen randomly, the epistemic-probability of ending up with a world with carbon chemistry is less than one part in 10^220.

If chance was not the driving factor to produce carbon molecules, what other factor do you suggest ????

1. God created a finite universe
2. Nothing was the origin of our universe. It simply popped up into existence from absolutely nothing.
3. The universe never began to exist, but existed always in some form or the other.

You think those are testable and well defined natural mechanisms? [/quote]

you completely miss the point. why do you think we need testable and well defined natural mechanisms to figure out, what explanation fits and explains best our existence ??

Failed assumption that everything needs an external cause, check out the Casimir effect for instance, where something arises from what, in conventional physics is "nothing" , in other words, for matter to be generated, NO external magic is required.

epic fail as shown above. the weakness of your position continues evident.

but i will rebut it with a different quote :

http://elshamah.heavenforum.com/astrono ... ns-t65.htm

In 1973, Edward Tryon suggested that our universe might originate from the quantum fluctuation. This requires extremely accurate cancellation between matter energy and gravitational energy. If the matter energy is just slightly (within 1 part in 1050) greater than the gravitational energy, the uncertainty principle would dictate the matter to disappear in a time period that is too short to have any physical meaning. For such gigantic fluctuation to occur spontaneously is almost impossible.

wanna try again ?

Who the fuck suggested String theory is the only explanation for the Universe? This is yet more mendacity trying to portray science as speculation, again, it must be noted that the String theory is more appropriately a mathematical model.

then please present another model which seems reasonable to you.

If an alternative isn't presented to bullshit, bullshit becomes true? Weird logic.

ah, ok. So you stick to the " we don't know yet " escape ?? well, that is not new to me, either.

DNA itself is an evolvable entity, and to try and use Popper's relatively ancient assertions in the light of modern evidence to try and refute the latter is a blatant piece of mendacity.

Bullshit.

http://elshamah.heavenforum.com/origin- ... r-t287.htm

Fundamental Law 1 (FL1)

A purely material entity, such as physicochemical processes, cannot create a nonmaterial entity. (Something material cannot create something nonmaterial.)

Physical entities include mass and energy (matter). Examples of something that is not material (nonmaterial entity) include thought, spirit, and volition (will).

Fundamental Law 2 (FL2)

Information is a nonmaterial fundamental entity and not a property of matter.
The information recorded on a CD is nonmaterial. If you weigh a modern blank CD, fill it with information, and weigh it again, the two weights will be the same. Likewise, erasing the information on the CD has no effect on the weight.
The same information can be transmitted on a CD, a book, a whiteboard, or using smoke signals. This means the information is independent of the material source. A material object is required to store information, but the information is not part of the material object. Much like people in an airplane are being stored and transferred in the plane, they are not part of the physical plane.
The first law of thermodynamics makes it clear that mass and energy (matter) can neither be created nor destroyed. All mass and energy in the universe is being conserved (the total sum is constant). However, someone can write a new complicated formula on a whiteboard and then erase the formula. This is a case of creating and destroying information.

Since the first law of thermodynamics states that mass and energy (matter) cannot be created or destroyed, and information (UDI) can be created and destroyed, information (UDI) must be nonmaterial.
The genetic information system is the software of life and, like the symbols in a computer, is purely symbolic and independent of its environment. Of course, the genetic message, when expressed as a sequence of symbols, is nonmaterial but must be recorded in matter and energy.5

Indeed, Einstein pointed to the nature and origin of symbolic information as one of the profound questions about the world as we know it. He could identify no means by which matter could bestow meaning to symbols. The clear implication is that symbolic information, or language, represents a category of reality distinct from matter and energy.6

First Law of Information (LI1)

Information cannot originate in statistical processes. (Chance plus time cannot create information no matter how many chances or how much time is available.)
There is no known law of nature, no known process, and no known sequence of events which can cause information to originate by itself in matter.7

Second Law of Information (LI2)

Information can only originate from an intelligent sender
Corollary 18
All codes result from an intentional choice and agreement between sender and recipient.

We observe daily a continual input of new information (UDI) from an intelligent source (human beings). At present, on earth, the only new information we have detected being created is from human beings. Careful examination of other systems will determine if there are any other intelligent sources of new UDI.
Corollary 2
Any given chain of information can be traced backward to an intelligent source.
For two people to effectively communicate, there must be some agreement on the language or code that is used.

Common ancestry for humans and chimps is also strongly supported by 1) Pseudogenes 2)

http://www.trueorigin.org/pseudogenes01.asp

As the function of more pseudogenes is being uncovered by testable and repeatable science, it is evident that these genetic elements, which are copiously spread in the genomes of different organisms, have been created with purpose. The recent finding of insertion hotspots also clarifies how pseudogenes may have appeared to evolutionists as shared mistakes and now invalidates their use in phylogenetic studies.

Chromosome fusion 3) ERV insertions, I hope you'll take the time to read the apposite scientific literature on the subject before continuing with your fuckwitted chain of assertions.

http://www.ideacenter.org/contentmgr/sh ... hp/id/1392

In other words, Miller has to explain why a random chromosomal fusion event which, in our experience ultimately results in offspring with genetic diseases, didn’t result in a genetic disease and was thus advantageous enough to get fixed into the entire population of our ancestors. Given the lack of empirical evidence that random chromosomal fusion events are not disadvantageous, perhaps the presence of a chromosomal fusion event is not good evidence for a Neo-Darwinian history for humans.

Miller may have found good empirical evidence for a chromosomal fusion event. But our experience with mammalian genetics tells us that such a chromosomal aberration could have created a non-viable mutant, or a normal individual who could not produce viable offspring. Thus, Neo-Darwinism has a hard time explaining why such a random fusion event was somehow advantageous.

A case of a tail in a 2-week-old infant is reported

thats not a tail.

http://www.icr.org/article/evolution-human-tail/

Don't want to have to actually discuss a topic, just use plagiarized copy pasta AND keep the misspelling. Three fucking threads of this.

Jireh wrote:
The universe is finely tuned to permit life on our planet. Over 120 fine tune constants are know up to know, and as more time pasts, more are discovered. This might be due to chance, to physical need, or to design. Chance is a very bad explanation. Some advocate a Multiverse. But to have just one life permitting universe, you need 1 to 10^500 attempts to get it done. Thats a 1 with 500 zeros. If we put it in comparison, that in our universe, there exist around 10^80 atoms, this shows how improbable it is, that a Multiverse could explain finetuning. Beside this, the Multiverse argument does not explain away God. A mechanism needs to be in place to trigger these multiverses. It could not be by physical need, since if so, why are there many planets, which are not life permitting, but our is ? So its best explained by design. Our earth/solar/moon system is a very strong evidence. Our solar system is embedded at the right position in our galaxy, neither too close, nor too far from the center of the galaxy. Its also the only location, which alouds us to explore the universe, In a other location, and we would not see more than stellar clouds. The earth has the right distance from the sun, and so has the moon from the earth. The size of the moon, and the earth, is the right one. Our planet has the needed minerals, and water. It has the right atmosphere, and a ozon protecting mantle. Jupiter attracts all asteroids , avoiding these to fall to the earth, and make life impossible. The earths magnetic field protects us from the deadly rays of the sun. The velocity of rotation of the earth is just right. And so is the axial tilt of the earth. Beside this, volcano activities, earth quakes, the size of the crust of the earth, and more over 70 different paramenters must be just right. To believe, all these are just right by chance, needs a big leap of faith. This is indeed maibe the strongest argument for theism.

http://www.thinkatheist.com/forum/topics/reasons-why-i-am-a-theist wrote:
2. The universe is finely tuned to permit life on our planet. Over 120 fine tune constants are know up to know, and as more time pasts, more are discovered. This might be due to chance, to physical need, or to design. Chance is a very bad explanation. Some advocate a Multiverse. But to have just one life permitting universe, you need 1 to 10^500 attempts to get it done. Thats a 1 with 500 zeros. If we put it in comparison, that in our universe, there exist around 10^80 atoms, this shows how improbable it is, that a Multiverse could explain finetuning. It could not be by physical need, since if so, why are there many planets, which are not life permitting, but our is ? So its best explained by design. Our earth/solar/moon system is a very strong evidence. Our solar system is embedded at the right position in our galaxy, neither too close, nor too far from the center of the galaxy. Its also the only location, which alouds us to explore the universe, In a other location, and we would not see more than stellar clouds. The earth has the right distance from the sun, and so has the moon from the earth. The size of the moon, and the earth, is the right one. Our planet has the needed minerals, and water. It has the right atmosphere, and a ozon protecting mantle. Jupiter attracts all asteroids , avoiding these to fall to the earth, and make life impossible. The earths magnetic field protects us from the deadly rays of the sun. The velocity of rotation of the earth is just right. And so is the axial tilt of the earth. Beside this, volcano activities, earth quakes, the size of the crust of the earth, and more over 70 different paramenters must be just right. To believe, all these are just right by chance, needs a big leap of faith. This is indeed maibe the strongest argument for theism.

Jireh wrote:

GenesForLife wrote:
A scientific theory, in case you did not get the memo, is an explanatory framework of scientifically verifiable facts, driven by empirical data, why do I get the impression this is a fuckwitted attempt at the fallacy of equivocation with the layman's meaning of "speculation"?

how can facts, that supposedly happened millions of years ago, be verified by empirical data ?

For one, remnants of an evolutionary ancestry in the genomes of extant organisms, which when treated statistically points towards universal common ancestry.

Universal common ancestry (UCA) is a central pillar of modern evolutionary theory1. As first suggested by Darwin2, the theory of UCA posits that all extant terrestrial organisms share a common genetic heritage, each being the genealogical descendant of a single species from the distant past3, 4, 5, 6. The classic evidence for UCA, although massive, is largely restricted to ‘local’ common ancestry—for example, of specific phyla rather than the entirety of life—and has yet to fully integrate the recent advances from modern phylogenetics and probability theory. Although UCA is widely assumed, it has rarely been subjected to formal quantitative testing7, 8, 9, 10, and this has led to critical commentary emphasizing the intrinsic technical difficulties in empirically evaluating a theory of such broad scope1, 5, 8, 9, 11, 12, 13, 14, 15. Furthermore, several researchers have proposed that early life was characterized by rampant horizontal gene transfer, leading some to question the monophyly of life11, 14, 15. Here I provide the first, to my knowledge, formal, fundamental test of UCA, without assuming that sequence similarity implies genetic kinship. I test UCA by applying model selection theory5, 16, 17 to molecular phylogenies, focusing on a set of ubiquitously conserved proteins that are proposed to be orthologous. Among a wide range of biological models involving the independent ancestry of major taxonomic groups, the model selection tests are found to overwhelmingly support UCA irrespective of the presence of horizontal gene transfer and symbiotic fusion events. These results provide powerful statistical evidence corroborating the monophyly of all known life.

http://www.nature.com/nature/journal/v4 ... 09014.html

Crimes without eyewitnesses and or video evidence are unseen, unobservable and in the unrepeatable past, so even if they do leave behind other evidence such as DNA, that says nothing about the truth, ey?

why do you think, so many people have been convicted falsly, just based on evidential data from the past ?

As opposed to the thousands of those who were convicted based on eyewitness accounts? Or all the guilty who escaped due to lack of evidence? This is a rhetorical question mind.

The fact is that the mechanisms of evolution and the natural processes postulated as part of the Theory of evolution are amenable to empirical testing, regardless of how much fuckwittery you continue to show it won't change, and the postulated processes are based on real world physical data that persist in ways ranging from the fossil record to the genomes of extant organisms, you fail pathetically at this asinine "were you there" canard.

how exactly do you feel the fossil record and genomes of exant organisms supports the theory of evolution ?

1) Concordance of molecular phylogenies with the fossil record, for one, it allows the verification of the results of phylogenetic analysis as being adequately representational of evolutionary history, secondly, phylogeny alone is based on the principle of inheritance and points towards a universal common ancestor, not separate creatio, the paper I posted above will explain.

2) Fossil record exhibits clear progression in the geological time frame, with multiple cladogenesis events, which , as described in point 1) is in perfect agreement with phylogeny, which itself has been corroborated by independent studies, both in the process of identifying the origins of HIV and in ancestral protein reconstructions, not to mention validation by comparing it in a double blind study with actual in-vitro evolution only to find that phylogeny itself, alone, is representative of the natural world.

Since humans cannot be trusted, and you didn't see yourself being born, can we safely assume that you weren't born because you didn't see yourself being born? Your existence today is the persistent physical evidence of your birth, and this doesn't make the "theory" of your birth any less valid.

how exactly does your example relate to the theory of evolution ?

My example relates to your attempt to ask "were you there?" as if it fundamentally means nothing is true if you weren't.

Wow, that is some amount of projection, what amount of empirical evidence do you have to describe Cali's posts as wishful thinking while your mythology apparently isn't? That is some level of hypocrisy, innit?

all the evidence i have, i show it here.

I take that as none?

Except Cali is backed up by evidence, what have you? Mythology?

i have the exact same historical record as Cali has. Maibe macroevolution is mythology ?[/quote]

Bullshit, at the very same moment I'll get you an empirical demonstration of a speciation (formation of a new species by loss of fertility between one population of ancestral species and the rest) event (which is macroevolution)

The paper in question can be found here http://www.hummingbirds.arizona.edu/Cou ... d_1989.pdf

According to the biological species concept, speciation is basically a problem of reproductive isolation.
Of the many ways to classify isolating mechanisms, the two main divisions are premating isolation, in which
mating is prevented from occurring, and postmating isolation, in which mating takes place but viable, fertile
offspring are not produced. There is much debate over which type of mechanism, premating or postmating,
is most likely to develop first and how the isolation comes about (e.g., see Dobzhansky, 1970; Mayr, 1963;
and Muller, 1949).

In an attempt to gain insight into the process of the development of reproductive isolation, eight populations
of Drosophilapseudoobscura were studied. These were first used by Powell and AndjelkoviE (1983) in a
study of the alpha-amylase (Amy) locus. Four were reared on a starch-based medium, and four were reared
on a maltose-based medium. These two media are both quite stressful; it initially took several months for the
populations to become fully established and healthy. Considering the pressure placed on the populations by
the media, one would expect to see some kind of adaptive divergence between the starch-reared and maltosereared
flies.

Several changes were in fact observed in the eight populations. Powell and AndjelkoviE noted an increase
in the "Just" allele of Amy in the starch populations as well as an increase in one of the patterns of amylase
activity in the midgut. However, no corresponding changes were seen in the maltose populations. Elsewhere
(Dodd, 1984), I have presented evidence that the populations have become differentially adapted to
the two media. In this study, it is shown that the populations have also developed behavioral isolation as a
pleiotropic by-product of this adaptive divergence.

This is just the introduction, anyone who is so inclined is welcome to read the paper.

All Abrahamic faiths are predicated upon starting off from a gene pool of two people and said mythology involves a global flood which the Egyptians and Chinese never encountered

http://www.morgenster.org/signs.htm

The fact that the oldest stories of the Bible can be found in Chines signs is an evidence that Chinese as well as Jews (= the modern name for the people of Israel) have common ancestors, who have lived these stories and have told them to their descendants. This proves that these stories are historical events in stead of inventions of the Jews.

The Chinese language contains about 600 basic symbols, which are basic words. Other words can be formed by combining these basic symbols to more complicated pictures. Sometimes a symbol is added to a word in order to present the pronunciation of that word. In this article we consider words without that pronunciation symbols.

http://www.creationism.org/csshs/v06n2p04.htm

An examination of Chinese tradition, and the legends of the equally ancient Far Eastern Miao tribes, suggests that China was colonised after a flood like that described in the Bible.

The flood was as important in the ancient mythologies of the peoples of China, as it is to Scripture. Many primitive peoples described it as a catastrophe of Biblical dimensions. The Miao Legend states that a single human couple escaped the deluge in a wooden drum, and then gave birth to the first members of post flood humanity.1 The Shu King, China's first "history", states:

destructive in their overflow are the waters of the inundation. In their vast extent they embrace the hills and overtop the great heights, threatening the heavens with their floods

How convenient to forget the Egyptians, who were very close by? I'll also tell you one more thing, starting a population with inbreds is a strict no-no.

If it is the Quran, "he is produced from a gushing fluid, which emanates from between the ribs and the loins" comes to mind, stuff which makes elementary errors in basic biology doesn't have anything going for it when explaining existence et cetera come to mind, got any friggin evidence to suggest otherwise?

i don't support the quran, so your mentioning it is not of interest to me.

Then let it go, but remember that whoever subscribes to that brand of mythology can assert that their version of a deity is no more unlikelier than yours.

The whole nature of "this is the truth" and the believe it or else dotted throughout, including threat of eternal torment, does that quite well, y'see.

we are well asked to study the bible, and not to believe it without thinking.

Citation please

I'll let someone deal with the finetuning canard that I suspect will be erected

why don't you deal by your own to clarify it just for yourself ? why is it not of interest for you ? [/quote]

Just short of time, but of course , you may want to read Harnik or Adam's work on the issue, showing that the possibility of the formation of life is more probable if the weak nuclear force were absent.

by the way, care to link us to proper peer-reviewed evidence in scientific journals pointing towards a creator?

you know well scientific journals hold on to the base of modern science, which relies on the philosophy of naturalism. Nothing shall be explained metaphysically.

Metaphysics has NEVER solved scientific problems, as the case of everyone sucking up to your cosmic sky daddy in 1348 reveals.

Secondly, a deistic creator doesn't automatically mean you can shove in your brand of magic man into the argument.

actually, i can. the cosmological argument fits excellently to the God of the bible, and not another one.

Evidence for this?

Since when did argument become tantamount to empirical evidence, got any, have you?

neither do you have any which supports macro-evolution. do you have any ?

I already posted one above, time for a few more

A whole-genome duplication occurred in a shared ancestor of the yeast species Saccharomyces cerevisiae, Saccharomyces castellii and Candida glabrata. Here we trace the subsequent losses of duplicated genes, and show that the pattern of loss differs among the three species at 20% of all loci. For example, several transcription factor genes, including STE12, TEC1, TUP1 and MCM1, are single-copy in S. cerevisiae but are retained in duplicate in S. castellii and C. glabrata. At many loci, different species have lost different members of a duplicated gene pair, so that 4–7% of single-copy genes compared between any two species are not orthologues. This pattern of gene loss provides strong evidence for speciation through a version of the Bateson–Dobzhansky–Muller mechanism, in which the loss of alternative copies of duplicated genes leads to reproductive isolation1, 2. We show that the lineages leading to the three species diverged shortly after the whole-genome duplication, during a period of precipitous gene loss. The set of loci at which single-copy paralogues are retained is biased towards genes involved in ribosome biogenesis and genes that evolve slowly, consistent with the hypothesis that reciprocal gene loss is more likely to occur between duplicated genes that are functionally indistinguishable. We propose a simple, unified model in which a single mechanism—passive gene loss—enabled whole-genome duplication and led to the rapid emergence of new yeast species.

http://www.nature.com/nature/journal/v4 ... 04562.html

This one uses molecular data from genome observation to demonstrate that speciation by gene duplication and gene loss were responsible for the origins of these species.

Try this review as well, the papers themselves are directly linked to at the bottom.

http://www.nature.com/news/2010/100707/ ... 6174a.html

In other words, your assertions are fucked.

abiogenesis cannot be explained. Human consciousness,ability of speech, and moral knowledge cannot be explained through science. And so many phenomenas remain unexplainable trough exclusion of the supernatural.

And the evidence for your blind assertion is what? If I'm guessing correctly, obfuscatory sweet fuck all.

your bias becomes truly obvious. feel free then to present rational and convincing explanations for the cited issues, above.

I am not asserting they're all explained by science now, there therefore is no onus on me to do so, on the other hand, YOU are making a positive claim that none of these can be explained through science, and YOU are required to substantiate it, an open question now doesn't mean a supernatural answer is the only one that is proposable, and nor does it mean a supernatural answer is the correct one, to suppose otherwise is a logical fallacy.

Unanswered questions don't mean you can propose shit as an answer.

Is that blog a peer-reviewed paper?

does your world view only rely on peer reviewed papers ? if so, why ?

I'm a scientist in waiting, that is why.

Since evolution is an ongoing process observable currently, this is yet another canard.

Show me macro-evolution then

See the literature documenting speciation, and weep.

Ellipses are used in threes, firstly, secondly, pointing out nonsense isn't tantamount to being arrogant, projection much?

the way its pointed out, is arrogant.

And the objective basis for that conclusion is? That you think so? (subjective)

cience isn't an argumentum ad populum, old chap, learn this lesson quickly, and if they accuse scientists of "interpreting" things differently based on personal bias, it is indeed defamatory.

Cali came up with this ....

He came up with an explanation of why the interpretation canard is dishonest, YOU tried to shoe in bias on the part of scientists and suggested that Cretinism is a valid interpretation.

Any evidence of any scientific progress ever achieved by not using materialism at all?

sure. Christianity played a important role of scientific progress :

http://www.bede.org.uk/sciencehistory.htm#conclusion

Christianity had an important impact on every step of the road to modern science. Let me now summarise exactly what they were:

The preservation of literacy in the Dark Ages

Because it is a literary religion based on sacred texts and informed by the writings of the early church fathers, Christianity was exclusively responsible for the preservation of literacy and learning after the fall of the Western Empire. This meant not only that the Latin classics were preserved but also that their were sufficient men of learning to take Greek thought forward when it was rediscovered.

The doctrine of the lawfulness of of nature

As they believed in a law abiding creator God, even before the rediscovery of Greek thought, twelfth century Christians felt they could investigate the natural world for secondary causes rather than put everything down to fate (like the ancients) or the will of Allah (like Moslems). Although we see a respect for the powers of reason by Arab scholars they did not seem to make the step of looking for universal laws of nature.

The need to examine the real world rather than rely on pure reason

Christians insisted that God could have created the world any way he like and so Aristotle's insistence that the world was the way it was because it had to be was successfully challenged. This meant that his ideas started to be tested and abandoned if they did not measure up.

The belief that science was a sacred duty

This is not so much covered in this essay, but features again and again in scientific writing. The early modern scientists were inspired by their faith to make their discoveries and saw studying the creation of God as a form of worship. This led to a respect for nature and the attempt to find simple, economical solutions to problems. Hence Copernicus felt he could propose a heliocentric model for no better reason that it seemed more elegant.

Not all these factors were unique to Christianity but they all came together in Western Europe to give the world its only case of scientific take off which has since seen its ideas spread to the rest of the world. An learned examination of why other civilisations failed to make the leap forward can be found here.

For the anti Christians desperate not to give credit for their own faith of scientism to the religion they hate, two questions must be answered. First, if the dominant world view of medieval Europe was as hostile to reason as they would like to suppose, why was it here rather than anywhere else that science arose? And secondly, given that nearly every one of the founders and pre founders of science were unusually devout (although not always entirely orthodox) even by the standards of their own time, why did they make the scientific breakthroughs rather than their less religiously minded contemporaries? I wonder if I will receive any answers.

Pfft, science itself is still materialistic, I asked for scientific progress made without using materialism at all, not whether religion was involved in some way or the other in the sociocultural environment in which science arose.
Way to miss the flippin' point.

Fail, you don't understand the differences between hypothesis, verified fact, laws and theories well, do you?
You are using the nature of hypotheses to argue against the whole of science, mendacious indeed...

its wellknown, modern science relies on the philosophy of naturalism. what is mendacious about that ?

You were asserting that the hypothetical nature of hypotheses counts against science as a whole, that IS mendacious, don't try to obfuscate.

bollocks, since evolution acts on extant creatures and is observable, and has been observed, this is combined with persistent physical and molecular evidence hallmarking the postulated processes in the past, may it be the fossil record or the phylogenetic trail.

how do you explain it, that some of our ancestors were far more sophisticated, than it was thought ? the phylogenetic trail should suggest. complexity is increasing. recent studies show the opposit......

Relaxation of selective pressure, and who the fuck told you that phylogeny should indicate that complexity should increase? It doesn't do that any more than your family tree would indicate you must be more complex, by the way, care to link to these studies? Cite or retract.

More blind assertions, and isn't this a repeat? Only that I've had to wade through so much of your nonsense I might've forgotten.

http://en.wikipedia.org/wiki/Karl_Popper

Karl Popper famously stated "Darwinism is not a testable scientific theory, but a metaphysical research program."

how true...

Someone states something that agrees with you, therefore it is the truth? The vast amount of extant data on Darwinism, ranging from selection to variation to speciation, shows that Popper was wrong, end of story.

But they themselves can never, by showing said scientific validity, and despite your assertions of thousands of scientists being creationists, cannot get their "interpretations" into proper scientific journals? Quelle surprise!

yes, they cannot. you should know by your own, why they can't.

Cause their interpretation is scientifically invalid, fucking deal with it, the only duplicitous thing cretinists can do, not least because they cannot produce any work in their favour, is to try and undermine science, and they fail at that too, like you are failing here.

http://elshamah.heavenforum.com/philosophy-and-god-f14/science-and-the-commitment-to-naturalistic-worldview-t335.htm

"Naturalistic science" points to naturalism, whether philosophical or methodological, both of which are essentially the same. Neither of which will allow the supernatural as a cause for anything in this world, even if logical. Natural causes must account for everything. So if scientific findings shows limits in natural causes, it doesn't matter because natural causes must have done everything. This shows that it is not the science that is important, but the reigning philosophy of naturalism. By definition, it will exclude any other possible explanation, whether presuppositional or logical or even rational, including the possibility of the supernatural, so it is true that naturalistic "science", or rather the naturalistic interpretation of scientific evidence will always miss a supernatural explanation. Whatever the supernatural is, the naturalistic mind will not accept it. That's why it is true that research today is not about finding real answers, but only confirming a naturalistic philosophy

here's a int - peer review rejects mere "interpretations" unless there is empirical data provided in support and warrants direct deduction, and Cretinists have none

peer review rejects answers, which are not based on naturalism.

Because non-naturalistic answers are not scientific... Creationism would, for instance, also leave natural evidence if it had occured, including the co-existence of all species that were created together at once instead of a gradual progression, barriers to speciation, barriers to cladogenesis, genetic integrity, freedom from selection, absence of a chromosome fusion event in the ancestor of the human lineage et cetera, the fact that none of what we'd expect to see if cretinism were to be the norm is seen rules out the possibility of both physical, and consequently metaphysical shoe-in of that as a valid explanation, learn to deal with it.

The evidence points to evolution and not to special cretardation, fucking deal with it.

how beautyful your bias is in evidence.....

Please at least learn to spell properly, and why don't you start putting up with requests for evidence or shutting the fuck up?

How does being any of that automatically mean that whatever they write down is true?

i've not said that. I just corrected cali's canard, the bible writers were just uneducated sheperds....
and even if they were : what evidence is there, they are automatically worthless to testify what they experienced , just based on their uneducated secular activity?

What evidence is there to suggest that their said experiences were actually divine and not schizophrenic hallucinations driven by the extant cultural norms?

Creation scientist is an oxymoron, since creationism makes no testable predictions.

Non of the historical sciences do.

Vapid blind assertion , big bang cosmology (historical science) makes testable predictions, as in the expected wavelength of the background radiation, and in the expansion of the universe, evolution makes testable predictions, ranging from divergence under differential selective pressures for instance, and most notably, in the case of human-ape ancestry, that humans would have to have one chromosome resulting from the fusion of two ancestral ape chromosomes if the ancestral link was true, guess what? they found telomeres in the central regions of a human chromosome and a second centromere, which only results from chromosome fusion...

Or how about the postulates that prebiotic conditions could give rise to amino acids, for instance (check the Urey-Miller experiment) which is from the field of abiogenesis research? or the postulate that there had to be ways in which DNA and RNA could self-replicate without proteins?

http://www.nature.com/nature/journal/v3 ... 218a0.html

MOLECULAR replication, a fundamental process of life, has in recent years been the subject of laboratory investigations using simple chemical systems1–10. Whereas the work of Rebek's group4,5 has focused on molecular architectures not known in living systems, self-replicating and template-based self-assembling systems based on nucleotides6–8 are regarded as potential models for exploring the evolution of replicating systems on the early Earth. Previous replicating oligonucleotides have been of the single-stranded, self-complementary type: small oligonucleotide fragments are assembled on a pre-existing template and linked to form an exact copy of the template. This process cannot easily be reiterated, however, because of the strong binding of the newly formed strand to the original template. Furthermore, DNA replication in living systems operates by complementarity rather than self-complementarity—each newly assembled strand is complementary to, rather than identical to, its template—and the replication process starts and finishes with double helices. Here we report the self-replication of palindromic (symmetrical) duplex DNA-like oligonucleotides, 24 monomers long, in the absence of enzymes by means of a cycle that transfers information from template to copy and is potentially capable of extension to include non-symmetrical sequences, selection and mutation. Replication proceeds by a chemical process involving the formation of an intermediate triplex structure, and is sequence-selective in the sense that mismatches impair its efficiency. These results indicate that DNA-like double-helical molecules can replicate without assistance from proteins, a finding that may be relevant both to the appearance of replicating systems on the early Earth and to the development of new approaches to DNA amplification.

http://www.springerlink.com/content/72ulpx8362t840n7/

Sea ice occurs abundantly at the polar caps of the Earth and, probably, of many other planets. Its static and dynamic properties that may be important for prebiotic and early biotic reactions are described. It concentrates substrates and has many features that are important for catalytical actions. We propose that it provided optimal conditions for the early replication of nucleic acids and the RNA world. We repeated a famous prebiotic experiment, the poly-uridylic acid-instructed synthesis of polyadenylic acid from adenylic acid imidazolides in artificial sea ice, simulating the dynamic variability of real sea ice by cyclic temperature variation. Poly(A) was obtained in high yield and reached nucleotide chain lengths up to 400 containing predominantly 3′→ 5′ linkages.

Try the fossil record

please show how the fossil record evidences macro-evolution.

Concordance with phylogeny.

then several cases of speciation

speciation is NOT macro-evolution. learn this.

acroevolution is a scale of analysis of evolution in separated gene pools.[1] Macroevolutionary studies focus on change that occurs at or above the level of species, in contrast with microevolution,[2] which refers to smaller evolutionary changes (typically described as changes in allele frequencies) within a species or population.

Show me organisms that exist above the species level, what part of new species formed by speciation, with time form new clades do you not understand? I hypothesized you would come up with this blatant attempt at apologetics, an attempt at goalpost shifting and an attempt to formulate a strawman that evolution doesn't propose, and then attempt to assert that said strawman somehow affects the validity of evolution.

Duplicitious lying of the most mendacious order, stuff yourself, please.

including Diane Dodd and Drosophila pseudoobscuraHeliconus heurippa and Hyla versicolor

that is speciacion, not macro-evolution.

More blatant fuckwittery and goalpost shifting, and lying, well done you.

and , off the top of my head, macroevolution is evolution at the species level, cause it is at the species level at best all organisms exist, microevolution occurs within populations of species.

your above examples of fruit flies etc. fail to present empirical evidence of macro-evolution.... wanna try again ??

More fuckwittery, more lying.

Ignorant bullshit, read the literature and come back, and trying to indulge in goalpost shifting by redefining macroevolution doesn't count, here's a hint, check wikipedia first for the definition of macroevolution.

I've done so. epic fail so far to provide hard empirical evidence of evolution on species level.

Speciation is the evolutionary process by which new biological species arise

http://en.wikipedia.org/wiki/Speciation

Lying again...

What objective standard do you use to assert fine tuning? is there an unfine tuned or a fine untuned universe which you no of to show the difference "design" makes?

you may have a study of the odds of a fine untuned universe, and then we talk. Your effort of credulity must be really overwhelming.... the finetuning of the universe is the strongest evidence for theism.

The more parsimonious explanation when dealing with our localized quantum fluctuations is that it is just one of many.

False dichotomy, chance and design aren't the only options, in fact, even with stochastic processes , there are variables involved which still follow basic, unaided natural processes.

which one ? please present them

The ability of the components necessary for life to be formed under prebiotic conditions, formulated based on the persistent physical evidence such conditions leave behind, is something that is currently under research, and Dr.Szostak's work is quite significant in this regard, among the work of many others, again, abiogenesis research is a field that still demands scientific rigour in testing postulates empirically, something that creotards don't get, don't understand, and never make an effort to do so when screaming "Goddidit, the babble says it"

you can struggle as much as you want. Abiogenesis is a lost case for atheists :

http://www.epm.org/resources/2010/Mar/1 ... t-exist-w/

To sum up the evolutionary dilemma: Even if the physical impossibility of forming and gathering the necessary physical building blocks of a cell were overcome, it would still require information. And it would still require a ‘language.” And it would need to immediately form a copying mechanism. Looking at it from a different angle, you need a cell to create a DNA molecule. But you need DNA to create a cell. What is required to create DNA and cells is information arising from intelligence. Which brings us back to the Biblical model. to sum up the evolutionary dilemma: even if the physical impossibility of forming and gathering the necessary physical building blocks of a cell were overcome, it would still require information. and it would still require a ‘language.” and it would need to immediately form a copying mechanism. looking at it from a different angle, you need a cell to create a DNA molecule. But you need DNA to create a cell. what is required to create DNA and cells is information arising from intelligence. which brings us back to the biblical model.

Fail, see the papers I already posted.

With respect to evolution, populations of real living organisms have been observed evolving in real time.

That is called micro-evolution. No creationist will defy this fact. Thats the only part of the theory of evolution, which can be called a fact.

Bullshit assertion, read the fucking literature first.

i've done so. prove me wrong.

You've presented absolutely bugger all evidence for having done so.

What scientists actually postulate, and they postulate this with respect to every observable phenomenon in the universe, is that well defined and testable mechanisms are responsible. Mechanisms that are amenable to empirical test and understanding, and in many cases, amenable to the development of a quantitative theory. Two such quantitative theories, namely general relativity and quantum electrodynamics, are in accord with observational reality to fifteen decimal places. As an aside, when someone can point to an instance of mythology producing something this useful, the critical thinkers will sit up and take notice, and not before.

I have not seen you here, postulating a other mechanism, than chance, to explain the existence of the universe, its fine-tuning to life, and abiogenesis. Wanna try again ? i give you a hint. It might be physical need ? you can try this one....

1) Quantum inflation

quantum inflation is a epic fail to explain the origin of our universe.

http://elshamah.heavenforum.com/astrono ... ns-t65.htm

"The recent use of such vacuum fluctuations is highly misleading. For virtual particles do not literally come into existence spontaneously out of nothing. Rather the energy locked up in a vacuum fluctuates spontaneously in such a way as to convert into evanescent particles that return almost immediately to the vacuum. As John Barrow and Frank Tipler comment, ". . . the modern picture of the quantum vacuum differs radically from the classical and everyday meaning of a vacuum-- nothing. . . . The quantum vacuum (or vacuua, as there can exist many) states . . . are defined simply as local, or global, energy minima (V'(O)= O, V"(O)>O)" ([1986], p. 440). The microstructure of the quantum vacuum is a sea of continually forming and dissolving particles which borrow energy from the vacuum for their brief existence. A quantum vacuum is thus far from nothing, and vacuum fluctuations do not constitute an exception to the principle that whatever begins to exist has a cause."

"In the case of quantum events, there are any number of physically necessary conditions that must obtain for such an event to occur, and yet these conditions are not jointly sufficient for the occurrence of the event. (They are jointly sufficient in the sense that they are all the conditions one needs for the event's occurrence, but they are not sufficient in the sense that they guarantee the occurrence of the event.) The appearance of a particle in a quantum vacuum may thus be said to be spontaneous, but cannot be properly said to be absolutely uncaused, since it has many physically necessary conditions. To be uncaused in the relevant sense of an absolute beginning, an existent must lack any non-logical necessary or sufficient conditions whatsoever."

"As Barrow and Tipler comment, "It is, of course, somewhat inappropriate to call the origin of a bubble Universe in a fluctuation of the vacuum 'creation ex nihilo,' for the quantum mechanical vacuum state has a rich structure which resides in a previously existing substratum of space-time, either Minkowski or de Sitter space-time. Clearly, a true 'creation ex nihilo' would be the spontaneous generation of everything--space-time, the quantum mechanical vacuum, matter--at some time in the past."([1986], p. 441)."

No evidence presented, quelle surprise, and no one said that the universe is creation ex-nihilo, so another strawman, quelle surprise again/

2) Life is fine-tuned to the universe by evolution

when we come to the hard questions, the light weight answers of atheists become VERY obvious, and their unreasonable faith construct becomes obvious as well.

we have simply BETTER explanations on hand for our universe, and that is evident for any honest rational thinker.

Better in what way? No evidence for designer means no evidence for design, deal with it, asserting something is better does not make it so.

The universe is finely tuned to permit life on our planet. Over 120 fine tune constants are know up to know, and as more time pasts, more are discovered. This might be due to chance, to physical need, or to design. Chance is a very bad explanation. Some advocate a Multiverse. But to have just one life permitting universe, you need 1 to 10^500 attempts to get it done. Thats a 1 with 500 zeros. If we put it in comparison, that in our universe, there exist around 10^80 atoms, this shows how improbable it is, that a Multiverse could explain finetuning. Beside this, the Multiverse argument does not explain away God. A mechanism needs to be in place to trigger these multiverses. It could not be by physical need, since if so, why are there many planets, which are not life permitting, but our is ? So its best explained by design. Our earth/solar/moon system is a very strong evidence. Our solar system is embedded at the right position in our galaxy, neither too close, nor too far from the center of the galaxy. Its also the only location, which alouds us to explore the universe, In a other location, and we would not see more than stellar clouds. The earth has the right distance from the sun, and so has the moon from the earth. The size of the moon, and the earth, is the right one. Our planet has the needed minerals, and water. It has the right atmosphere, and a ozon protecting mantle. Jupiter attracts all asteroids , avoiding these to fall to the earth, and make life impossible. The earths magnetic field protects us from the deadly rays of the sun. The velocity of rotation of the earth is just right. And so is the axial tilt of the earth. Beside this, volcano activities, earth quakes, the size of the crust of the earth, and more over 70 different paramenters must be just right. To believe, all these are just right by chance, needs a big leap of faith. This is indeed maibe the strongest argument for theism.

The sheer number of stars and galaxies in the universe make that probability, that these conditions are due to sheer dumb combination of factors close to certainty, no evidence presented and your discoursive elision is duly noted.

3) Chemical reactions, none of the three are chance, get that? They're driven by well defined natural processes.

to produce life, you need carbon molecules.

Carbon is a product of fusion in stars, and can be disseminated by supernovae, no magic required.

http://elshamah.heavenforum.com/astronomy-cosmology-and-god-f15/the-fine-tune-constants-close-examination-one-by-one-t191.htm

Lee Smolin (a world-class physicist and a leader in quantum gravity) estimates that if the physical constants of the universe were chosen randomly, the epistemic-probability of ending up with a world with carbon chemistry is less than one part in 10^220.

If chance was not the driving factor to produce carbon molecules, what other factor do you suggest ????

Fusion is not chance.

1. God created a finite universe
2. Nothing was the origin of our universe. It simply popped up into existence from absolutely nothing.
3. The universe never began to exist, but existed always in some form or the other.

You think those are testable and well defined natural mechanisms?

you completely miss the point. why do you think we need testable and well defined natural mechanisms to figure out, what explanation fits and explains best our existence ??

Without evidence , any explanation would have to be considered valid, and thus they answer nothing.

Failed assumption that everything needs an external cause, check out the Casimir effect for instance, where something arises from what, in conventional physics is "nothing" , in other words, for matter to be generated, NO external magic is required.

epic fail as shown above. the weakness of your position continues evident.

The generation of matter doesn't require an external agency, what part of that do you still not get? it is funny that you should continue to blabber on blithely, if YOU postulate a first cause, YOU must show it is necessary, and in the case of our localized region of the Universe, there is NO indication that a knob jockey was required.

but i will rebut it with a different quote :

http://elshamah.heavenforum.com/astrono ... ns-t65.htm

In 1973, Edward Tryon suggested that our universe might originate from the quantum fluctuation. This requires extremely accurate cancellation between matter energy and gravitational energy. If the matter energy is just slightly (within 1 part in 1050) greater than the gravitational energy, the uncertainty principle would dictate the matter to disappear in a time period that is too short to have any physical meaning. For such gigantic fluctuation to occur spontaneously is almost impossible.

wanna try again ?

Serial trials fallacy.

Who the fuck suggested String theory is the only explanation for the Universe? This is yet more mendacity trying to portray science as speculation, again, it must be noted that the String theory is more appropriately a mathematical model.

then please present another model which seems reasonable to you.

There are many, ranging from Guth's inflationary models to M-theory to Steinhardt and Turok's derivation thereof, again you are using extant hypotheses to target all of science, mendacity indeed.

If an alternative isn't presented to bullshit, bullshit becomes true? Weird logic.

ah, ok. So you stick to the " we don't know yet " escape ?? well, that is not new to me, either.

It is not an escape, it is called being honest, and if you hadn't noticed before it is integral to scientific research, but then, why would anyone expect liars for doctrine to understand the concept of intellectual honesty?

DNA itself is an evolvable entity, and to try and use Popper's relatively ancient assertions in the light of modern evidence to try and refute the latter is a blatant piece of mendacity.

Bullshit.

http://elshamah.heavenforum.com/origin- ... r-t287.htm

Fundamental Law 1 (FL1)

A purely material entity, such as physicochemical processes, cannot create a nonmaterial entity. (Something material cannot create something nonmaterial.)

Physical entities include mass and energy (matter). Examples of something that is not material (nonmaterial entity) include thought, spirit, and volition (will).

Fundamental Law 2 (FL2)

Information is a nonmaterial fundamental entity and not a property of matter.
The information recorded on a CD is nonmaterial. If you weigh a modern blank CD, fill it with information, and weigh it again, the two weights will be the same. Likewise, erasing the information on the CD has no effect on the weight.
The same information can be transmitted on a CD, a book, a whiteboard, or using smoke signals. This means the information is independent of the material source. A material object is required to store information, but the information is not part of the material object. Much like people in an airplane are being stored and transferred in the plane, they are not part of the physical plane.
The first law of thermodynamics makes it clear that mass and energy (matter) can neither be created nor destroyed. All mass and energy in the universe is being conserved (the total sum is constant). However, someone can write a new complicated formula on a whiteboard and then erase the formula. This is a case of creating and destroying information.

Since the first law of thermodynamics states that mass and energy (matter) cannot be created or destroyed, and information (UDI) can be created and destroyed, information (UDI) must be nonmaterial.
The genetic information system is the software of life and, like the symbols in a computer, is purely symbolic and independent of its environment. Of course, the genetic message, when expressed as a sequence of symbols, is nonmaterial but must be recorded in matter and energy.5

Information is a mathematical REPRESENTATION of the extant physical data in a system, learn some basic information theory before you start using it, the "information" in DNA is a representation of material chemistry, just to bitchslap your stupidity I'll bring up a paper showing the evolution of a novel genetic code with a quadruplet coding in-vitro.

The in vivo, genetically programmed incorporation of designer amino acids allows the properties of proteins to be tailored with molecular precision1. The Methanococcus jannaschii tyrosyl-transfer-RNA synthetase–tRNACUA (MjTyrRS–tRNACUA)2, 3 and the Methanosarcina barkeri pyrrolysyl-tRNA synthetase–tRNACUA (MbPylRS–tRNACUA)4, 5, 6 orthogonal pairs have been evolved to incorporate a range of unnatural amino acids in response to the amber codon in Escherichia coli 1, 6, 7. However, the potential of synthetic genetic code expansion is generally limited to the low efficiency incorporation of a single type of unnatural amino acid at a time, because every triplet codon in the universal genetic code is used in encoding the synthesis of the proteome. To encode efficiently many distinct unnatural amino acids into proteins we require blank codons and mutually orthogonal aminoacyl-tRNA synthetase–tRNA pairs that recognize unnatural amino acids and decode the new codons. Here we synthetically evolve an orthogonal ribosome8, 9 (ribo-Q1) that efficiently decodes a series of quadruplet codons and the amber codon, providing several blank codons on an orthogonal messenger RNA, which it specifically translates8. By creating mutually orthogonal aminoacyl-tRNA synthetase–tRNA pairs and combining them with ribo-Q1 we direct the incorporation of distinct unnatural amino acids in response to two of the new blank codons on the orthogonal mRNA. Using this code, we genetically direct the formation of a specific, redox-insensitive, nanoscale protein cross-link by the bio-orthogonal cycloaddition of encoded azide- and alkyne-containing amino acids10. Because the synthetase–tRNA pairs used have been evolved to incorporate numerous unnatural amino acids1, 6, 7, it will be possible to encode more than 200 unnatural amino acid combinations using this approach. As ribo-Q1 independently decodes a series of quadruplet codons, this work provides foundational technologies for the encoded synthesis and synthetic evolution of unnatural polymers in cells.

http://www.nature.com/nature/journal/v4 ... 08817.html

If you read the paper, you'll notice they mutated the 23S peptidyltransferase unit of the ribosome, changing the ribosome meant that the same sequence of DNA which produced a particular protein based on it being read in threes by the normal ribosome would produce something totally different when read by a quadruplet encoding ribosome, in other words, the "information content" of said DNA has been altered by mutated ribosomes in the process, with the new information having a material source, fucking deal with it.

Indeed, Einstein pointed to the nature and origin of symbolic information as one of the profound questions about the world as we know it. He could identify no means by which matter could bestow meaning to symbols. The clear implication is that symbolic information, or language, represents a category of reality distinct from matter and energy.6

First Law of Information (LI1)

Information cannot originate in statistical processes. (Chance plus time cannot create information no matter how many chances or how much time is available.)
There is no known law of nature, no known process, and no known sequence of events which can cause information to originate by itself in matter.7

Second Law of Information (LI2)

Information can only originate from an intelligent sender
Corollary 18
All codes result from an intentional choice and agreement between sender and recipient.

We observe daily a continual input of new information (UDI) from an intelligent source (human beings). At present, on earth, the only new information we have detected being created is from human beings. Careful examination of other systems will determine if there are any other intelligent sources of new UDI.
Corollary 2
Any given chain of information can be traced backward to an intelligent source.
For two people to effectively communicate, there must be some agreement on the language or code that is used.

Bollocks, read the papers on the material mutagenic modification of the "information" in DNA and weep.

Common ancestry for humans and chimps is also strongly supported by 1) Pseudogenes 2)

http://www.trueorigin.org/pseudogenes01.asp

As the function of more pseudogenes is being uncovered by testable and repeatable science, it is evident that these genetic elements, which are copiously spread in the genomes of different organisms, have been created with purpose. The recent finding of insertion hotspots also clarifies how pseudogenes may have appeared to evolutionists as shared mistakes and now invalidates their use in phylogenetic studies.

Pseudogenes are duplicate copies with an absent start codon, insertion hotspots apply to ERVs and not pseudogenes, learn to at least attribute the right features to the right processes.

Chromosome fusion 3) ERV insertions, I hope you'll take the time to read the apposite scientific literature on the subject before continuing with your fuckwitted chain of assertions.

http://www.ideacenter.org/contentmgr/sh ... hp/id/1392

In other words, Miller has to explain why a random chromosomal fusion event which, in our experience ultimately results in offspring with genetic diseases, didn’t result in a genetic disease and was thus advantageous enough to get fixed into the entire population of our ancestors. Given the lack of empirical evidence that random chromosomal fusion events are not disadvantageous, perhaps the presence of a chromosomal fusion event is not good evidence for a Neo-Darwinian history for humans.

Simple reason being that the fusion ostensibly didn't result in any deletion of genetic segments.

Miller may have found good empirical evidence for a chromosomal fusion event. But our experience with mammalian genetics tells us that such a chromosomal aberration could have created a non-viable mutant, or a normal individual who could not produce viable offspring. Thus, Neo-Darwinism has a hard time explaining why such a random fusion event was somehow advantageous.

Robertsonian fusion, a common occurrence, may not have any phenotypic effects, the idea that the fusion itself had to be selected for is a blatant lie too, since Robertsonian fusion may not have any effect on the phenotype.

A Robertsonian translocation in balanced form results in no excess or deficit of genetic material and causes no health difficulties.

http://en.wikipedia.org/wiki/Robertsonian_translocation

A case of a tail in a 2-week-old infant is reported

thats not a tail.

http://www.icr.org/article/evolution-human-tail/

Did you read the fucking paper? INCLUDING the differentiation they themselves make between true tails and pseudotails, and indicate the observed mechanisms behind each? More discoursive elision, dishonesty and lying.

In case anybody can't wait a month for Jireh to come back, he's just appeared on LoR.

http://forums.leagueofreason.co.uk/view ... 82&start=0

A true troll, this one.

Jireh → joint intertubez-related extensible homomeme? Or some other kind of bot?

Jireh wrote:

GenesForLife wrote:
A scientific theory, in case you did not get the memo, is an explanatory framework of scientifically verifiable facts, driven by empirical data, why do I get the impression this is a fuckwitted attempt at the fallacy of equivocation with the layman's meaning of "speculation"?

how can facts, that supposedly happened millions of years ago, be verified by empirical data ?

Crimes without eyewitnesses and or video evidence are unseen, unobservable and in the unrepeatable past, so even if they do leave behind other evidence such as DNA, that says nothing about the truth, ey?

why do you think, so many people have been convicted falsely, just based on evidential data from the past ?

Ah, you do know that the methods used to verify that the original conclusion was wrong is the very methods you are hand-waving away? Rarely, and certainly without consistency or predictability, do the other methods produce reasonable results. They are so bad even proponents don't always rely on them with consistency.

No one suggests that the scientific methods are perfect. Just that they have been shown repeatedly to be the best options we have. Over time their inherent redundancy is far better than the occasionally correct suppositions.

You keep scorning naturalism for the times when has been used incorrectly or shown to be wrong because the naturalist methods didn't have all the information available at the time. It still produces the best results we know how to produce, consistently. Of course, I'm not aware of another system that works to produce knowledge without relying on naturalism methodologies. Please teach us these non-naturalist methods (in other threads though.)

If you do have a better method to propose that adequately incorporates all the knowledge, methodologies and theories we have gathered so, as well as makes predictable and testable results about subjects we do not know conclusively, feel free to explain it. Perhaps in another thread though to leave this one on topic. It will be questioned and discarded by millions until it has be verified as effective. Once we have established its reliability, we can rescind this thread. You or your colleagues will be heroes. A win for everyone!

Awww... I was really hoping to find out about the consistent non-naturalist methodologies. Can't you make exceptions this time?

err... seems I forgot to refresh my browser windows. I only missed by 12-13 hours.

Hi there! I really like this FAQ you made. It's full of good info, but I think I found some things that could do with some updates. I hope you don't mind... Here are some things I have some problems with.

For example, Claude Shannon provided a rigorous treatment of information, but a treatment that was strictly applicable to information transmission, and NOT applicable to information storage.

This is pretty much false. It is totally immaterial if information is being transmitted or stored. One is simply a dynamical notion other one is a statical one. It's still information and it's measured in any way that is valid. The computer storage devices store information in bits, just as Shannon defined them, in the equation –log2p(x). And we can clearly see the amount of data we have as bits, that is – megabytes, which is a measure of Shannon information.

Therefore, application of Shannon information to information storage in the genome is a misuse of Shannon's work.

No it is not, you can use it if you want. There is absolutely no reason not to do so. Unless you want to use some other measure. But Shannon measure is still fine.

The correct information analysis to apply to storage is Kolmogorov's analysis, which erects an entirely different measure of information content that is intended strictly to be applicable to storage.

There is no "correct" measure. We are not dealing here with ultimate truths, we are dealing with descriptions. There are plenty of different measures of information, and yes Kolmogorov complexity is also a valid one. The only thing we should be careful about is which measure to use, becasue differnet measures are applicable to differnet problems.

Ultimately, "information" is nothing more than the observational data that is extant about the current state of a system.

This is one of many different and equally valid definitions, yes.

Turing alighted upon this notion when he wrote his landmark paper on computable numbers, and used the resulting theory to establish that Hilbert's conjecture upon decidability in formal axiomatic systems was false. Of course, it's far easier to visualise the process at work, when one has an entity such as a Turing machine to analyse this - a Turing machine has precise, well-defined states, and precise, well-defined interactions that take place when the machine occupies a given state. But this is precisely what we have with DNA - a system that can exist in a number of well-defined states, whose states determine the nature of the interactions that occur during translation, and which result in different outcomes for different states.

Exactly, and Turing machines are designed, so that should pretty much follow for DNA as well. Shouldn't it?

As for the canard that "mutations cannot produce new information", this is manifestly false. Not only does the above analysis explicitly permit this, the production of new information (in the form of new states occupied by DNA molecules) has been observed taking place in the real world and documented in the relevant scientific literature.

I agree to an extent, but what the real problem actually is, is that information that is being produced is not what is needed for biological evolution. Neither Shannon information, nor Kolmogorov information can account for biological functions. Thus generating Shannon information or Kolmogorov complexity, does not equal generating biological information. What we need is a different type of measure, and that is Functional information. This measure takes into account the functional nature of sequences. That is, it takes into account the fact that only some sequences out of all possible sequences in the sequence space is considered functional. Unlike with Shannon information, were any sequence is considered information, and with Kolmogorov complexity, where the measure is only concerned with the shortest description of a given sequence.

Functional Sequence Complexity requires this added programming dimension of uncoerced selection at successive decision nodes in the string. Shannon information theory measures the relative degrees of RSC and OSC. Shannon information theory cannot measure FSC. FSC is invariably associated with all forms of complex biofunction, including biochemical pathways, cycles, positive and negative feedback regulation, and homeostatic metabolism.

link

Indeed, the extant literature not only covers scientific papers explicitly dealing with information content in the genome, such as Thomas D. Schneider's paper handily entitled Evolution And Biological Information to make your life that bit easier, but also papers on de novo gene origination, of which there are a good number, several of which I have presented here in the past in previous threads.

Indeed. And I would like to point out that Schneider uses Shannon information measure in his paper. Which, contradicts your first claim that it can't be used in biological application. The second thing I would like to point out is that even though his paper is valid, it does not address the evolution of biological functions, obviously because he did not use a measure that can measure biological functions properly.

Царь Славян wrote:Hi there! I really like this FAQ you made. It's full of good info, but I think I found some things that could do with some updates. I hope you don't mind... Here are some things I have some problems with.

Hi, I suppose you are new here? How is your name typed out in English?

Царь Славян wrote:

For example, Claude Shannon provided a rigorous treatment of information, but a treatment that was strictly applicable to information transmission, and NOT applicable to information storage.

This is pretty much false. It is totally immaterial if information is being transmitted or stored. One is simply a dynamical notion other one is a statical one. It's still information and it's measured in any way that is valid. The computer storage devices store information in bits, just as Shannon defined them, in the equation –log2p(x). And we can clearly see the amount of data we have as bits, that is – megabytes, which is a measure of Shannon information.

Shannon information as per the Shannon-Hartley theorem is defined in terms of information entropy during transmission.
firstly, secondly, your equation doesn't have two variables, would you mind completing it?

Having read the paper you linked to later in the post it appears to me you may have committed a significant error, namely that Shannon information and Shannon Uncertainty, as measured by entropy, as far as I know are two different things.

Looking at the Shannon-Hartley Theorem, we have this.

C is the channel capacity in bits per second;
B is the bandwidth of the channel in hertz (passband bandwidth in case of a modulated signal);
S is the total received signal power over the bandwidth (in case of a modulated signal, often denoted C, i.e. modulated carrier), measured in watt or volt2;
N is the total noise or interference power over the bandwidth, measured in watt or volt2; and
S/N is the signal-to-noise ratio (SNR) or the carrier-to-noise ratio (CNR) of the communication signal to the Gaussian noise interference expressed as a linear power ratio (not as logarithmic decibels).

http://en.wikipedia.org/wiki/Shannon%E2 ... ey_theorem

Clearly is a model where one would expect data to be transmitted with noise involved in the transmission. With DNA mutations do not add noise, they change the signal itself assuming that reproduction entails transmission.

Therefore, application of Shannon information to information storage in the genome is a misuse of Shannon's work.

No it is not, you can use it if you want. There is absolutely no reason not to do so. Unless you want to use some other measure. But Shannon measure is still fine.

Considering that there is no transmitter and receiver involved in reproduction, and even if we assume that gamete transfer is transmission mutations still happen a priori I think there is every reason not to use it.
Secondly, you may have noticed that the Creationist Canard that is frequently encountered is "Mutations cannot produce new information at all" and not just "Mutations cannot produce Shannon information"

The correct information analysis to apply to storage is Kolmogorov's analysis, which erects an entirely different measure of information content that is intended strictly to be applicable to storage.

There is no "correct" measure. We are not dealing here with ultimate truths, we are dealing with descriptions. There are plenty of different measures of information, and yes Kolmogorov complexity is also a valid one. The only thing we should be careful about is which measure to use, becasue differnet measures are applicable to differnet problems.

And I contend Kolmogorov information is better suited to DNA.

Ultimately, "information" is nothing more than the observational data that is extant about the current state of a system.

This is one of many different and equally valid definitions, yes.

Skip, no qualms with that.

Turing alighted upon this notion when he wrote his landmark paper on computable numbers, and used the resulting theory to establish that Hilbert's conjecture upon decidability in formal axiomatic systems was false. Of course, it's far easier to visualise the process at work, when one has an entity such as a Turing machine to analyse this - a Turing machine has precise, well-defined states, and precise, well-defined interactions that take place when the machine occupies a given state. But this is precisely what we have with DNA - a system that can exist in a number of well-defined states, whose states determine the nature of the interactions that occur during translation, and which result in different outcomes for different states.

Exactly, and Turing machines are designed, so that should pretty much follow for DNA as well. Shouldn't it?[/quote]

Nope, except that the "information" in DNA is the result of chemistry acting upon it, by mutating the components involved in said chemistry it is possible to arrive at different outputs while using the same DNA sequence as an input, I will produce a relevant post on the demonstrated experimental evidence for this after this post.

As for the canard that "mutations cannot produce new information", this is manifestly false. Not only does the above analysis explicitly permit this, the production of new information (in the form of new states occupied by DNA molecules) has been observed taking place in the real world and documented in the relevant scientific literature.

I agree to an extent, but what the real problem actually is, is that information that is being produced is not what is needed for biological evolution. Neither Shannon information, nor Kolmogorov information can account for biological functions. Thus generating Shannon information or Kolmogorov complexity, does not equal generating biological information. What we need is a different type of measure, and that is Functional information. This measure takes into account the functional nature of sequences. That is, it takes into account the fact that only some sequences out of all possible sequences in the sequence space is considered functional. Unlike with Shannon information, were any sequence is considered information, and with Kolmogorov complexity, where the measure is only concerned with the shortest description of a given sequence.

Skip.

Functional Sequence Complexity requires this added programming dimension of uncoerced selection at successive decision nodes in the string. Shannon information theory measures the relative degrees of RSC and OSC. Shannon information theory cannot measure FSC. FSC is invariably associated with all forms of complex biofunction, including biochemical pathways, cycles, positive and negative feedback regulation, and homeostatic metabolism. link

Indeed, the extant literature not only covers scientific papers explicitly dealing with information content in the genome, such as Thomas D. Schneider's paper handily entitled Evolution And Biological Information to make your life that bit easier, but also papers on de novo gene origination, of which there are a good number, several of which I have presented here in the past in previous threads.

Indeed. And I would like to point out that Schneider uses Shannon information measure in his paper. Which, contradicts your first claim that it can't be used in biological application. The second thing I would like to point out is that even though his paper is valid, it does not address the evolution of biological functions, obviously because he did not use a measure that can measure biological functions properly.

But the evolvability of the genetic code, and the documentation of de-novo functional origination through mutational processes render this irrelevant.

That paper by Abel also appears to be outdated with respect to several claims, and I will bring a few of these up in further posts.

Now onto the origin of "information" in DNA from the interactions of the chemistry acting thereupon.

The "code" is the result of base pairing between tRNA and mRNA, and the binding of amino acid to tRNA, and the catalysis of a bond in between them. And the fact that mutations in the components of the translational machinery lead to the formation of of divergent genetic codes or alter the fundamental nature of the genetic code is empirically and experimentally demonstrated, in other words, shove your assertions back up the same orifice you produced it out off.

And of course, the fact that the illusion of a code written into DNA is due to the nature of the translational machinery and that altering the latter should change the "code" itself is also an evidentially supported fact.

What follows is some snippets from the extant literature that should cover why the genetic code has evolvability and also demonstrate that there is no code inherent to DNA but that any appearance of a code is a function of the translational apparatus that cells use to process their DNA into proteins.

Translation is a function of ribosomal structure and the way it interacts with mRNA, firstly , and secondly the interactions of tRNA with mRNA held in the ribosome, and the interaction of tRNAs with amino acids, which is affected by the action of enzymes called aminoacyl tRNA synthetases.

Changing these parameters allows the "code" to be modified, and since these components are themselves the result of translation and transcription of their respective genes, mutations in the latter will tend to affect the former.

With this in mind we can now look at some of the literature regarding documented examples of mutant codes resulting from mutant components of the translational machinery.

We investigated directed deviations from the universal genetic code. Mutant tRNAs that incorporate cysteine at positions corresponding to the isoleucine AUU, AUC, and AUA and methionine AUG codons were introduced in Escherichia coli K12. Missense mutations at the cysteine catalytic site of thymidylate synthase were systematically crossed with synthetic suppressor tRNACys genes coexpressed from compatible plasmids. Strains harboring complementary codon/anticodon associations could be stably propagated as thymidine prototrophs. A plasmid-encoded tRNACys reading the codon AUA persisted for more than 500 generations in a strain requiring its suppressor activity for thymidylate biosynthesis, but was eliminated from a strain not requiring it. Cysteine miscoding at the codon AUA was also enforced in the active site of amidase, an enzyme found in Helicobacter pylori and not present in wild-type E. coli. Propagating the amidase missense mutation in E. coli with an aliphatic amide as nitrogen source required the overproduction of Cys-tRNA synthetase together with the complementary suppressor tRNACys. The toxicity of cysteine miscoding was low in all our strains. The small size and amphiphilic character of this amino acid may render it acceptable as a replacement at most protein positions and thus apt to overcome the steric and polar constraints that limit evolution of the genetic code.

http://www.genetics.org/cgi/content/full/150/2/543

In this case, they used mutant tRNAs to encode cysteine instead of isoleucine and methionine, they noted that the inclusion of cysteine instead of the other amino acids was not deleterious because of the nature of the amino acid.
But that is rather superfluous to requirements here, the important thing to note is that mutant tRNAs can cause different amino acids to be incorporated for the same codon on mRNA, they had therefore, by mutation and artificial selection, evolved a new codon assignment, in other words, they'd fundamentally changed the genetic code by evolution.

At this juncture I would also like to cite/present another paper, showing that such an approach is applicable to other amino acids too, in this case Tyrosine.

Abstract.

A unique transfer RNA (tRNA)/aminoacyl-tRNA synthetase pair has been generated that expands the number of genetically encoded amino acids in Escherichia coli. When introduced into E. coli, this pair leads to the in vivo incorporation of the synthetic amino acid O-methyl-L-tyrosine into protein in response to an amber nonsense codon. The fidelity of translation is greater than 99%, as determined by analysis of dihydrofolate reductase containing the
unnatural amino acid. This approach should provide a general method for increasing the genetic repertoire of living cells to include a variety of amino acids with novel structural, chemical, and physical properties not found in the
common 20 amino acids.

The abstract and the full paper can be found here at http://uregina.ca/suhdaey/courses/04%20 ... 20coli.pdf

In this particular case, they chose to reconfigure a stop codon (UAG) into one that would code for Tyrosine.
I now move on to quote what in my opinion are the relevant (to this discussion) snippets of the paper.

What follows is an example of sheer scientific elegance in ensuring that the new modified code was orthogonal (i.e did not affect the translation of the native genetic code in E.coli) and building in selectability.

An orthogonal tRNA/synthetase pair in E.coli can be generated by importing a pair from a different organism if cross-species aminoacylation is inefficient and the anticodon loop is not a key determinant of synthetase recognition. One such candidate pair is the tyrosyl tRNA/synthetase pair of Methanococcus jannaschii, an archaebacterium
whose tRNATyr identity elements differ from those of E. coli tRNATyr (in particular, the first base pair of the acceptor stem is GC in E.coli and CG in M. jannaschii), and whose tyrosyl-tRNA synthetase (TyrRS) has only a minimalist anticodon loop binding domain (13). In addition, the M. jannaschii TyrRS does not have an editing mechanism (14)
and, therefore, should not proofread an unnatural amino acid ligated to the tRNA. We have shown that the M. jannaschii TyrRS efficiently aminoacylates an amber suppressor tRNA derived from its cognate tRNATyr (15), but does not aminoacylate E. coli tRNAs (13). Moreover, the M. jannaschiit RNA Tyr CUA is a poor substrate for the E. coli synthetases but functions efficiently in protein translation in E. coli (15).

[1] The problem of orthogonality was solved by importing the tRNA that carries tyrosine and the coresponding aminoacyl tRNA synthetase pair from the bacterial species Methanococcus jannaschii

[2] This choice was made due to two primary reasons, one - the elements that the synthetase uses to identify the amino acid was different to the one the synthetase present in E.coli uses. In other words, the E.coli native synthetase would not recognize the tRNA from Methanococcus and two- that the said synthetase has minimal interactions with the anticodon loop, which means it could still recognize the tRNA for Tyrosine and attach the amino acid to it. Just to help you grasp the work being discussed you may refer to the diagram of tRNA below.



The anticodon arm binds to mRNA by complementary base pairing, in this case, they had to reconfigure said mRNA by
altering the anticodon loop on the Tyrosine tRNA such that it bound to the amber codon on mRNA instead of the native codon for Tyrosine, and this is where the importance of the second reason becomes apparent.

[3] They subjected these to mutation and selection and evolved the new codon assignment, the method of selection they used follows below.

To further reduce recognition of the M. jannaschii tRNA Tyr CUA by E. coli synthetases, 11 nucleotides of the tRNA that do not interact directly with the M. jannaschii TyrRS (C16, C17, U17a, U20, C32, G37, A38, U45, U47, A59, and U60) were randomly mutated to generate a suppressor tRNA library. This tRNA library
was passed through a negative selection (suppression of amber mutations in the barnase gene), which removes tRNAs that are aminoacylated by E. coli synthetases, and then a positive selection for tRNAs that are efficiently
aminoacylated by M. jannaschii TyrRS (suppression of amber mutations in the b-lactamase gene)

So they generated a library of mutants, which is akin to a gene pool of mutant alleles. They then had two methods they employed for selection.

[1] the expression of barnase is lethal to the cell in the absence of barstar, so whether this is expressed or not can be used for purifying selection. These researchers eliminated those mutant tRNAs that were bound to amino acids by E.coli synthetases (if an amber mutation is suppressed by such activity it would trigger the expression of fully functional barnase and all bacterial colonies that contained that particular gene would go kaput, in other words, non orthologonality was eliminated, and we were left with just those mutant tRNAs which would only react with the imports from M.jannaschii

[2] the expression of beta lactamase would enable bacteria to survive and proliferate in the presence of Beta-lactam antibiotics such as Penicillin. Here, they chose tRNAs that had passed the first round of selection to see if they'd incorporate an amino acid when they met an amber stop codon in a gene for beta lactamase which had a nonsense mutation somewhere in the middle. (in other words, we were now looking at reconfiguring a codon which incorporated nothing previously such that it incorporated an amino acid, allowing the fully functional beta lactamase enzyme to be produced.

Those that were successfully tagged with amino acids by the imported aminoacyl tRNA synthetase allowed their carriers to reproduce. This led to the selection of a set of mutant tRNA/tRNA synthetase pairs that were both orthogonal and capable of introducing amino acids instead of the stop codon.

The following bit leads us to the conclusion they found.

Aminoacylation of a transformed suppressor tRNA by any endogenous E. coli synthetase results in cell growth in the presence of ampicillin. E. coli transformed with the M. jannaschii tRNACUATyr and
pBLAM survive at 55 ug/ml ampicillin.

When the best mutant suppressor tRNA (mutRNACUATyr ) selected from the library was
expressed (17), cells survive at only 12 ug/ml ampicillin; similar values are obtained in the absence of any suppressor tRNA. When the M. jannaschii TyrRS is coexpressed with this mutRNACUA Tyr , cells survive at 440 ug/ml ampicillin.

ug = (Mu)g = Micrograms, just thought I should make that clear.

Just expressing the mutant tRNA alone resulted in an extremely low treshold for survival in the presence of ampicillin, and this was no more than the survival if the amber mutation were not suppressed, in other words, the native synthetases from E.coli had no effect (no codon reconfiguration in other words)

Adding both the imported synthetase and the best mutant tRNA they selected from the library led to dose tolerance that was 36 times higher, in other words, reconfiguration successful, new codon assignment successfully evolved.

The paper then goes on to describe the incorporation of unnatural amino acids, but I'll let the discerning reader figure it out themselves

I also said I would illustrate how modifying the ribosome can change the genetic code. I will let Chin et al do the job.

The abstract follows...

The in vivo, genetically programmed incorporation of designer amino acids allows the properties of proteins to be tailored with molecular precision1. The Methanococcus jannaschii tyrosyl-transfer-RNA synthetase–tRNACUA (MjTyrRS–tRNACUA)2, 3 and the Methanosarcina barkeri pyrrolysyl-tRNA synthetase–tRNACUA (MbPylRS–tRNACUA)4, 5, 6 orthogonal pairs have been evolved to incorporate a range of unnatural amino acids in response to the amber codon in Escherichia coli 1, 6, 7. However, the potential of synthetic genetic code expansion is generally limited to the low efficiency incorporation of a single type of unnatural amino acid at a time, because every triplet codon in the universal genetic code is used in encoding the synthesis of the proteome. To encode efficiently many distinct unnatural amino acids into proteins we require blank codons and mutually orthogonal aminoacyl-tRNA synthetase–tRNA pairs that recognize unnatural amino acids and decode the new codons. Here we synthetically evolve an orthogonal ribosome8, 9 (ribo-Q1) that efficiently decodes a series of quadruplet codons and the amber codon, providing several blank codons on an orthogonal messenger RNA, which it specifically translates8. By creating mutually orthogonal aminoacyl-tRNA synthetase–tRNA pairs and combining them with ribo-Q1 we direct the incorporation of distinct unnatural amino acids in response to two of the new blank codons on the orthogonal mRNA. Using this code, we genetically direct the formation of a specific, redox-insensitive, nanoscale protein cross-link by the bio-orthogonal cycloaddition of encoded azide- and alkyne-containing amino acids10. Because the synthetase–tRNA pairs used have been evolved to incorporate numerous unnatural amino acids1, 6, 7, it will be possible to encode more than 200 unnatural amino acid combinations using this approach. As ribo-Q1 independently decodes a series of quadruplet codons, this work provides foundational technologies for the encoded synthesis and synthetic evolution of unnatural polymers in cells.

They developed new orthogonal ribosomes through mutations such that they read in fours instead of threes, firstly, and followed it up by adding two unnatural amino acids to the newly evolved quadruplet code using the new blank codons that were generated. They now have loads of codons to work with just by changing the nature of the code, and they are heralding a new era in synthetic biology where we can write stuff into the genome without affecting any of the native translation of the recipient cells.

The full paper is indeed available for this and I would encourage the discerning reader to read this, and the link is
http://ase.tufts.edu/chemistry/kumar/jc ... n_2010.pdf

Empirical demonstrations of the evolvability of the genetic code, without a mind directing said changes. Just mutation and selection. (the selection here was artificial because they were applying it with a specific purpose in mind, therefore they chose to determine which mutant genetic code would survive.

we have seen evidence that

[1] Mutating the peptidyltransferase subunit of ribosomes as in the work of Chin et al leads to codons being read in fours instead of threes.
[2] Mutant tRNAs incorporate different amino acids even when the same codon assignment is maintained, by virtue of mutability of the chemistry of the interactions of the binding of amino acids with tRNA and their synthetase enzymes.
[3] Mutant tRNAs can incorporate an amino acid in response to another codon assignment.

Let us come to Abel's paper now.

RNA chemistry is extremely challenging in a prebiotic context. Ribonucleotides are difficult to activate (charge). And even oligoribonucleotides are extremely hard to form, especially without templating. The maximum length of such single strands in solution is usually only eight to ten monomers (mers).

No, this is an outdated assertion.

Abstract

The synthesis of RNA chains from 3′,5′-cAMP and 3′,5′-cGMP was observed. The RNA chains formed in water, at moderate temperatures (40–90 °C), in the absence of enzymes or inorganic catalysts. As determined by RNase analyses, the bonds formed were canonical 3′,5′-phosphodiester bonds. The polymerizations are based on two reactions not previously described: 1) oligomerization of 3′, 5′-cGMP to ∼25-nucleotide-long RNA molecules, and of 3′,5′-cAMP to 4- to 8-nucleotide-long molecules. Oligonucleotide A molecules were further extended by reciprocal terminal ligation to yield RNA molecules up to >120 nucleotides long and 2) chain extension by terminal ligation of newly polymerized products of 3′,5′-cGMP on preformed oligonucleotides. The enzyme- and template-independent synthesis of long oligomers in water from prebiotically affordable precursors approaches the concept of spontaneous generation of (pre)genetic information.

http://www.jbc.org/content/284/48/33206.short?rss=1

Little empirical evidence exists to contradict the contention that untemplated sequencing is dynamically inert (physically arbitrary). We are accustomed to thinking in terms of base-pairing complementarity determining sequencing. It is only in researching the pre-RNA world that the problem of single-stranded metabolically functional sequencing of ribonucleotides (or their analogs) becomes acute. And of course highly-ordered templated sequencing of RNA strands on natural surfaces such as clay offers no explanation for biofunctional sequencing. The question is never answered, "From what source did the template derive its functional information?" In fact, no empirical evidence has been presented of a naturally occurring inorganic template that contains anything more than combinatorial uncertainty. No bridge has been established between combinatorial uncertainty and utility of any kind.

[1] 8 - 10 again? Outdated claim but I will give him the benefit of doubt given it is an old paper.
[2] No bridge? I think such a bridge for an inorganic template is not necessitated anymore, the evidence refuting [1] also does away with requirements for an inorganic template.

Biopolymeric messenger molecules were instructing biofunction not only long before Homo sapiens existed, but also long before metazoans existed. Many eubacteria and archaea depend upon nearly 3,000 highly coordinated genes. Genes are linear, digital, cybernetic sequences. They are meaningful, pragmatic, physically instantiated recipes.
One of the requirements of any semantic/semiotic system is that the selection of alphanumeric characters/units be "arbitrary"[47]. This implies that they must be contingent and independent of causal determinism. Pattee [72-74] and Rocha [58] refer to this arbitrariness of sequencing as being "dynamically inert." "Arbitrary" does not mean in this context "random," but rather "unconstrained by necessity." Contingent means that events could occur in multiple ways. The result could just as easily have been otherwise. Unit selection at each locus in the string is unconstrained. The laws of physics and chemistry apply equally to whatever sequencing occurs. The situation is analogous to flipping a "fair coin." Even though the heads and tails side of the coin are physically different, the outcome of the coin toss is unrelated to dynamical causation. A heads result (rather than a tails) is contingent, unconstrained by initial conditions or law.

Yes, point being? Any assertions about complexity often fail to take into account the Mullerian two-step for the evolution of Irreducible Complexity.

In the rest of the paper he argues that biological functions need to be specified and cannot emerge through purely stochastic processes, I argue that they can.

Our current understanding of biology suggests that early life relied predominantly on RNA for catalysis and replication. Here, we report the isolation of an RNA polymerase ribozyme called B6.61 that exhibits superior extension and fidelity relative to its progenitor, the Round-18 polymerase. The B6.61 polymerase was selected from a mutagenized pool containing ∼ 9 × 1014 sequence variants through the use of a novel large-scale in vitro compartmentalization system. B6.61 polymerized all tested primer–template (PT) complexes faster than the Round-18 variant. For one PT, B6.61 exhibited dramatically faster elongation past one full helical turn and incorporated at least 20 nucleotides of sequence, setting a new extension record for an RNA polymerase ribozyme. The increased efficiency of the B6.61 construct was related to improvements in fidelity, with the new variant incorporating less incorrect wobble base pairs than its parent. This new polymerase demonstrates the feasibility of evolving an artificial RNA replicase ribozyme in the foreseeable future.

http://rnajournal.cshlp.org/content/13/7/1017.full
Evolved function there.

An indispensable step in protein biosynthesis is the 2′(3′) aminoacylation of tRNA by aminoacyl-tRNA synthetases. Here we show that a similar activity exists in a tiny, 5-nt-long RNA enzyme with a 3-nt active center. The small ribozyme initially trans-phenylalanylates a partially complementary 4-nt RNA selectively at its terminal 2′-ribose hydroxyl using PheAMP, the natural form for activated amino acid. The initial 2′ Phe-RNA product can be elaborated into multiple peptidyl-RNAs. Reactions do not require divalent cations, and have limited dependence on monovalent cations. Small size and minimal requirements for regiospecific translational activity strongly support the hypothesis that minuscule RNA enzymes participated in early forms of translation.

http://www.pnas.org/content/early/2010/02/12/0912895107

And there, just to name two instances.

No empirical or rational basis exists for granting to chemistry non-dynamic capabilities of functional sequencing. Naturalistic science has always sought to reduce chemistry to nothing more than dynamics. In such a context, chemistry cannot explain a sequencing phenomenon that is dynamically inert. If, on the other hand, chemistry possesses some metaphysical (beyond physical; beyond dynamics) transcendence over dynamics, then chemistry becomes philosophy/religion rather than naturalistic science. But if chemistry determined functional sequencing dynamically, sequences would have such high order and high redundancy that genes could not begin to carry the extraordinary prescriptive information that they carry.

And this assertion in the paper is [1] Uncited [2] Evidentially unsupported.

Algorithms are processes or procedures that produce a needed result, whether it is computation or the end-products of biochemical pathways. Such strings of decision-node selections are anything but random. And they are not "self-ordered" by redundant cause-and-effect necessity. Every successive nucleotide is a quaternary "switch setting." Many nucleotide selections in the string are not critical. But those switch-settings that determine folding, especially, are highly "meaningful." Functional switch-setting sequences are produced only by uncoerced selection pressure. There is a cybernetic aspect of life processes that is directly analogous to that of computer programming. More attention should be focused on the reality and mechanisms of selection at the decision-node level of biological algorithms. This is the level of covalent bonding in primary structure. Environmental selection occurs at the level of post-computational halting. The fittest already-computed phenotype is selected.

Nope, the fitness landscape necessarily isn't one peaked, selection works by eliminating lethal mutants.

We can hypothesize that metabolism "just happened," independent of directions, in a prebiotic environment billions of years ago. But we can hypothesize anything. The question is whether such hypotheses are plausible. Plausibility is often eliminated when probabilities exceed the "universal probability bound" [132]. The stochastic "self-organization" of even the simplest biochemical pathways is statistically prohibitive by hundreds of orders of magnitude.

Without algorithmic programming to constrain (more properly "control") options, the number of possible paths in sequence space for each needed biopolymer is enormous. 1015 molecules are often present in one test tube library of stochastic ensembles. But when multiple biopolymers must all converge at the same place at the same time to collectively interact in a controlled biochemically cooperative manner, faith in "self-organization" becomes "blind belief." No empirical data or rational scientific basis exists for such a metaphysical leap.

And he makes no references to where biologists actually propose this strawman caricature where the whole of metabolism just popped into place. But yes, there is substantial evidence to suggest that there are ribozymes that can carry out functions such as peptide bond formation et cetera, there are self replicating ribozymes, there are translational ribozymes of a very small length. I close this post with

Abstract

A main unsolved problem in the RNA World scenario for the origin of life is how a template-dependent RNA polymerase ribozyme emerged from short RNA oligomers obtained by random polymerization on mineral surfaces. A number of computational studies have shown that the structural repertoire yielded by that process is dominated by topologically simple structures, notably hairpin-like ones. A fraction of these could display RNA ligase activity and catalyze the assembly of larger, eventually functional RNA molecules retaining their previous modular structure: molecular complexity increases but template replication is absent. This allows us to build up a stepwise model of ligation-based, modular evolution that could pave the way to the emergence of a ribozyme with RNA replicase activity, step at which information-driven Darwinian evolution would be triggered.

http://rnajournal.cshlp.org/content/ear ... na.1488609

and

The RNA world hypothesis regarding the early evolution of life relies on the premise that some RNA sequences can catalyze RNA replication. In support of this conjecture, we describe here an RNA molecule that catalyzes the type of polymerization needed for RNA replication. The ribozyme uses nucleoside triphosphates and the coding information of an RNA template to extend an RNA primer by the successive addition of up to 14 nucleotides—more than a complete turn of an RNA helix. Its polymerization activity is general in terms of the sequence and the length of the primer and template RNAs, provided that the 3′ terminus of the primer pairs with the template. Its polymerization is also quite accurate: when primers extended by 11 nucleotides were cloned and sequenced, 1088 of 1100 sequenced nucleotides matched the template.

full paper at http://citeseerx.ist.psu.edu/viewdoc/do ... 1&type=pdf

Hi, I suppose you are new here? How is your name typed out in English?

Well hello there. My name would be "King of The Slavs" in English. A quick look at google translator makes wonders!

Shannon information as per the Shannon-Hartley theorem is defined in terms of information entropy during transmission.
firstly, secondly, your equation doesn't have two variables, would you mind completing it?

Here we have the complete equation from Shannon himself.

Having read the paper you linked to later in the post it appears to me you may have committed a significant error, namely that Shannon information and Shannon Uncertainty, as measured by entropy, as far as I know are two different things.

I'm sorry but those two are considered the same.

In information theory, entropy is a measure of the uncertainty associated with a random variable. In this context, the term usually refers to the Shannon entropy, which quantifies the expected value of the information contained in a message, usually in units such as bits. Equivalently, the Shannon entropy is a measure of the average information content one is missing when one does not know the value of the random variable. The concept was introduced by Claude E. Shannon in his 1948 paper "A Mathematical Theory of Communication".

link

Looking at the Shannon-Hartley Theorem, we have this.[/quote]

Clearly is a model where one would expect data to be transmitted with noise involved in the transmission. With DNA mutations do not add noise, they change the signal itself assuming that reproduction entails transmission.

Okay, but the point I made is that it's measured in bits. Whatever is happening with that information it's measured in bits, and it does not matter if it is standing still or being transmitted, it's still meaasured in bits in the same way.

Oh, and yes, the reproduction process is not perfect, so noise does arise. Mutations can decrease, increase or modify the gentic content, leading to noise.

Considering that there is no transmitter and receiver involved in reproduction, and even if we assume that gamete transfer is transmission mutations still happen a priori I think there is every reason not to use it.

But there is a transmitter and receiver. The parent is the transmitter and the offspring is the receiver. The same would be the case in ERV's transmission of it's own genetic material to another species.

Secondly, you may have noticed that the Creationist Canard that is frequently encountered is "Mutations cannot produce new information at all" and not just "Mutations cannot produce Shannon information"

Well that would be their idea, not mine...

And I contend Kolmogorov information is better suited to DNA.

Depending on what you want to measure.

Nope, except that the "information" in DNA is the result of chemistry acting upon it, by mutating the components involved in said chemistry it is possible to arrive at different outputs while using the same DNA sequence as an input, I will produce a relevant post on the demonstrated experimental evidence for this after this post.

More generally, they are results of mechanical actions and physical electric interactions, right? Well, yeah, so are turing machines, i.e. computers. And they were most certainly designed. So yeah, it would seem we have an analogy here, and it should follow that they are both designed.

But the evolvability of the genetic code, and the documentation of de-novo functional origination through mutational processes render this irrelevant.

Not really it simply means that there is a certain amount of information that can be inputed into the genome of living organisms by outside forces. There is nothing wrong with that. That does not in any way contradict the fact that biological information can not be properlly measured with Shannon information. Let me give you an example.

If we have a 10 bit string of 0 and 1, and ascribe functions to only some of them we would have 10 bits of information according to Shannon for every single sequence. Which means that "0000000000", "1111111111" and "1011100110" all have 10 bits of Shannon information since they are 10 bits long.

Now let's take a look at teh original paper on FSC, and see the equation for measuring it.


link

Let's asign a function to let's say 100 sequences of all possible sequences. Their Ex = 1, and all other sequences have Ex = 0. Also, all the possible sequences that can be produced with 10 bits, which is 10^2, is 1024 sequences. This would now mean that some sequences will not have any corresponding function. Which means that only some sequences are considered to have functional information. Only those 100 sequences that have Ex = 1. So all other sequences (924 of them), have Ex = 0, thus having no functional information.

Let's say that a sequence "1011100110", has a function and the sequence "1111010100" has none. We would measure information like this, according to the FSC description. For the first sequence since it's Ex = 1 it would be:

-log2[100/1024] = 3,356 bits.

And for the other one, it's Ex = 0, thus it's FSC is 0.

As you can see, there is only about 3,356 bits, and 0 bits for the second sequence, while with Shannon information, there would be 10 bits for every sequence.

This description corresponds well to biological information, because not all sequences of DNA have a biological function, thus FSC is well suited to be a mesure of biological complexity.

That paper by Abel also appears to be outdated with respect to several claims, and I will bring a few of these up in further posts.

Please do.

More generally, they are results of mechanical actions and physical electric interactions, right? Well, yeah, so are turing machines, i.e. computers. And they were most certainly designed. So yeah, it would seem we have an analogy here, and it should follow that they are both designed.

Mechanical actions? since when did chemistry become a matter of solely mechanical actions? The analogy fails when we talk about Turing machines et cetera, since there is direct evidence of humans building these Turing machines, otherwise the analogy would still fail given that there is no rigorous method for the verification of design.

And I disagree when you say mutations involve transmission from parent to offspring, the offspring don't exist until purported transmission through reproduction is complete. In other words you cannot transmit to a receiver that only starts existing after the message has been received without involving storage until the latter happens, but since DNA is a storage molecule itself briging in transmission here is rather superfluous to requirements.

Also, mutations do not add noise in the process of purported transmission during reproduction, because these mutations happen prior to reproduction. Reproduction is an imperfect process because the imperfections are introduced through mutations before it occurs.

Now onto the origin of "information" in DNA from the interactions of the chemistry acting thereupon.

The "code" is the result of base pairing between tRNA and mRNA, and the binding of amino acid to tRNA, and the catalysis of a bond in between them. And the fact that mutations in the components of the translational machinery lead to the formation of of divergent genetic codes or alter the fundamental nature of the genetic code is empirically and experimentally demonstrated, in other words, shove your assertions back up the same orifice you produced it out off.

And of course, the fact that the illusion of a code written into DNA is due to the nature of the translational machinery and that altering the latter should change the "code" itself is also an evidentially supported fact.

What follows is some snippets from the extant literature that should cover why the genetic code has evolvability and also demonstrate that there is no code inherent to DNA but that any appearance of a code is a function of the translational apparatus that cells use to process their DNA into proteins.

Translation is a function of ribosomal structure and the way it interacts with mRNA, firstly , and secondly the interactions of tRNA with mRNA held in the ribosome, and the interaction of tRNAs with amino acids, which is affected by the action of enzymes called aminoacyl tRNA synthetases.

Changing these parameters allows the "code" to be modified, and since these components are themselves the result of translation and transcription of their respective genes, mutations in the latter will tend to affect the former.

With this in mind we can now look at some of the literature regarding documented examples of mutant codes resulting from mutant components of the translational machinery.

Actually I agree with everything you said. The only thing you seem to fail to notice is that the same thing applies to computers. The code they understand is nothing more than a bunch of electrical and mechanical interactions. Which yes, can be changed. Just look at how differently Macs, and any other computer like the old Spectrum might interpret the same bit string. It's all due to their programming, which is just a different configuration of their mechanical parts. And, yes both Macs and Spectrums were designed.

In this case, they used mutant tRNAs to encode cysteine instead of isoleucine and methionine, they noted that the inclusion of cysteine instead of the other amino acids was not deleterious because of the nature of the amino acid.
But that is rather superfluous to requirements here, the important thing to note is that mutant tRNAs can cause different amino acids to be incorporated for the same codon on mRNA, they had therefore, by mutation and artificial selection, evolved a new codon assignment, in other words, they'd fundamentally changed the genetic code by evolution.

At this juncture I would also like to cite/present another paper, showing that such an approach is applicable to other amino acids too, in this case Tyrosine.

Great paper. It clearly shows how people, ie. Intelligent agents, can manipulate the genetic code.

The abstract and the full paper can be found here at http://uregina.ca/suhdaey/courses/04%20 ... 20coli.pdf

In this particular case, they chose to reconfigure a stop codon (UAG) into one that would code for Tyrosine.
I now move on to quote what in my opinion are the relevant (to this discussion) snippets of the paper.

What follows is an example of sheer scientific elegance in ensuring that the new modified code was orthogonal (i.e did not affect the translation of the native genetic code in E.coli) and building in selectability.

Again, a great paper, showing how scientist, ie. Intelligent agents can modify teh genetic code as they see fit.

[1] The problem of orthogonality was solved by importing the tRNA that carries tyrosine and the coresponding aminoacyl tRNA synthetase pair from the bacterial species Methanococcus jannaschii

[2] This choice was made due to two primary reasons, one - the elements that the synthetase uses to identify the amino acid was different to the one the synthetase present in E.coli uses. In other words, the E.coli native synthetase would not recognize the tRNA from Methanococcus and two- that the said synthetase has minimal interactions with the anticodon loop, which means it could still recognize the tRNA for Tyrosine and attach the amino acid to it. Just to help you grasp the work being discussed you may refer to the diagram of tRNA below.
The anticodon arm binds to mRNA by complementary base pairing, in this case, they had to reconfigure said mRNA by altering the anticodon loop on the Tyrosine tRNA such that it bound to the amber codon on mRNA instead of the native codon for Tyrosine, and this is where the importance of the second reason becomes apparent.

[3] They subjected these to mutation and selection and evolved the new codon assignment, the method of selection they used follows below.

So, you are saying that they intelligently manipulated, that is, they intelligently selected the specific codons? Yes, I would have thought so. A pretty nice example of what intelligent agents can do.

So they generated a library of mutants, which is akin to a gene pool of mutant alleles. They then had two methods they employed for selection.

[1] the expression of barnase is lethal to the cell in the absence of barstar, so whether this is expressed or not can be used for purifying selection. These researchers eliminated those mutant tRNAs that were bound to amino acids by E.coli synthetases (if an amber mutation is suppressed by such activity it would trigger the expression of fully functional barnase and all bacterial colonies that contained that particular gene would go kaput, in other words, non orthologonality was eliminated, and we were left with just those mutant tRNAs which would only react with the imports from M.jannaschii

[2] the expression of beta lactamase would enable bacteria to survive and proliferate in the presence of Beta-lactam antibiotics such as Penicillin. Here, they chose tRNAs that had passed the first round of selection to see if they'd incorporate an amino acid when they met an amber stop codon in a gene for beta lactamase which had a nonsense mutation somewhere in the middle. (in other words, we were now looking at reconfiguring a codon which incorporated nothing previously such that it incorporated an amino acid, allowing the fully functional beta lactamase enzyme to be produced.

Those that were successfully tagged with amino acids by the imported aminoacyl tRNA synthetase allowed their carriers to reproduce. This led to the selection of a set of mutant tRNA/tRNA synthetase pairs that were both orthogonal and capable of introducing amino acids instead of the stop codon.

The following bit leads us to the conclusion they found.

A perfect example of an intelligent agency producing the final design from it's starting idea. They wanted to produce the different populations with different allele frequencies, and for that they used their intelligent to select those individuals that were most fit.

ug = (Mu)g = Micrograms, just thought I should make that clear.

Just expressing the mutant tRNA alone resulted in an extremely low treshold for survival in the presence of ampicillin, and this was no more than the survival if the amber mutation were not suppressed, in other words, the native synthetases from E.coli had no effect (no codon reconfiguration in other words)

Adding both the imported synthetase and the best mutant tRNA they selected from the library led to dose tolerance that was 36 times higher, in other words, reconfiguration successful, new codon assignment successfully evolved.

The paper then goes on to describe the incorporation of unnatural amino acids, but I'll let the discerning reader figure it out themselves

I also said I would illustrate how modifying the ribosome can change the genetic code. I will let Chin et al do the job.

The abstract follows...

Yes it did evolve. It was ntelligently evelved, which is a great example of intelligent design and what it can produce.

They developed new orthogonal ribosomes through mutations such that they read in fours instead of threes, firstly, and followed it up by adding two unnatural amino acids to the newly evolved quadruplet code using the new blank codons that were generated. They now have loads of codons to work with just by changing the nature of the code, and they are heralding a new era in synthetic biology where we can write stuff into the genome without affecting any of the native translation of the recipient cells.

The full paper is indeed available for this and I would encourage the discerning reader to read this, and the link is
http://ase.tufts.edu/chemistry/kumar/jc ... n_2010.pdf

Empirical demonstrations of the evolvability of the genetic code, without a mind directing said changes. Just mutation and selection. (the selection here was artificial because they were applying it with a specific purpose in mind, therefore they chose to determine which mutant genetic code would survive.

Excuse me but no, the mind was present all the time. The mind of the scientists that did the selection. They are the ones that were intelligently selecting/designing the outcome.

we have seen evidence that

[1] Mutating the peptidyltransferase subunit of ribosomes as in the work of Chin et al leads to codons being read in fours instead of threes.
[2] Mutant tRNAs incorporate different amino acids even when the same codon assignment is maintained, by virtue of mutability of the chemistry of the interactions of the binding of amino acids with tRNA and their synthetase enzymes.
[3] Mutant tRNAs can incorporate an amino acid in response to another codon assignment.

I totally agree, and all of those eveidence was produced by intelligently selecting them.

Since when did Macs and spectrums begin to reproduce? Or mutate stochastically?