Intelligent Design, the best explanation of Origins

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Some questions for Atheists

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1 Some questions for Atheists on Fri Jan 06, 2017 8:27 am

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Some questions for Atheists

http://reasonandscience.heavenforum.org/t2408-some-questions-for-atheists

How can a proponent of philosophical naturalism provide a better worldview based on naturalism/strong atheism over a proponent of creationism / intelligent design ?  Anyone trying to explain the origin of our reality has to take into account following points :

1. What caused the universe to exist?
2. The universe works orderly based on physical laws.
3. The original conditions of the universe, the fundamental forces, our galaxy, and the earth are finely tuned to permit life. How comes?
4. Stars and planets exist
5. Life exists
6. Cells are complex factories, full of molecular machines, and assembly lines.
7. Cells use various codes and hierarchical levels of information, based on complex hardware/information processing machines ( computers )
8. Genes have two layers of codes and information
9. DNA has the highest information storage density physically  possible
10. Cells use metabolic pathways and literally manufacturing and production assembly lines
11. Cells are interdependent and irreducible complex ( a minimal genome, proteome, and metabolome size is required to give life a first go )
12. Cells are self-replicating
13. Cells have error detection and check mechanisms
14. Cells require homeostasis
15. There are 3 domains of life and the virus world. Biological cells and viruses are interdependent. There would be no viruses without life, and vice-versa
16. There is consciousness
17. There are objective moral values
18. Language, logic, reasoning, free will, and moral values are not grounded in physics.
19. How did DNA and amino acids arise?
20. How do irreducibly complex enzyme chains evolve?
21. How do we account for the origin of 116 distinct language families?
22. Why did cities suddenly appear all over the world between 3,000 and 1,000BC?
23. How is independent thought possible in a world ruled by chance and necessity?
24. How do we account for self-awareness?
25. How is free will possible in a material universe?
26. How do we account for conscience?
27. On what basis can we make moral judgments?
28. Why does suffering matter?
29. Why do human beings matter?
30. Why care about justice?
31. How do we account for the almost universal belief in the supernatural?
32. What is the evidence that the natural world is all there is?
33. How can we know if there is no conscious existence after death?
34. What accounts for the empty tomb, resurrection appearances, and growth of the church?
35. Is the Bible just fiction?



How do these facts support naturalism / strong atheism?

Creationism / ID is false, therefore, (strong) atheism is true.   This is one of the most frequent logical fallacies of atheists/skeptics/agnostics etc. That is called affirmative conclusion from a negative premise  This illicit negative occurs when a categorical syllogism has a positive conclusion, but one or two negative premises. Atheists must be able to present and adopt a well-articulated, thorough-going positive worldview based on positive evidence that results in good reasons to infer naturalism. What the debater must present, is a positive case for strong atheism by reference to the evidence that favors a naturalistic interpretation of reality. Asking to provide positive, compelling evidence that points to the fact that the natural world can have an origin on its own, is not the same as to ask for evidence that God does not exist. If atheists are going to argue that adequate answers exist without the need for God, they are at least going to have to provide sufficient reasons and explanations.

If we held the position that no deities are needed and that adequate answers exist based on natural causes on their own, without the need of a God, we are at least going to have to provide sufficient positive compelling explanations based on philosophical naturalism.  Some things happen because of an intelligent agency, some things don't.  Materialists don't believe in agency at all. So, how can this view be backed up rationally?  

This view implies that we need good answers of how absolutely nothing magically can turn into a Big Bang and a life-supporting universe and create the physical laws simultaneously, or if we propose that the universe is eternal in any kind of form, like a multiverse, oscillating universe etc. , and had no beginning;  how we can reach the present and now from eternity. If we add one event after the other starting now, whenever we stop, the timelapse will always be a defined timespan. How can we then reach now from ( past ) eternity by adding one event after the other? Furthermore, we have to explain how the second law of thermodynamics would be overcome. Since useful energy winds down, and the universe exists from eternity, we would have reached maximum entropy, and the universe would be in a state of heat death.

Then, its required that we  give good reasons of how random unguided forces  finetuned successfully the expansion of the Big Bang out of 10^55 attempts and possibilities ( that's a 10 with 55 zeroes ), the four fundamental forces like gravity, which strength  is finely tuned to a precision of  one of 14 billion billion billion settings, and hundreds of physical parameters, and the conditions to permit life on earth. It's not that life adapted to the universe. The parameters had to be finely tuned right from the start;  If not, no universe could exist at all.  How can life emerge from non-life and produce cells ?

The cell is an interdependent functional city. We state, “The cell is the most detailed and concentrated organizational structure known to humanity. It is a lively microcosmic city, with factories for making building supplies, packaging centers for transporting the supplies, trucks that move the materials along highways, communication devices, hospitals for repairing injuries, a massive library of information, power stations providing usable energy, garbage removal, walls for protection and city gates for allowing certain materials to come and go from the cell.” The notion of the theoretical first cell arising by natural causes is a perfect example of irreducible complexity. Life cannot exist without many numerous interdependent complex systems, each irreducibly complex on their own, working together to bring about a grand pageant for life to exist.

How could cells emerge through unguided, accidental random events, and luck was able to create  the storage device of information in DNA, transcription and translation machinery inside cells, invent an optimal genetic code, better and committing less errors  than one million alternatives, a translation system ( a genetic cipher, that equals to translation from English to Chinese ) , an incalculable amount of precise instructions to create the first  self-replicating cell with a minimal number of precisely dimensioned and fitting parts, precise energy supply where needed for various chemical reactions, a error check and repair system all along the cellular processes, and  millions of amazingly diverse species with the ability to evolve and adapt to the environment, and explain the emergence of conscient intelligent minds from inanimate  matter. Furthermore, we have to give good reasons why it could be justified in exceptional circumstances to torture, rape and kill little babies for fun. If we can't, we would grant that absolute, objective moral values exist. Since they are prescriptive, we would have to grant the existence of a moral giver or moral code prescriber above us.

We can also not afford us to commit the logical fallacy to make affirmative conclusions based on a negative premise. This illicit negative occurs when a categorical syllogism has a positive conclusion, but one or two negative premises. We need to be able to present and adopt a well-articulated, thorough-going positive worldview based on positive evidence that results in good reasons to infer naturalism. What we have to present, is a positive case for  strong atheism by reference to the evidence that favors a naturalistic interpretation of reality. Asking to provide positive, compelling evidence that points to the fact that the natural world can have an origin on its own, is not the same as to ask for evidence that God does not exist. If we are going to argue that adequate answers exist without the need for a creative intelligent powerful agency with a will, we are at least going to have to provide sufficient naturalistic explanations.

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2 Re: Some questions for Atheists on Mon Nov 20, 2017 3:36 am

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1. No idea what caused the universe to exist, but I don't have to know. We haven't developed a decernable method to determine the causation of the universe, if it is a universe. That said, the "big bang" or expansion is the best model so far, as it does account for many phenomena we observe within the observable limits of the universe.


The Kalaam Cosmological Argument

http://reasonandscience.heavenforum.org/t1333-the-kalaam-cosmological-argument

The Kalam Cosmological Argument
(1) Everything that has a beginning of its existence has a cause of its existence.
(2) The universe has a beginning of its existence.
Therefore:
(3) The universe has a cause of its existence.
(4) If the universe has a cause of its existence then that cause is God.
Therefore:
(5) God exists.

Some try to substitute God as first cause by claiming that energy was always there, eternally, stored in a singularity, and caused the universe into being by a quantum fluctuation event. Planck regarded matter/energy as derivative from consciousness. What would be the contrary? Consciousness derivative from energy. If it were so, over an unknown length of time, energy would have become cognitive and self-aware, even learning the how's and why's of becoming other perceivable forms. It would gain  perception, thinking, free will, moral judgment, and memory.  Einstein recognized the absurdity of this claim. He  described the "gulf' that logically separates the concrete world of hard objects on the one hand from the abstract world of ideas on the other. A small part of the materialists problem is that hard objects are never observed spontaneously to transform themselves (on their own recognizance) into abstract ideas.

W.L.Craig writes : 
The only way to have an eternal cause but a temporal effect would seem to be if the cause is a personal agent who freely chooses to create an effect in time. For example, a man sitting from eternity may will to stand up; hence, a temporal effect may arise from an eternally existing agent. Indeed, the agent may will from eternity to create a temporal effect, so that no change in the agent need be conceived. Thus, we are brought not merely to the first cause of the universe, but to its personal Creator.

Only the God of the Bible is described with the following characteristics:
• Supernatural in nature (as He exists outside of His creation)
• Incredibly powerful (to have created all that is known)
• Eternal (self-existent, as He exists outside of time and space)
• Omnipresent (He created space and is not limited by it)
• Timeless and changeless (He created time)
• Immaterial (because He transcends space)
• Personal (the impersonal can’t create personality)
• Necessary (as everything else depends on Him)
• Infinite and singular (as you cannot have two infinites)
• Diverse yet has unity (as all multiplicity implies a prior singularity)
• Intelligent (supremely, to create everything)
• Purposeful (as He deliberately created everything)
• Moral (no moral law can exist without a lawgiver)
• Caring (or no moral laws would have been given)

The universe requires a cause because it had a beginning … God, unlike the universe, had no beginning, so doesn’t need a cause. In addition, Einstein’s general relativity, which has much experimental support, shows that time is linked to matter and space. So time itself would have begun along with matter and space. Since God, by definition, is the creator of the whole universe, he is the creator of time. Therefore He is not limited by the time dimension He created, so has no beginning in time.

Therefore, The God of the Bible fits the description of the cause and infers that He exists and is the best explanation of the cause of the universe.



2. Laws in physics are not the same as political laws. There isn't a library that scientists visit to check out various laws on the universe, such are determined through observation and reverse engineering, sort of. We determine these laws, the same way someone would determine the laws of a nation by merely observing the actions and consequences of the actions. This isn't 100% acurate and updates are made to these laws when it can be demonstrated as necessary.


Laws of Physics, where did they come from? 

http://reasonandscience.heavenforum.org/t1336-laws-of-physics-where-did-they-come-from

The physical universe and the laws of physics are interdependent and irreducible. There would not be one without the other. Origins make only sense in face of Intelligent Design.

"The naive view implies that the universe suddenly came into existence and found a complete system of physical laws waiting to be obeyed. Actually, it seems more natural to suppose that the physical universe and the laws of physics are interdependent." —*WH. McCrea, "Cosmology after Half a Century," Science, Vol. 160, June 1968, p. 1297.

Paul Davies: The universe obeys mathematical laws; they are like a hidden subtext in nature. Science reveals that there is a coherent scheme of things, but scientists do not necessarily interpret that as evidence for meaning or purpose in the universe.

The only rational explanation is however that God created this coherent scheme of things since there is no other alternative explanation. That's why atheists rather than admit that, prefer to argue of " not knowing " of its cause.  

The following quotations from Einstein are all in Jammer’s book 2:
“Every scientist becomes convinced that the laws of nature manifest the existence of a spirit vastly superior to that of men.”
“Everyone who is seriously involved in the pursuit of science becomes convinced that a spirit is manifest in the laws of the universe – a spirit vastly superior to that of man.”
“The divine reveals itself in the physical world.”
“My God created laws… His universe is not ruled by wishful thinking but by immutable laws.”
“I want to know how God created this world. I want to know his thoughts.”
“What I am really interested in knowing is whether God could have created the world in a different way.”
“This firm belief in a superior mind that reveals itself in the world of experience, represents my conception of God.”
“My religiosity consists of a humble admiration of the infinitely superior spirit, …That superior reasoning power forms my idea of God.”

The argument of the supervision of order
1. We find in nature many laws like the law of gravitation, the laws of motion, the laws of thermodynamics.
2. Just as in any state, the government or the king makes different laws and supervises their subjects that the laws are carried out, so the laws of nature had to be generated and supervised by some intelligent being.
3. So, for everything that happens according to those laws there has to be a supervisor or controller.
4. Man can create small laws and control limited things in his domain, but nature’s grand laws had to be created by a big brain, an extraordinarily powerful person who can supervise that those laws are carried out.
5. Such an extraordinary, omnipotent person can be only God.
6. Hence, God exists.

The argument of the nature of established laws
1. Physical or scientific law is a scientific generalization based on empirical observations of physical behavior. Law is defined in the following ways:
a. Absolute. Nothing in the universe appears to affect them. (Davies, 1992:82)
b. Stable. They are unchanged since they were first discovered (although they may have been shown to be approximations of more accurate laws).
c. Omnipotent. Everything in the universe apparently must comply with them (according to observations). (Davies, 1992:83)
2. Some of the examples of scientific or nature’s laws are:
a. The law of relativity by Einstein.
b. The four laws of thermodynamics.
c. The laws of conservation of energy.
d. The uncertainty principle etc.
e. Biological laws
i. Life is based on cells.
ii. All life has genes.
iii. All life occurs through biochemistry.
iv. Mendelian inheritance.
f. Conservation Laws.
i. Noether's theorem.
ii. Conservation of mass.
iii. Conservation of energy, momentum and angular momentum.
iv. Conservation of charge .
3. Einstein said that the laws already exist, man just discovers them.
4. Only an omnipotent, absolute eternal person can give absolute, stable and omnipotent laws for the whole universe.
5. That person all men call God.
6. Hence God exists.


3. What original conditions? According to scientific study, the younger universe was far harsher than it is today. Further, this planet is fairly lethal to life, in fact most species that have ever lived have died in this planet. Even fuether, this planet is the only one in our solar system to have observable life so far, that is 1/8, hardly "fine tuning."

Fine-tuning of the  fundamental forces of the universe

http://reasonandscience.heavenforum.org/t1339-fine-tuning-of-the-fundamental-forces-of-the-universe

Faber, a professor at the University of California, Santa Cruz, was referring to the idea that there is something uncannily perfect about our universe. The laws of physics and the values of physical constants seem, as Goldilocks said, “just right.” If even one of a host of physical properties of the universe had been different, stars, planets, and galaxies would never have formed. Life would have been all but impossible.

Take, for instance, the neutron. It is 1.00137841870 times heavier than the proton, which is what allows it to decay into a proton, electron and neutrino—a process that determined the relative abundances of hydrogen and helium after the big bang and gave us a universe dominated by hydrogen. If the neutron-to-proton mass ratio were even slightly different, we would be living in a very different universe: one, perhaps, with far too much helium, in which stars would have burned out too quickly for life to evolve, or one in which protons decayed into neutrons rather than the other way around, leaving the universe without atoms. So, in fact, we wouldn’t be living here at all—we wouldn’t exist.



Examples of such “fine-tuning” abound. Tweak the charge on an electron, for instance, or change the strength of the gravitational force or the strong nuclear force just a smidgen, and the universe would look very different, and likely be lifeless. The challenge for physicists is explaining why such physical parameters are what they are.

This challenge became even tougher in the late 1990s when astronomers discovered dark energy, the little-understood energy thought to be driving the accelerating expansion of our universe. All attempts to use known laws of physics to calculate the expected value of this energy lead to answers that are 10120 times too high, causing some to label it the worst prediction in physics.

“The great mystery is not why there is dark energy. The great mystery is why there is so little of it,” said Leonard Susskind of Stanford University, at a 2007 meeting of the American Association for the Advancement of Science. “The fact that we are just on the knife edge of existence, [that] if dark energy were very much bigger we wouldn’t be here, that’s the mystery.” Even a slightly larger value of dark energy would have caused spacetime to expand so fast that galaxies wouldn’t have formed.

That night in Hawaii, Faber declared that there were only two possible explanations for fine-tuning. “One is that there is a God and that God made it that way,” she said. But for Faber, an atheist, divine intervention is not the answer.

“The only other approach that makes any sense is to argue that there really is an infinite, or a very big, ensemble of universes out there and we are in one,” she said.

This ensemble would be the multiverse. In a multiverse, the laws of physics and the values of physical parameters like dark energy would be different in each universe, each the outcome of some random pull on the cosmic slot machine. We just happened to luck into a universe that is conducive to life. After all, if our corner of the multiverse were hostile to life, Faber and I wouldn’t be around to ponder these questions under stars.

This “anthropic principle” infuriates many physicists, for it implies that we cannot really explain our universe from first principles. “It’s an argument that sometimes I find distasteful, from a personal perspective,” says Lawrence Krauss of Arizona State University in Tempe, Arizona, author of A Universe From Nothing. “I’d like to be able to understand why the universe is the way it is, without resorting to this randomness.”

And he’s not the only one who feels this way. Nobel laureate Steven Weinberg of the University of Texas at Austin once told me, “I would, and most physicists would, prefer not to have to rely on anything like the anthropic principle, but actually to be able to calculate things.”

http://www.pbs.org/wgbh/nova/physics/blog/2012/03/is-the-universe-fine-tuned-for-life/



Is the universe hostile to life ?

http://reasonandscience.heavenforum.org/t1896-is-the-universe-hostile-to-life

http://www.reasonablefaith.org/is-the-universe-hostile-to-life

The fact to be explained is why the universe is life-permitting rather than life-prohibiting. That is to say, scientists have been surprised to discover that in order for embodied, interactive life to evolve anywhere at all in the universe, the fundamental constants and quantities of nature have to be fine-tuned to an incomprehensible precision. Were even one of these constants or quantities to be slightly altered, the universe would not permit the existence of embodied, interactive life anywhere in the cosmos. These finely-tuned conditions are necessary conditions of life in a universe governed by the present laws of nature. it would be obtuse to think that the universe is not life-permitting because regions of the universe are not life-permitting!

If the expansion rate of the universe were not finely adjusted, our universe would not exist.

http://www.focus.org.uk/lennox.php

A H Guth ‘Inflationary Universe,’ Physical Review, D, 23, 1981, p. 348.

an alteration in the ratio of the expansion and contraction forces by as little as 1 part in 1055 at the Planck time (just 10-43 seconds after the origin of the universe), would have led either to too rapid expansion of the universe with no galaxies forming or to too slow an expansion with consequent rapid collapse.

http://home.earthlink.net/~almoritz/cosmological-arguments-god.htm

It should be obvious by now that the fine-tuning argument holds in the relation to the universe as a whole, and is not meant to address the question of why you cannot live on the sun or breathe on the moon. Of course sources of energy (stars) are needed to drive life and evolution, and of course you cannot live on them. Nor can you live in the, by necessity, frighteningly large stretches of empty space between them and planets. So what is the point? Nobody would deny that the light bulb is an invention that greatly enhances modern life. But when you would try to hold your hand around a light bulb that is turned on, you would burn it to pieces. Is the light bulb then "hostile to life"? Certainly not. This modest example, however, indicates how utterly irrelevant the argument really is – one of those false arguments that appear to be brought forth and rehashed solely in order to avoid the deeper issues.


4. Stars and planets exist due to the gravitaional pull of atoms, and that the more mass there is in a confined space, the more other masses will be attracted to it.

Stellar evolution and the problem of the ‘first’ stars

http://reasonandscience.heavenforum.org/t1922-chronology-and-timeline-of-origins-of-the-universe-life-and-biodiversity-the-lack-of-explanatory-power-open-questions-and-refuted-claims-of-naturalism

Fred Hoyle, The Intelligent Universe, London, 1984, p. 184-185
The big bang theory holds that the universe began with a single explosion. Yet as can be seen below, an explosion merely throws matter apart, while the big bang has mysteriously produced the opposite effect–with matter clumping together in the form of galaxies.

Through a process not really understood, astronomers think that stars form from clouds of gas. Early in the universe, stars supposedly formed much more rapidly than they do today, though the reason for this isn’t understood either. Astronomers really don’t know how stars form, and there are physical reasons why star formation cannot easily happen. 1)
According to proponents of naturalism, the first chemical elements heavier than hydrogen, helium and lithium formed in nuclear reactions at the centres of the first stars. Later, when these stars exhausted their fuel of hydrogen and helium, they exploded as supernovas, throwing out the heavier elements. These elements, after being transformed in more generations of stars, eventually formed asteroids, moons and planets. But, how did those first stars of hydrogen and helium form? Star formation is perhaps the weakest link in stellar evolution theory and modern big bang cosmology. Especially problematic is the formation of the first stars—Population III stars as they are called.

There were no dust grains or heavy molecules in the primordial gas to assist with cloud condensation and cooling, and form the first stars. (Evolutionists now believe that molecular hydrogen may have played a role, in spite of the fact that molecular H almost certainly requires a surface—i.e. dust grains—to form.) Thus, the story of star formation in stellar evolution theory begins with a process that astronomers cannot observe operating in nature today. 2)

Neither hydrogen nor helium in outer space would clump together. In fact, there is no gas on earth that clumps together either. Gas pushes apart; it does not push together. Separated atoms of hydrogen and/or helium would be even less likely to clump together in outer space.

Because gas in outer space does not clump, the gas could not build enough mutual gravity to bring it together. And if it cannot clump together, it cannot form itself into stars. The idea of gas pushing itself together in outer space to form stars is more scienceless fiction. Fog, whether on earth or in space, cannot push itself into balls. Once together, a star maintains its gravity quite well, but there is no way for nature to produce one. Getting it together in the first place is the problem. Gas floating in a vacuum cannot form itself into stars. Once a star exists, it will absorb gas into it by gravitational attraction. But before the star exists, gas will not push itself together and form a star—or a planet, or anything else. Since both hydrogen and helium are gases, they are good at spreading out, but not at clumping together. 

"Attempts to explain both the expansion of the universe and the condensation of galaxies must be largely contradictory so long as gravitation is the only force field under consideration. For if the expansive kinetic energy of matter is adequate to give universal expansion against the gravitational field, it is adequate to prevent local condensation under gravity, and vice versa. That is why, essentially, the formation of galaxies is passed over with little comment in most systems of cosmology.

"—*F. Hoyle and *T. Gold, quoted in *D.B. Larson, Universe in Motion (1984). p. 8.


Harwit’s research dealt with the mathematical likelihood that hydrogen atoms could stick together and form tiny grains of several atoms, by the random sticking of interstellar atoms and molecules to a single nucleus as they passed by at a variable speed. Using the most favorable conditions and the maximum possible sticking ability for grains, Harwit determined that the amount of time needed for gas or other particles to clump together into a size of just a hundred-thousandth of a centimeter in radius—would take about 3 billion years! Using more likely rates, 20 billion years would be required—to produce one tiny grain of matter stuck together out in space. As with nearly all scientists quoted in our (*M. Harwit, Astrophysical Concepts, 1973, p. 394).



5. Life does exist, how is this a problem? Unless you admit that the universe isn't fine tuned, this making #3 a useless question.


Abiogenesis is impossible

HOW DID LIFE BEGIN?

Did life originate in what Darwin envisaged as a “warm little pond,” perhaps a tidal pool repeatedly dried and refreshed? Or might life be rooted among hydrothermal vents? Could life’s origins even lie beyond Earth? 6

The origin of life stands as one of science’s deepest and most challenging questions. It is a historical problem that emerged during a time with little-recorded history, so it must be approached mostly through theory and experiment— imaginative efforts to re-create our planet’s early conditions and establish plausible chemical routes to the emergence of life. The goal of understanding life’s beginnings has attracted scientists from geology and from many overlapping disciplines, especially subfields of organic chemistry and molecular biology. In an age of planetary exploration, the origin of life is also an astrobiological issue, currently investigated on Mars, where a sedimentary record of earliest planetary history is preserved, and potentially across the wider stretch of Universe where planets have been detected. Some of the most fundamental mysteries about the origin of life are geological in nature: From what materials did life originate? When, where, and in what form did life first appear? At its most basic physical level, life is a chemical phenomenon, and because it arose billions of years ago, geologists are intensely interested in creating an accurate picture of the chemical building blocks available to early life.

Louis Pasteur, Darwin’s great Parisian contemporary, went a step further. Pasteur decisively refuted the doctrine of spontaneous generation, the long-held view that life can arise de novo from nonliving materials, declaring instead, that life springs always from life (Pasteur, 1922- 1939).

Essential to our understanding of how life emerged from prebiotic chemicals is accurate knowledge of the kinds of catalysts present in the environment. A catalyst is a substance that increases the speed of a chemical reaction, often dramatically. In every cell, the complex and coordinated chemical reactions that support life require the action of catalysts, usually enzymatic proteins. Many prebiotic reactions require catalysts as well, not only to support energy-yielding reactions but also to permit the synthesis of the long-chain molecules such as nucleic acids and proteins that make up living systems. Some of the most essential catalysts used in experimental approaches to prebiotic
chemistry are metal ions, which coordinate chemical reactions in developing metabolism, and mineral surfaces, which provide templates and catalysis in synthesizing biopolymers.

By chance? - Not a chance !!

http://reasonandscience.heavenforum.org/t1279-abiogenesis-is-impossible

Single proteins do not have any function on their own unless interconnected correctly in a living cell. In order for life to begin naturally, all essential proteins required for life to start would have had to emerge randomly on a prebiotic earth, protein super-complexes like ribosomes would have had to join the subparts together to get the right protein-protein interactions, like lock and key. A miracle would have had to prevent them to be burned by UV radiation. Then start to interconnect in the correct order to create a functional metabolic network and multi-protein production lines , where the joint venture of several enzymes began to produce functional products, hand them over to carrier mechanisms, tag them in order to be transported to the right locations. Somehow, all this would have had to begin in a protected environment, so a protective envelope would have had to exist. That envelope had to emerge fully functional with " gates " that permit the right materials in, and the waste product out. 

Once the data storage system (DNA) emerged, a language based on a code system had to be established, and the blueprint to store the information to make all parts of the cell had to be stored within it, and DNA replication errors had to be reduced 10.000.000.000 times. 

Let's suppose that a self-replicating RNA molecule would appear miraculously on early earth.  that does not explain the origin of the information to make all life essential parts in the cell.
It is as to go just from a hard drive storage device to a self replicating factory with the ability of self replication of the entire factory once ready, to respond to changing environmental demands and regulate its metabolic pathways, regulate and coordinate all cellular processes, such as molecule and building block biosynthesis according to the cells demands, depending on growth, and other factors.

The ability of uptake of nutrients, to be structured, internally compartmentalized and organized, being able to check replication errors and minimize them, and react to stimuli, and changing environments. That's is, the ability to adapt to the environment is a must right from the beginning.

If just ONE single protein or enzyme - of many - is missing, no life. If topoisomerase II or helicase are missing - no replication - no perpetuation of life.


Somehow, that envelope had to create a homeostatic environment, diminishing the calcium concentration in the cell 10000 times below the external environment, to permit signaling. At the same time, a signaling code would have had to be established, and immediately begin to function, with a common agreement between sender and receiver................energy supply would have been a major problem, since almost all life forms depend on the supply of glucose, which is a product of complex metabolic pathways, and not readily available on a prebiotic earth. Most proteins require active metal clusters in their reaction centers.

These clusters are in most cases ultracomplex, each cluster had to have the right atoms interconnected in the right way, and get the correct 3-dimensional form. They require the complex uptake of the basic materials, like iron and sulfur, molybdenum, and complex biosynthesis processes, and after the correct assembling, the insertion in the right way and form inside the proteins. All these processes require energy, in form of ATP, not readily available - since ATP is the product of complex nano-factories, like ATP synthase - which by themselves depend on a proton gradient. Sorry------- not by chance !!




6. Yes, some cells are complex, remember, early life was single celled organisms. Same with some microbes.



LUCA—The Last Universal Common Ancestor 1

The last universal common ancestor represents the primordial cellular organism from which diversified life was derived

http://reasonandscience.heavenforum.org/t2176-lucathe-last-universal-common-ancestor#3995

Even the most conservative models of the composition of LUCA paint it as a quite complex system, a true organism. A system like this would be very difficult to imagine arising directly from purely prebiotic chemical reactions.
ASTROBIOLOGY An Evolutionary Approach    page 131

From analyses of bacterial microfossils, (some of which may be up to 3.48 billion years old) we know that the most primitive life was nearly as complex as today’s bacteria. Unfortunately, the (micro)fossil record can’t really tell us how we got from the simple chemicals to living, working, bacterial cells. 
http://origins.case.edu/2017/07/01/some-assembly-required-the-ingredients-of-life/

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2478661/
LUCA does not appear to have been a simple, primitive, hyperthermophilic prokaryote but rather a complex community of protoeukaryotes with a RNA genome, adapted to a broad range of moderate temperatures, genetically redundant, morphologically and metabolically diverse.

Life was born complex and the LUCA displayed that heritage.

Recent comparative genomic studies support the latter model and propose that the urancestor was similar to modern organisms in terms of gene content.
[/h3]

[url=http://isites.harvard.edu/fs/docs/icb.topic635406.files/Becerra et al 2007.pdf]http://isites.harvard.edu/fs/docs/icb.topic635406.files/Becerra%20et%20al%202007.pdf[/url]
Theoretical estimates of the gene content of the Last Common Ansestor’s genome suggest that it was not a progenote or a protocell, but an entity similar to extant prokaryotes.

http://news.illinois.edu/news/11/1005LUCA_ManfredoSeufferheld_JamesWhitfield_Caetano_Anolles.html
New evidence suggests that LUCA was a sophisticated organism after all, with a complex structure recognizable as a cell, researchers report. Their study appears in the journal Biology Direct. The study lends support to a hypothesis that LUCA may have been more complex even than the simplest organisms alive today, said James Whitfield, a professor of entomology at Illinois and a co-author on the study.


http://www.ncbi.nlm.nih.gov/pubmed/16431085
the estimate of LUCA's gene content appears to be substantially higher than that proposed previously, with a typical number of over 1000 gene families, of which more than 90% are also functionally characterized.a fairly complex genome similar to those of free-living prokaryotes, with a variety of functional capabilities including metabolic transformation, information processing, membrane/transport proteins and complex regulation, shared between the three domains of life, emerges as the most likely progenitor of life on Earth


7. DNA can be metaphircally compared to binary code, but it is a fairly poor comparison. Not every line of "code" in a cell is put to use. Much of many complex organisms DNA is "junk" DNA.


DNA stores literally coded information

http://reasonandscience.heavenforum.org/t1281-dna-stores-literally-coded-information

CRISPR–Cas encoding of a digital movie into the genomes of a population of living bacteria
DNA is an excellent medium for archiving data. Recent efforts have illustrated the potential for information storage in DNA using synthesized oligonucleotides assembled in vitro. A relatively unexplored avenue of information storage in DNA is the ability to write information into the genome of a living cell by the addition of nucleotides over time. Using the Cas1–Cas2 integrase, the CRISPR–Cas microbial immune system stores the nucleotide content of invading viruses to confer adaptive immunity. When harnessed, this system has the potential to write arbitrary information into the genome. Here we use the CRISPR–Cas system to encode the pixel values of black and white images and a short movie into the genomes of a population of living bacteria. In doing so, we push the technical limits of this information storage system and optimize strategies to minimize those limitations. We also uncover underlying principles of the CRISPR–Cas adaptation system, including sequence determinants of spacer acquisition that are relevant for understanding both the basic biology of bacterial adaptation and its technological applications. This work demonstrates that this system can capture and stably store practical amounts of real data within the genomes of populations of living cells.
http://www.nature.com.ololo.sci-hub.cc/nature/journal/vaop/ncurrent/full/nature23017.html

Feature The digital code of DNA 
http://www.nature.com/nature/journal/v421/n6921/full/nature01410.html

The discovery of the structure of DNA transformed biology profoundly, catalysing the sequencing of the human genome and engendering a new view of biology as an information science. Two features of DNA structure account for much of its remarkable impact on science: its digital nature and its complementarity, whereby one strand of the helix binds perfectly with its partner. DNA has two types of digital information — the genes that encode proteins, which are the molecular machines of life, and the gene regulatory networks that specify the behaviour of the genes. The discovery of the double helix in 1953 immediately raised questions about how biological information isencoded in DNA. A remarkable feature of the structure is that DNA can accommodate almost any sequence of base pairs — any combination of the bases adenine (A), cytosine (C), guanine (G) and thymine (T) — and, hence any digital message or information. During the following decade it was discovered that each gene encodes a complementary RNA transcript, called messenger RNA (mRNA), made up of A, C, G and uracil (U), instead of T. The four bases of the DNA and RNA alphabets are related to the 20 amino acids of the protein alphabet by a triplet code — each three letters (or ‘codons’) in a gene encodes one amino acid. For example, AGT encodes the amino acid serine. The dictionary of DNA letters that make up the amino acids is called the genetic code. There are 64 different triplets or codons, 61 of which encode an amino acid (different triplets can encode the same amino acid), and three of which are used for ‘punctuation’ in that they signal the termination of the growing protein chain. The molecular complementary of the double helix — whereby each base on one strand of DNA pairs with its complementary base on the partner strand (A with T, and C with G) — has profound implications for biology. As implied by James Watson and Francis Crick in their landmark paper, base pairing suggests a template copying mechanism that accounts for the fidelity in copying of genetic material during DNA replication . It also underpins the synthesis of mRNA from the DNA template, as well as processes of repairing damaged DNA.

DNA Is Multibillion-Year-Old Software
Nature invented (sic) software billions of years before we did. “The origin of life is really the origin of software,” says Gregory Chaitin. Life requires what software does (it’s foundationally algorithmic).
1. “DNA is multibillion-year-old software,” says Chaitin (inventor of mathematical metabiology). We’re surrounded by software, but couldn’t see it until we had suitable thinking tools.
2. Alan Turing described modern software in 1936, inspiring John Von Neumann to connect software to biology. Before DNA was understood, Von Neumann saw that self-reproducing automata needed software. We now know DNA stores information; it's a biochemical version of Turning’s software tape, but more generally: All that lives must process information. Biology's basic building blocks are processes that make decisions.
http://bigthink.com/errors-we-live-by/dna-is-multibillion-year-old-software


How Junk DNA confirms intelligent design predictions

http://reasonandscience.heavenforum.org/t2359-how-junk-dna-confirms-intelligent-design-predictions



As far back as 1994, pro-ID scientist and Discovery Institute fellow Forrest Mims had warned in a letter to Science[1] against assuming that 'junk' DNA was 'useless.'" Science wouldn't print Mims' letter, but soon thereafter, in 1998, leading ID theorist William Dembski repeated this sentiment in First Things:
[Intelligent] design is not a science stopper. Indeed, design can foster inquiry where traditional evolutionary approaches obstruct it. Consider the term "junk DNA." Implicit in this term is the view that because the genome of an organism has been cobbled together through a long, undirected evolutionary process, the genome is a patchwork of which only limited portions are essential to the organism. Thus on an evolutionary view we expect a lot of useless DNA. If, on the other hand, organisms are designed, we expect DNA, as much as possible, to exhibit function. And indeed, the most recent findings suggest that designating DNA as "junk" merely cloaks our current lack of knowledge about function. For instance, in a recent issue of the Journal of Theoretical Biology, John Bodnar describes how "non-coding DNA in eukaryotic genomes encodes a language which programs organismal growth and development." Design encourages scientists to look for function where evolution discourages it. 15

The more scientific knowledge advances and unravels, important biochemical functions of junk dna are discovered, which doesn't favour the views of proponents of naturalism.  Complex instructional information is used on various levels, not only in the genome, but also in the epigenome, and a big responsability goes to the noncoding DNA regions, and what was supposed to be Junk DNA, HAS been uncovered to have several essential functions to form complex organisms. 

 Dr. Mae-Wan Ho mentions " a vast RNA underworld where RNA agents not only decide which bits of text to copy, which copies get destroyed, which bits to delete and splice together, which copies to be transformed into a totally different message and finally, which resulting message - that may bear little resemblance to the original text - gets translated into protein. RNAs even get to decide which parts of the sacred text to rewrite or corrupt. The whole RNA underworld also resembles an enormous espionage network in which genetic information is stolen, or gets re-routed as it is transmitted, or transformed, corrupted, destroyed, and in some cases, returned to the source file in a totally different form. 

RNA's of course do not decide anything ( thats one of the often used anthropomorphised language that should be tabu in evolutionary writings ) . RNA's, transcribed from " junk dna" are PROGRAMMED, or INSTRUCTED to exercise many tasks in the organism. These instructions can only be the result of preloading by intelligence, since a stepwise evolutionary manner is not possible. Jerry Coynes assertion that natural selection is capable of the task is unsupported pseudoscientific nonsense. 

An interesting paper reports that eukaryotic cells use a variety of strategies to control their transcriptional output that employ a large number of regulatory factors that, in turn, must be tightly regulated. Introns, as genetic entities or RNA segments ( previously held as junk ), facilitate or participate in this amazing regulation feat by sheltering information for small regulatory RNAs allowing for concerted expression of multiple molecules in a given context, influencing where and when a messenger RNA is spliced and translated, preventing or attenuating translation off context or, on the contrary, diversifying the type and function of the molecules produced depending on the internal and external environment.

Observe the nomenclature, which goes like a redline through many scientific biology papers: strategies, control, regulatory, tightly regulated, amazing regulation feat, concerted expression, preventing or attenuating translation. All this is far from useless , random , genetic junk and waste, but is essential  coded, instructional complex genetic information. A stepwise arise  is not possible; either the process is fully regulated and setup right from the beginning, or nothing goes. 

8. Genes are double helix for sexually reproductive species yes, not sure about asexual; but I am not a biologist, nor do I see the relevance to the discussion.


Codes Within Codes: How Dual-Use Codons Challenge Statistical Methods for Inferring Natural Selection

http://reasonandscience.heavenforum.org/t2185-the-second-code-of-dna

The argument of the double function of the genetic code
 1. An “overlapping language” has been found in the genetic code, according to HealthDay News at MedLine Plus from the National Institutes of Health (NIH).
2. One language describes how proteins are made, and the other helps direct genetic activity in cells. One language is written on top of the other, which is why this other language went undiscovered for so long, according to the report in the 2013 Dec. 13 issue of Science.
3. The original paper by Stergachis et al. writes  about “evolutionary constraints” of the overlapping codes. They wrote: “Our results indicate that simultaneous encoding of amino acid and regulatory information within exons is a major functional feature of complex genomes. The information architecture of the received genetic code is optimized for superimposition of additional information, and this intrinsic flexibility has been extensively exploited by natural selection. Although TF [transcription factor] binding within exons may serve multiple functional roles, our analyses above is agnostic to these roles, which may be complex.”
4. According to the research, natural selection constrains or eliminates change (purifying selection) is not helpful for creating new organs or functions. 
5. Thus, for Darwinists to explain unguided physical processes is already impossible and with this new discovery they are even in bigger trouble.
6. The words: information, architecture, optimized, and function are always and only referring to a person with thinking feeling and willing. Other proposed agents cannot on their own give information, design, optimize or execute tasks. This has never been shown.
7. Such an intelligently designed complex genetic code with double or even triple functions could have been created only by God, the Supreme Designer.
8. God exists.


9. No, it doesn't.


The amazing DNA information storage capacity

http://reasonandscience.heavenforum.org/t2052-the-amazing-dna-information-storage-capacity

The evidence of DNA storage
1. In the scientific magazine ‘Nature,’ in January 2013, Nick Goldman et al. reported a successful use of DNA to store large amounts of data.
2. “Here we describe a scalable method that can reliably store more information than has been handled before. We encoded computer files totaling 739 kilobytes of hard-disk storage and with an estimated Shannon information of 5.2× 106 bits into a DNA code, synthesized this DNA, sequenced it and reconstructed the original files with 100% accuracy. Theoretical analysis indicates that our DNA-based storage scheme could be scaled far beyond current global information volumes and offers a realistic technology for large-scale, long-term and infrequently accessed digital archiving. In fact, current trends in technological advances are reducing DNA synthesis costs at a pace that should make our scheme cost-effective for sub-50-year archiving within a decade.”
3. "DNA-based storage has potential as a practical solution to the digital archiving problem and may become a cost-effective solution for rarely accessed archives," said Goldman. 
4. DNA far surpasses any current manmade technology and can last for thousands of years. To get a handle on this, consider that 1 petabyte is equivalent to 1 million gigabytes of information storage. This paper reports an information storage density of 2.2 petabytes per gram.
5. Scientists needed many decades to find out such an incredibly useful design of the DNA made, as they say, by nature. The discovery of the complex design of the DNA needed intelligence. How one can deny a superior intelligence that designed hundreds of different DNA’s, necessary for the survival of all the species.
6. That intelligence of nature is actually the intelligence of God since intelligence is only a property of a person.
7. Thus God inevitably exists.

Perry Marshall, Evolution 2.0, page 192
Ultra-High-Density Data Storage and Compression 
Your cells contain at least 92 strands of DNA and 46 double-helical chromosomes. In total, they stretch 6 feet (1.8 meters) end to end. Every human DNA strand contains as much data as a CD. Every DNA strand in your body stretched end to end would reach from Earth to the sun and back 600 times. When you scratch your arm, the dead skin cells that flake off contain more information than a warehouse of hard drives. Cells store data at millions of times more density than hard drives, 1021 bits per gram . Not only that, they use that data to store instructions vastly more effectively than human-made programs; consider that Windows takes 20 times as much space (bits) as your own genome. We don’t quite know how to quantify the total information in DNA. The genome is unfathomably more elegant, more sophisticated, and more efficient in its use of data than anything we have ever designed. Even with the breathtaking pace of Moore’s Law—the principle that data density doubles every two years and its cost is cut in half—it’s hard to estimate how many centuries it may take for human technology to catch up. Hopefully the lessons we learn from DNA can speed our efforts. A single gene can be used a hundred times by different aspects of the genetic program, expressed in a hundred different ways (248). The same program provides unique instructions to the several hundred different types of cells in the human body; it dictates their relationships to each other in three-dimensional space to make organs, as well as in a fourth dimension, the timeline of growth and development. It knows, for instance, that boys’ voices need to change when they’re 13 and not when they’re 3. It’s far from clear how this information is stored and where it all resides. Confining our understanding of DNA data to computer models is itself a limiting paradigm. This is all the more reason why our standard for excellence ought to be the cell and not our own technology:

• DNA is a programming language, a database, a communications protocol, and a highly compressed
storage device for reading and writing data—all at the same time.
• As a programming language it’s more versatile than C, Visual Basic, or PHP.
• As a database it’s denser than Oracle or MySQL.
• As a communications protocol it wastes far less space than TCP/IP and it’s more robust than
Ethernet.
• As a compression algorithm it’s superior to WinZip or anything else we’ve dreamed of.
• As a storage medium it’s a trillion times denser than a CD, and packs information into less space
than any hard drive or memory chip currently made.
• And even the smallest bacterium is capable of employing all these mechanisms to dominate its
environment and live in community with other cells.

Dawkins, The Blind Watchmaker, pp. 116–117.... 
there is enough information capacity in a single human cell to store the Encyclopaedia Britannica, all 30 volumes of it, three or four times over. ... There is enough storage capacity in the DNA of a single lily seed or a single salamander sperm to store the Encyclopaedia Britannica 60 times over. Some species of the unjustly called ‘primitive’ amoebas have as much information in their DNA as 1,000 Encyclopaedia Britannicas.


10. Assembly line is analogous, you do realize that assmbly lines are far older than abrahamic religion. Analogies aren't arguments, just ways of simplifying a complex process to better explain to high schoolers and college freshmen.


Amazing molecular assembly lines and non ribosomal amino-acid chain formation pathways come to light

http://reasonandscience.heavenforum.org/t2445-new-amazing-molecular-assembly-lines-and-non-ribosomal-amino-acid-chain-formation-pathways-come-to-light



 To make these siderophores, incredible assembly lines in the cell are used: 

Its remarkable, how Nature magazine describes in the article Enzymes line up for assembly ,  how non-ribosomal peptide synthetase (NRPS) work ( we are back at the starting point of this article ) :

Nearly 100 years ago, Henry Ford demonstrated the full strength of economist Adam Smith’s insights into productivity and the division of labour when he established the first moving assembly line. By shuttling partially constructed cars mechanically from one worker to the next, each performing a single specific task, Ford’s assembly line could issue a new Model T every three minutes. This manufacturing method provided the foundation of modern mass production. But nature employed much the same approach for constructing molecules long before humans existed to ponder questions of economy and efficiency.  Walsh and colleagues  identify a previously unrecognized link in one such biological assembly line — an enzyme that could some day be exploited by chemists to modify complex, naturally occurring compounds. The enzymes that form the polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS) families are responsible for the biosynthesis of many useful compounds, including the antibiotics erythromycin and vancomycin, and the antitumour drug epothilone. These multi-subunit enzymes are the molecular equivalents of moving assembly lines: growing substrate molecules are handed, bucket-brigade style, from one specialized catalytic site to the next, with each site performing a specific and predictable function. The PKS assembly line starts by recruiting The PKS assembly line starts by recruiting small building-blocks (such as acetate and propionate molecules, which contain ‘acyl’ chemical groups) onto carrier proteins. The building-blocks are then bonded together in reactions catalysed by a ‘ketosynthase’ region of the PKS. The resulting substrate may then be chemically tailored by various other enzyme domains, before being passed on to another ketosynthase for a further round of extension and modification. The cycle is repeated until the finished molecule is finally offloaded. The various catalytic domains may exist as discrete enzymes (as in type II PKS), or be connected end to end, like beads on a string (as in type I PKS), but in both cases the biosynthetic strategy remains the same. The NRPS cycle is very similar to that of PKS enzymes, except that it uses amino acids as building-blocks. Thus, amino acids become bound to peptidyl carrier proteins (PCPs); PCP-bound amino acids are joined together with amide bonds to form peptides, in catalytic sites known as condensation domains; tailoring regions may then modify the newly formed peptide before passing it along for further cycles of extension and tailoring; and finally, the finished product is cleaved from the enzyme. The PKS and NRPS enzymes each produce very different products, but the logic they use is strikingly similar — so similar, in fact, that they can easily cooperate to construct hybrid PKS–NRPS products such as epothilone.

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3 Re: Some questions for Atheists on Mon Nov 20, 2017 4:01 am

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11. Cells aren't irreducible complex, see answer #6.


The irreducible, code-instructed process to make cell factories and machines points to intelligent design

http://reasonandscience.heavenforum.org/t2364-the-irreducible-code-instructed-process-to-make-cell-factories-and-machines-points-to-intelligent-design

Would you also say that it is plausible that a tornado over a junkyard could produce a 747?
Would you also say that it is plausible that mindless random chance can write a book?

The cell is a factory, that has various computer like hierarchically organized systems of  hardware and software, various language based  informational systems, a translation system, hudge amounts of precise instructional/specified, complex information stored and extract systems to make all parts needed to produce the factory and replicate itself, the scaffold structure, that permits the build of the indispensable protection wall, form and size of its building, walls with  gates that permits  cargo in and out, recognition mechanisms that let only the right cargo in, has specific sites and production lines, "employees", busy and instructed to produce all kind of necessary products, parts and subparts  with the right form and size through the right materials, others which mount the parts together in the right order, on the right place, in the right sequence, at the right time,   which has sophisticated check and error detection mechanisms all along the production process, the hability to compare correctly produced parts to faulty ones and discard the faulty ones, and repeat the process to make the correct ones;  highways and cargo carriers that have tags which recognize where  to drop the cargo where it's needed,  cleans up waste and has waste bins and sophisticated recycle  mechanisms, storage departments, produces its energy and shuttles it to where its needed, and last not least, does reproduce itself.

The salient thing is that the individual parts and compartments have no function by their own. They had to emerge ALL AT ONCE, No stepwise manner is possible, all systems are INTERDEPENDENT and IRREDUCIBLE. And it could not be through evolution, since evolution depends on fully working self-replicating cells, in order to function.

How can someone rationally argue that the origin of the most sophisticated factory in the universe would be probable to be based on natural occurrence, without involving any guiding intelligence?

chemist Wilhelm Huck, professor at Radboud University Nijmegen 
A working cell is more than the sum of its parts. "A functioning cell must be entirely correct at once, in all its complexity,"

To go from a bacterium to people is less of a step than to go from a mixture of amino acids to a bacterium. — Lynn Margulis

Evolution has been a central point of the origins debate. Abiogenesis, however, provides far better elucidation of what mechanisms  explain  the origin of biological systems better: an intelligent designer, through power, information input, wisdom, will, or natural, non-guided, non-intelligent  mechanisms, that is: random chance or physical necessity, long periods of time, mutation and natural selection, or self-organisation of matter.

Behe's definition of  Irreducible complexity can be expanded and applied not only to biological systems, but also to systems, machines, and factories created by man,  that require a minimal number of parts to exercise a specific function, and this minimal number of parts cannot be reduced to keep the basic function. The term applies as well to processes, production methods and proceedings of various sorts. To reach a certain goal, a minimal number of manufacturing steps must be gone through. That applies in special to processes in living cells, where a minimal set of basic processes must be fully functional and operational, in order to maintain cells alive.

Following  irreducible processes and parts  are required to keep cells alive and illustrate mount improbable to get life a first go: 
Reproduction. Reproduction is essential for the survival of all living things.
Metabolism. Enzymatic activity allows a cell to respond to changing environmental demands and regulate its metabolic pathways, both of which are essential to cell survival. 
Nutrition. This is closely related to metabolism. Seal up a living organism in a box for long enough and in due course, it will cease to function and eventually die. Nutrients are essential for life.
Complexity. All known forms of life are amazingly complex. Even single-celled organisms such as bacteria are veritable beehives of activity involving millions of components. 
Organization. Maybe it is not complexity per se that is significant but organized complexity. 
Growth and development. Individual organisms grow and ecosystems tend to spread (if conditions are right). 
Information content. In recent years scientists have stressed the analogy between living organisms and computers. Crucially, the information needed to replicate an organism is passed on in the genes from parent to offspring. 
Hardware/software entanglement. All life of the sort found on Earth stems from a deal struck between two very different classes of molecules: nucleic acids and proteins. 
Permanence and change. A further paradox of life concerns the strange conjunction of permanence and change.
Sensitivity. All organisms respond to stimuli— though not always to the same stimuli in the same ways.
Regulation. All organisms have regulatory mechanisms that coordinate internal processes.



The cell is irreducibly complex

http://reasonandscience.heavenforum.org/t1299-the-cell-is-irreducibly-complex

chemist Wilhelm Huck, professor at Radboud University Nijmegen
A working cell is more than the sum of its parts. "A functioning cell must be entirely correct at once, in all its complexity
http://www.ru.nl/english/@893712/protocells-formed/

Behes definition of  Irreducible complexity can be expanded, and applied not only  to biological systems, but also to systems , machines and factories created by man,  that require a minimal number of parts to exercise a specific function, and this minimal number of parts cannot be reduced to keep the basic function. The term applies as well  to processes, production methods and proceedings of various sorts. To reach a certain goal, a minimal number of manufacturing  steps must be gone through. That applies in special to  processes in living cells, where  a minimal set of basic processes must be fully functional and operational, in order to maintain cells alive.

Following  irreducible processes and parts  are required to keep cells alive, and illustrate mount improbable to get life a first go: 
Reproduction. Reproduction is essential for the survival of all living things.
Metabolism. Enzymatic activity allows a cell to respond to changing environmental demands and regulate its metabolic pathways, both of which are essential to cell survival. 
Nutrition. This is closely related to metabolism. Seal up a living organism in a box for long enough and in due course it will cease to function and eventually die. Nutrients are essential for life. 
Complexity. All known forms of life are amazingly complex. Even single-celled organisms such as bacteria are veritable beehives of activity involving millions of components. 
Organization. Maybe it is not complexity per se that is significant, but organized complexity. 
Growth and development. Individual organisms grow and ecosystems tend to spread (if conditions are right). 
Information content. In recent years scientists have stressed the analogy between living organisms and computers. Crucially, the information needed to replicate an organism is passed on in the genes from parent to offspring. 
Hardware/software entanglement. All life of the sort found on Earth stems from a deal struck between two very different classes of molecules: nucleic acids and proteins. 
Permanence and change. A further paradox of life concerns the strange conjunction of permanence and change.
Sensitivity. All organisms respond to stimuli— though not always to the same stimuli in the same ways.
Regulation. All organisms have regulatory mechanisms that coordinate internal processes.


12. Cells can self replicate yes, and? How is mitosis or meiosis relevant to this?


DNA replication, and its mind boggling nano technology  that defies naturalistic explanations

http://reasonandscience.heavenforum.org/t1849-dna-replication-of-prokaryotes


The Argument of the Original Replicator
In prokaryotic cells, DNA replication involves more than thirty specialized proteins to perform tasks necessary for building and accurately copying the genetic molecule.
Each of these proteins is essential and required for the proper replicating process. Not a single one of these proteins can be missing, otherwise the whole process breaks down, and is unable to perform its task correctly. DNA repair mechanisms must also be in place,  fully functional and working properly, otherwise the mutation rate will be too high, and the cell dies. 18
The individual parts and proteins require by themselves complex assembly proteins to be built.
The individual parts, assembly proteins, and proteins individually would have no function by their own. They have only function interconnected in the working whole. 
The individual parts must be readily available on the construction site of the rna replication complex, being correctly interlocked, interlinked, and have the right interface compatibility to be able to interact correctly together. All this requires information and meta information ( information that directs the expression of the genomic information for construction of the individual proteins, and correct timing of expression, and as well the information of the correct assembly sequence. )
Evolution is not a capable driving force to make the dna replicating complex, because evolution depends on cell replication through the very own mechanism we try to explain. It takes proteins to make DNA replication happen. But it takes the DNA replicationprocess to make proteins. That’s a catch 22 situation.
DNA replication requires coded, complex, specified information and meta-information, and the DNA replication process is irreducibly complex.
Therefore, DNA replication is best explained through design. 


13. Cells don't have error detection necessarily, if they did, cancer wouldn't be an issue.


DNA damage and repair
http://reasonandscience.heavenforum.org/t2043-dna-repair?highlight=dna+repair
http://reasonandscience.heavenforum.org/t1849p30-dna-replication-of-prokaryotes#4401

Replication forks may stall frequently and require some form of repair to allow completion of chromosomal duplicationFailure to solve these replicative problems comes at a high price, with the consequences being genome instability, cell death and, in higher organisms, cancer. Replication fork repair and hence reloading of DnaB may be needed away from oriC at any point within the chromosome and at any stage during chromosomal duplication. The potentially catastrophic effects of uncontrolled initiation of chromosomal duplication on genome stability suggests that replication restart must be regulated as tightly as DnaA-directed replication initiation at oriC. This implies reloading of DnaB must occur only on ssDNA at repaired forks or D-loops rather than onto other regions of ssDNA, such as those created by blocks to lagging strand synthesis.Thus an alternative replication initiator protein, PriA helicase, is utilized during replication restart to reload DnaB back onto the chromosome 

Question: Could the first cell, with its required complement of genes coded for by DNA, have successfully reproduced for a significant number of generations without a proofreading function ? A further question is how the function of synthesis of the lagging strand could have arisen, and the machinery to do so. That is, the Primosome, and the function of Polymerase I to remove the short peaces of RNA that the cell uses to prime replication, allowing the polymerase III function to fill the gap. These functions all require precise regulation, and coordinated functional machine-like steps. These are all complex, advanced functions and had to be present right from the beginning. How could this complex machinery have emerged in a gradual manner ? the Primosome had to be fully functional, otherwise polymerisation could not have started, since a prime sequence is required.


14. You have taken biology 101, yey. How is this relevant


Homeostasis  in cells, and origin of life scenarios

http://reasonandscience.heavenforum.org/t2447-homeostasis-in-cells-and-origin-of-life-scenarios

One of the key properties of life is Regulation, including homeostasis.

Freeman Dyson, Origins of Life, page 73:
The essential characteristic of living cells is homeostasis, the ability to maintain a steady and more-or-less constant chemical balance in a changing environment. Homeostasis is the machinery of chemical controls and feedback cycles that make sure that each molecular species in a cell is produced in the right proportion, not too much and not too little. Without homeostasis, there can be no ordered metabolism and no quasi-stationary equilibrium deserving the name of life. The question Why is life so complicated? means, in this context, Given that a population of molecules is able to maintain itself in homeostatic equilibrium at a steady level of metabolism, how many different molecular species must the population contain? From the fact that bacteria have generally refused to shrink below a certain level of complexity, we may deduce that this level is in some sense an irreducible minimum.  I am conjecturing that the minimum population size required for homeostasis would be  ten or twenty thousand monomer units. And more important, I am suggesting that the most promising road to an understanding of the origin of life would be to do experiments like the Spiegelman and Eigen experiments but this time concerned with homeostasis rather than with replication.

The essence of life from the beginning was homeostasis based on a complicated web of molecular structures. Life by its very nature is resistant to simplification, whether on the level of single cells or ecological systems or human societies. Life could tolerate a precisely replicating molecular apparatus only by incorporating it into a translation system that allowed the complexity of the molecular web to be expressed in the form of software. After the transfer of complication from hardware to software, life continued to be a complicated interlocking web in which the replicators were only one component. The replicators were never as firmly in control as Dawkins imagined. In my version the history of life is counterpoint music, a two-part invention with two voices, the voice of the replicators attempting to impose their selfish purposes upon the whole network and the voice of homeostasis tending to maximize diversity of structure and flexibility of function. The tyranny of the replicators was always mitigated by the more ancient cooperative structure of homeostasis that was inherent in every organism.

Homeostasis is the mechanistic fundament of biology, beginning with the protocell 1 Two fundamental properties of life as we recognize it are homeostasis and redox chemistry. Redox homeostasis is defined here as the maintenance of a constant electrochemical potential and ionic concentration gradient across a cellular boundary, despite fluctuations in the electrochemical potential of the external environment and despite changing identities and activities of electron donors and acceptors. 2  The transition to free-living cells depends on the proto-cells’ ability to maintain a proton motive force for energy conversion, providing for metabolism, for active transport, and for synthesis of informational and structural macromolecules.  A feature that distinguishes living from non-living matter  is homeostasis – the maintenance of a constant internal environment despite changes in the external environment. A second feature of all known life  is that living things are composed of spatial compartments, called cells. Cellular homeostasis requires a system of integrated feedback and feedforward, producing adaptive responses to, and anticipation of, ultimately uncontrollable changes in the properties of the outside world.

I have been trying to imagine a framework for the origin of life, guided by a personal philosophy that considers the primal characteristics of life to be homeostasis rather than replication, diversity rather than uniformity, the flexibility of the genome rather than the tyranny of the gene, the error tolerance of the whole rather than the precision of the parts.

A Massachusetts General Hospital (MGH) research team investigating how the earliest stages of life might have developed has discovered a way the first living cells could have met a key challenge -- maintaining a constant internal environment, a process called homeostasis, even when external conditions change. "Modern cells are constantly regulating what they are doing -- synthesizing, degrading and exporting a whole suite of RNAs and proteins -- depending on the cell's particular needs at the time," says Aaron Engelhart, PhD, of the MGH Department of Molecular Biology and the Center for Computational and Integrative Biology, lead author of the paper. "One would expect that the earliest cells weren't nearly as complex as today's cells, but they still had the need to regulate their internal environment. 1



Iron Uptake and Homeostasis in Cells 1

http://reasonandscience.heavenforum.org/t2443-iron-uptake-and-homeostasis-in-prokaryotic-microorganisms

The origin of life required two processes that dominated: 
(1) the generation of a proton gradient and 
(2) linking this gradient to ATP production in part and in part to uptake of essential chemicals and rejection of others. The generation of a proton gradient required especially appropriate amounts of iron (Fe2+), levels for electron transfer and the ATP production depended on controlling H+, Mg2+ and phosphate in the cytoplasm. 8

Iron serves essential functions in both prokaryotes and eukaryotes, and cells have highly specialized mechanisms for acquiring and handling this metal. 2
Organisms use a variety of transition metals as catalytic centers in proteins, including iron, copper, manganese, and zinc. Iron is well suited to redox reactions due to its capability to act as both an electron donor and acceptor. In eukaryotic cells, iron is a cofactor for a wide variety of metalloproteins involved in energy metabolism, oxygen binding, DNA biosynthesis and repair, synthesis of biopolymers, cofactors, and vitamins, drug metabolism, antioxidant function, and many others. Because iron is so important for survival, organisms utilize several techniques to optimize uptake and storage to ensure maintenance of sufficient levels for cellular requirements. However, the redox properties of iron also make it extremely toxic if cells have excessive amounts. Free iron can catalyze the formation of reactive oxygen species such as the hydroxyl radical, which in turn can damage proteins, lipids, membranes, and DNA. Cells must maintain a delicate balance between iron deficiency and iron overload that involves coordinated control at the transcriptional, post-transcriptional, and post-translational levels to help fine tune iron utilization and iron trafficking.  4

Question: Had this coordination not have to be fully setup right when cells first became alive ? 



How  intracellular Calcium signaling,  gradient and its role as a universal intracellular regulator points to design

http://reasonandscience.heavenforum.org/t2448-howintracellular-calcium-signaling-gradient-and-its-role-as-a-universal-intracellular-regulator-points-to-design

In view of the importance of calcium (Ca2+) as a universal intracellular regulator, its essential role in cell signaling and communication in many biological intra and extra cellular processes,  it is surprising how little it is mentioned in the origins ( evolution/ID) debate. Most discussions about the origin of life start with RNA worlds versus metabolism first scenarios, panspermia, hydrothermal vent theory etc. The origin of life cannot be elucidated, without taking into consideration and explaining how the calcium signaling machinery and cell homeostasis appeared. 

The Calcium gradient :
The ability of cells to maintain a large gradient of calcium across their outer membrane is universal. All biological cells have a low cytosolic (liquid found inside Cells ) calcium concentration, can and must keep this even when the free calcium outside is up to 20,000 times higher concentrated!  The first forms of life required an effective Ca2+ homeostatic system, which maintained intracellular Ca2+ at comfortably low concentrations—somewhere around 100 nanomolar, this being ∼10,000–20,000 times lower than that in the extracellular milieu.  Damage the ability of the plasma membrane to maintain this gradient and calcium will flood into the cell, precipitating calcium phosphate, damaging the ATP-generating machinery, and kill the cell. At millimolar concentrations, calcium competes with Mg2+ ( magnesium), binds to DNA and RNA, and clogs it up. Ca2+ binds to nucleotides, so they do not work properly. And crucially Ca2+, at too high concentrations, precipitates carbonate, phosphate, and sulfate. So if a primeval cell was to work, it had to get rid of Ca2+, lowering it at least to submillimolar levels, if not submicromolar. In fact, without control of intracellular Ca2+,  life would never have got off the ground! Control of intracellular Ca2+ had to be a crucial step in allowing the original cells to survive and replicate, even before RNA or DNA synthesis could begin in earnest. The evidence we have from molecular biology, together with the toxic nature of prolonged high Ca2+ levels inside cells, argues strongly that primeval cells must have had  Ca2+ pumps to keep their free intracellular Ca2+ low, setting the scene for the ‘calcium pressure’ across then plasma membrane to be exploited to act as the source for cell activation.

In order to maintain such a low cytosolic calcium concentration, Ca2+ ions thus have to be transported against a steep concentration gradient. In addition, the positively charged molecules are often transported against a very negative membrane potential, contributing to a large electrochemical gradient for Ca2+ ions.   The concentration is tightly regulated by Ca 2+ -binding proteins, Ca 2+ pumps and other transporters. This gradient has to be maintained by the continuous exclusion of Ca2+ from the cell. The removal of Ca2+ by active extrusion requires energy to pump the Ca2+ against the electrochemical gradient. The metabolic apparatus that serves this function involves Ca2+ protein-based and non-proteinaceous channels, Ca2+ antiporters (Ca2+/2H+, Ca2+/Na+), and ATP-dependent Ca2+ pumps.

The making of a power gradient ( which is a thermodynamically uphill process )  is always an engineering achievement, and a lot of knowledge,  planning, and intelligence is required for setup. Hydroelectric dams are highly complex, and always the result of years of planning by the most skilled, educated and knowledge engineers  of large companies. As for many human inventions, the engineering solutions discovered by man are employed in nature at least since life began in a far more elaborate and sophisticated way. So inanimate chemistry had the innate drive of trials and errors to produce a cell membrane, and amongst tons of other things, a Ca+ gradient through highly complex [b]Calcium channels to keep a 10 000-fold higher concentration of calcium outside the cell than inside the cytosol in order to create a environment suited for a protocell to keep its vital functions and not to die ? Why would chemical elements do that? Did they have the innate drive and goal to become alive and keep an  ambiance prerequisite, homeostasis of various elements, to permit life ?[/b]


15. Yes, this is called symbiotic relationships. How is this fine tuning or relevant?


Viruses, another mistery of origin of life scenarios

http://reasonandscience.heavenforum.org/t1433-viruses-another-mistery-of-origin-of-life-scenarios?highlight=viruses

http://christiananswers.net/q-crs/abiogenesis.html

Many bacteria and all viruses possess less complexity than required for an organism normally defined as “living,” and for this reason must live as parasites which require the existence of complex cells in order to reproduce. For this reason Trefil noted that the question of where viruses come from is an “enduring mystery” in evolution. Viruses usually are much smaller than parasitic bacteria and are not considered alive because they must rely on their host even more than bacteria do. Viruses consist primarily of a coat of proteins surrounding DNA or RNA that contains a handful of genes, and

since they do not reproduce in the normal way, its hard to see how they could have gotten started.
 One theory: they are parasites who, over a long period of time, have lost the ability to reproduce independently… Viruses are among the smallest of “living” things. A typical virus, like the one that causes ordinary influenza, may be no more than a thousand atoms across. This is in comparison with cells which may be hundreds or even thousands of times that size. Its small size is one reason that it is so easy for a virus to spread from one host to another--its hard to filter out anything that small (Trefil, 1992, p. 91).


In order to reproduce, a virus's genes must invade a living cell and take control of its much larger DNA. A bacterium is 400 times greater in size than the smallest known virus, while a typical human cell averages 200 times larger than the smallest known bacterium. The QB virus is only 24 nanometers long, contains only 3 genes and is almost 20 times smaller than Escherichia coli, billions of which inhabit the human intestines. E. coli is 1,000 nanometers long compared to a typical human cell that is about 10,000 nanometers long (1 nanometer equals 1 billionth of a meter, or about 1/25-millionths of an inch) and contains an estimated 100,000 genes. Researchers have detected microbes in human and bovine blood that are only 2-millionths of an inch in diameter, but these organisms cannot live on their own because they need more than simple inorganic, or common inorganic molecules to survive. 

Since parasites lack many of the genes (and other biological machinery) required to survive on their own, in order to grow and reproduce they must obtain the nutrients and other services they require from the organisms that serve as their hosts. Independent free-living creatures such as people, mice and roses are far more complex than organisms like parasites and viruses that are dependent on these complex free-living organisms. Abiogenesis theory requires that the first life forms consisted of free-living autotrophs (i.e. organisms that are able to manufacture their own food) since the complex life forms needed to sustain heterotrophs (organisms that cannot manufacture their own food) did not exist until later.

The simplest microorganisms, Chlamydia and Rickettsea, are the smallest living things known, but also are both parasites and thus too simple to be the first life. Only a few hundred atoms across, they are smaller than the largest virus and have about half as much DNA as do other species of bacteria. Although they are about as small as possible and still be living, these two forms of life still possess the millions of atomic parts necessary to carry out the biochemical functions required for life, yet they still are too simple to live on their own and thus must use the cellular machinery of a host in order to live (Trefil, 1992, p. 28). Many of the smaller bacteria are not free living, but are parasite like viruses that can live only with the help of more complex organisms (Galtier et al., 1999).

The gap between non-life and the simplest cell is illustrated by what is believed to be the organism with the smallest known genome of any free living organism Mycoplasma genitalium (Fraser et al., 1995). M. genitalium is 200 nanometers long and contains only 482 genes or over 0.5 million base pairs which compares to 4,253 genes for E. coli (about 4,720,000 nucleotide base pairs), with each gene producing an enormously complex protein machine (Fraser et al., 1995). M. genitalium also must live off other life because they are too simple to live on their own. They invade reproductive tract cells and live as parasites on organelles that are far larger and more complicated but which must first exist for the survival of parasitic organisms to be possible.


16. Yes, consciousness exists, it's how life responds to it's environment. Hell, we could argue plants have consciousness, as they will adjust their growth to obtain more life, some release hormones and scents to trigger other plants of infestations, and some are carnivorous and can determine edible from not.


What comes first, mind or matter?

http://reasonandscience.heavenforum.org/t1380-what-comes-first-mind-or-matter

Energy, rather than an eternal, conscious mind as the first cause of the universe?

Some try to substitute God as a first cause by claiming that energy was always there, eternally, stored in a singularity, and caused the universe suddenly into being by a quantum fluctuation event. Planck regarded matter/energy as derivative from consciousness. What would be the contrary? Consciousness derivative from energy. If it were so, over an unknown length of time, energy would have become cognitive and self-aware, even learning the how's and why's of becoming other perceivable forms. It would gain perception, thinking, free will, moral judgment, and memory.  But logical laws must be already a priori existent to make distinctions, syllogistic thinking with induction and deduction at play. Einstein recognized the absurdity of this claim. He described the "gulf' that logically separates the concrete world of hard objects on the one hand from the abstract world of ideas on the other. A small part of the materialist's problem is that hard objects are never observed spontaneously to transform themselves (on their own recognizance) into abstract ideas.

W.L.Craig writes :
The only way to have an eternal cause but a temporal effect would seem to be if the cause is a personal agent who freely chooses to create an effect in time. For example, a man sitting from eternity may will to stand up; hence, a temporal effect may arise from an eternally existing agent. Indeed, the agent may will from eternity to create a temporal effect, so that no change in the agent need be conceived. Thus, we are brought not merely to the first cause of the universe, but to its personal Creator.


Near Death experience , evidence of dualism
http://reasonandscience.heavenforum.org/t1284-near-death-experience-evidence-of-dualism

The Mind is Not The Brain
http://reasonandscience.heavenforum.org/t1662-the-mind-is-not-the-brain#2581

Quantum Mechanics and Consciousness: 5 Experiments
https://docs.google.com/document/d/1rqqkxxQighIbyqtE0VeBZmu9D3GvUQfO5v1xwOTyp_E/edit




17. Morality is not objective. We can make well reasoned generalizations about morality, but it is not objective.


The moral argument for Gods existence

http://reasonandscience.heavenforum.org/t1369-the-moral-argument-for-gods-existence

If you agree, that its wrong in any circumstances to rape, torture and kill little babies for fun,  then you agree that objective moral values exist. Since that is the case,  this takes you to really believe much more than you might think you do. This is a very big thing that you are admitting here. I don't think you realized how big. You are saying that you are confident -- you have a reasonable certainty -- that something exists somewhere in a realm which you can't see, taste, touch, smell or hear. You believe something exists that you can't prove empirically. Think for a moment about a moral absolute. Where did it come from?

 The implications of this fact  you believe that that rule applies to everyone, in other words, it is a moral absolute, then you have just affirmed a belief in something that is immaterial that you don't access by your five senses but you do access with some certainty by some other means. There is a sense of moral intuition that has a play here. If a moral absolute exists, it's fair to ask the question, what kind of thing is it? It's not a physical thing. A moral thing is not physical. It doesn't extend into space, it doesn't weigh something, it has no physical qualities or characteristics. It is a non-physical thing that really exists. It's an immaterial thing, something that you know exists but you can't get at with any of your five senses. If it seems that the moral thing exists and has moralforce on our behavior, then it seems to me the most reasonable option is that Someone made that moral thing and so that moral rule is a rule of Somebody's, and it's not just a disembodied principle. When you break the moral rule, you offend the Person Who made the rule itself.

That's true for a lot of people who object to the idea of God because they can't find Him with their senses.   In other words, there are other ways to learn about things than just the five senses.   I think there is a sense of moral intuition that has a play here. But in any event, you can be considered rational in believing that such a rule actually exists. Once you do that, it does a lot of work for you.

Well, when you say that a thing like an absolute moral rule exists, you've made an admission that has profound implications for many other beliefs. In other words, a whole bunch of other beliefs are bound up in that statement.

For example, when you say that some absolute moral laws exist, you're saying that immaterial things -- like moral laws which aren't made out of physical stuff -- certainly do exist. Therefore, materialism as a worldview is false. Instead, it is reasonable to believe in things you don't see and can't test with the five senses. Strict empiricism would be false, then. Now this is a big step, because in the case of many atheists one of their frequent  arguments against God is that He hasn't shown Himself to us. But by your own admission, it can be reasonable to believe in something you simply can't see. In other words, there are different ways to "show" things to people, ways that don't involve the senses.

Given that this moral rule is out there somewhere, where did it come from?

You have only a limited number of options.

1.  It could have just come into existence out of nowhere. It could have just "poofed" into existence.
2.  It could have self-created itself. Though if it did then one could ask how is it that an arbitrary thing like a moral rule could have any moral force?  If it is an accident, if it just comes from nowhere, why would it have any moral force on me? And part of our argument is that a moral rule does have moral force. Maybe it assembled itself by accident out of available immaterial stuff floating around in wherever that world is that morals float around in. Of course, if it happened by accident then you'd still have to answer the question, how does an accidental thing have moral force? Or,
3.  it could be that the moral law was made by Someone Who lives in that immaterial realm. Now, those are your options. I don't know how many other options there are, but it seems to me you are stuck with these three.

You see, you do not have the liberty of standing in a neutral place on this issue. You've got to believe something. If you refuse to believe God made moral laws, given that you admit that they are there, then you're opting for one of the other two alternatives. And if you say that they just popped into existence or that they assembled themselves by chance, you have new problems to solve. In other words, I don't think those are tenable alternatives.

My point is to look at what seems to be the obvious existence of moral absolutes and to then look and see where that observation leads us, and it seems to lead us to the existence of a God who makes those moral rules because moral rules are designed kinds of things that don't make themselves, it appears. And it seems that a very good explanation for their existence is that a God with moral character made a set of moral rules that express His character and those rules then become absolutes which are incumbent upon us

Apart from God, there is no ultimate reference point to distinguish between what is human and what is inhuman. There is no ontological human compass - certain actions may be held in contempt by society because those actions jeopardise the safety and flourishing of others, but there is no ultimate anchor in which to place those OPINIONS – no commandments from the Divine to endorse or condemn


18. Logic is influenced and inspired by physics, same with reasoning, but true, these are social inventions of a civilized society. Now we are entering anthropology and philosophy...more my department.


 The Practical Impossibility of Atheism

http://reasonandscience.heavenforum.org/t1375-schaeffer-the-practical-impossibility-of-atheism

 “Supposing there was no intelligence behind the universe, no creative mind. In that case, nobody designed my brain for the purpose of thinking. It is merely that when the atoms inside my skull happen, for physical or chemical reasons, to arrange themselves in a certain way, this gives me, as a by-product, the sensation I call thought. But, if so, how can I trust my own thinking to be true? It's like upsetting a milk jug and hoping that the way it splashes itself will give you a map of London. But if I can't trust my own thinking, of course I can't trust the arguments leading to Atheism, and therefore have no reason to be an Atheist, or anything else. Unless I believe in God, I cannot believe in thought: so I can never use thought to disbelieve in God.”

― C.S. Lewis

Atheism shoots science in the foot and then shoots itself in the head! Atheism cannot account for the existence of logic and it has to deny the existence of truth ( Darwin himself doubted that the human brain which was the result of irrational processes could be trusted to be rational ) Without this two science is impossible! If you take the view of common ancestry and macroevolution as true, you cannot trust anything about what you think is true. How are you sure your thoughts are logical if they derive from a lucky evolutionary accident that was not logical at all?

http://www.goodreads.com/quotes/344552-but-then-with-me-the-horrid-doubt-always-arises-whether
“But then with me, the horrid doubt always arises whether the convictions of man's mind, which has been developed from the mind of the lower animals, are of any value or at all trustworthy. Would anyone trust in the convictions of a monkey's mind, if there are any convictions in such a mind?
[ Charles Darwin To William Graham 3 July 1881]”

You believe ON SHEER FAITH, that something came from nothing (absolutely nothing?) -for no reason. Therefore, according to your belief system, non-material entities such as objective truth is a myth since even the most basic principles of logic are all produced by a random accident, as is even your brain. This, in turn, means that your every thought is a random, meaningless chemical fizz. So, if your belief system is true, then the comment you just made is nothing more than the accidental result of a meaningless chemical reaction, in a randomly formed chunk of brain matter. Newsflash my friend. No one gives a hoot about any so-called data produced by a randomly programmed computer. Such a computer would be inherently unreliable and the data would be presumed faulty. Therefore, when atheists say that the Universe is an accident, and nothing within it is designed for a purpose, including their own brains, they cede any right to have their randomly produced thoughts taken seriously. So, when you call anything "superstitious", your comment is nothing more than a bad joke, or more accurately, a self-deception that you pull on yourself. Like all atheists, you want to have your cake and eat it too when you claim that 1. God is a superstition and 2. You'd do well to constantly remind yourself that your thoughts,(according to atheism) are completely meaningless chemical reactions, occurring in a long chain of cause and effect from mechanical, purposeless physical forces acting on your equally random and accidentally produced brain chemistry and therefore, within an atheistic framework, your thoughts could never be meaningful or worth sharing.

The difference is not in the existence of the soul, or mind itself but in the concept of a designed, planned product of an intelligent Mind, as opposed to an accident generated from blind random chance. If your brain is designed to think according to rational, logical patterns and if it comes with an organic version of pre- installed software that allows it not only to function rationally but also to recognize its own rationality, then you can proceed to analyze problems with confidence that your thoughts truly possess rationality, meaning, value, and purpose.

The only design gives you that certainty of rationality, meaning, value and purpose. Blind chance can only produce a more random blind chance. Without the prospect of an Eternal Mind, all is meaningless. Plato and Aristotle recognized this and hence their concepts of non-material Forms and the Unmoved Mover. Later, Aquinas realized that the great minds of Plato and Aristotle had paved a road that can only possibly lead to the Triune God of the Christianity.

from all practical appearances we just shouldn't be here but here we are, you and i, and although we disagree on fundamental issues of life we are both apparently rational beings. But where does rationality come from? Ask that and we're back in the loop of causation. Every effect has a cause. That is, as you well know, one of the Basic Principles of Logic. It follows then that no effect is greater than its cause and as we observe our material world, sure enough, we can point to nothing that was not caused by something that was powerful enough as a secondary, instrumental, or material cause, to cause that effect. But when we come to the sticky, no material effects that we observe and even intuitively acknowledge, such as rationality, morality, objective truth, and objective standards of aesthetics, as well as the Virtues such as, "love of our family and fellow man is better than hate" suddenly atheism chokes!  Thanks to Mac Howell 

If a man, obviously drunk, whom you have never met, stumbles up to you on the street and says to you "Your mother told me to tell you not to go home, the house is full of spiders." You will not trust what he says. Why? Because he is irrational, because, he is drunk, and we know that we cannot trust irrational sources.
But if our brains are ultimately the product of a series of blind, irrational causes then how could we possibly know what truth is?
You might suggest that natural selection is not blind in the sense of being irrational, it picks the best, or picks what works. But blind, deaf, senseless random mutation has to produce anything and everything from which natural selection selects. Natural selection cannot create ANYTHING. It cannot select a green bug from four brown bugs. It is totally dependent on totally random forces.
It may select what works, but how or why would we imagine we could know "truth". Why would we imagine the idea of truth? Why would we imagine? And yet we do. And we believe there is such a thing as truth and that we can know it. Credit to Rick Swindell


19. DNA very well may have arisen from early proteins in the right conditions, again; if it is so fine tunes, how is this a problem for you? Are you admitting that the universe wasn't designed for us, and that life is a beautiful rarity?


DNA synthesis - what came first, the enzymes to make DNA, or DNA to make the enzymes that synthesize DNA?

These are some enzyme names of de novo Purine and Pyrimidine biosynthesis, essential to make DNA, and supposedly extant at LUCA ( last universal common ancestor )

to make purines:

amidophosphoribosyltransferase, 2.4.2.14
phosphoribosylamine-glycine ligase, 6.3.4.13
phosphoribosylglycinamide formyltransferase, 2.1.2.2
phosphoribosylformylglycinamidine synthase, 6.3.5.3
phosphoribosylformylglycinamidine cyclo-ligase, 6.3.3.1

and these to make pyrimidines :

Carbamoyl phosphate synthase II
Aspartate carbamoyltransferase
Dihydroorotase
Dihydro Orotate Dehydrogenase
Orotate Phosphoribosyl transferase
Orotidine 5'-phosphate decarboxylase
Nucleoside-phosphate kinase  & Nucleoside-diphosphate kinase

How did these enzymes emerge on a prebiotic earth ???

It takes DNA to make these enzymes. And it takes these enzymes to make DNA.......

Biosynthesis of the DNA double helix, evidence of design
http://reasonandscience.heavenforum.org/t2028-biosynthesis-of-the-dna-double-helix-evidence-of-design


20. An irreducibly complex enzyme would have been the starting point, or, perhaps it isn't irreducibly complex. Also, do you know how evolution works?


What might be a Cell’s minimal requirement of parts ?  [url=file:///E:/Desktop/apdf files/FirstGeneCh10.pdf]1[/url]

http://reasonandscience.heavenforum.org/t2110-what-might-be-a-protocells-minimal-requirement-of-parts

How Many Genes Can Make a Cell: The Minimal-Gene-Set Concept
https://www.ncbi.nlm.nih.gov/books/NBK2227/
Several theoretical and experimental studies have endeavored to derive the minimal set of genes that are necessary and sufficient to sustain a functioning cell under ideal conditions, that is, in the presence of unlimited amounts of all essential nutrients and in the absence of any adverse factors, including competition. A comparison of the first two completed bacterial genomes, those of the parasites Haemophilus influenzae and Mycoplasma genitalium, produced a version of the minimal gene set consisting of ~250 genes.

Following  irreducible processes and parts  are required to keep cells alive, and illustrate mount improbable to get life a first go: 
Reproduction. Reproduction is essential for the survival of all living things.
Metabolism. Enzymatic activity allows a cell to respond to changing environmental demands and regulate its metabolic pathways, both of which are essential to cell survival. 
Nutrition. This is closely related to metabolism. Seal up a living organism in a box for long enough and in due course it will cease to function and eventually die. Nutrients are essential for life. 
Complexity. All known forms of life are amazingly complex. Even single-celled organisms such as bacteria are veritable beehives of activity involving millions of components. 
Organization. Maybe it is not complexity per se that is significant, but organized complexity. 
Growth and development. Individual organisms grow and ecosystems tend to spread (if conditions are right). 
Information content. In recent years scientists have stressed the analogy between living organisms and computers. Crucially, the information needed to replicate an organism is passed on in the genes from parent to offspring. 
Hardware/software entanglement. All life of the sort found on Earth stems from a deal struck between two very different classes of molecules: nucleic acids and proteins. 
Permanence and change. A further paradox of life concerns the strange conjunction of permanence and change.
Sensitivity. All organisms respond to stimuli— though not always to the same stimuli in the same ways.
Regulation. All organisms have regulatory mechanisms that coordinate internal processes.

For a nonliving system, questions about irreducible complexity are even more challenging for a totally natural non-design scenario, because natural selection — which is the main mechanism of Darwinian evolution — cannot exist until a system can reproduce.  For an origin of life we can think about the minimal complexity that would be required for reproduction and other basic life-functions.  Most scientists think this would require hundreds of biomolecular parts.  And current science has no plausible theories to explain how the minimal complexity required for life (and the beginning of biological natural selection) could have been produced by natural process before the beginning of biological natural selection.

In order to make life, and specially multicellular complex life,  the building blocks of life, cells, have to be made, which are the tiniest living entities. To build  cells requires information and programming, complex protein manufacturing machines and assembly lines, energy, nutrient supply chains, quality control , waste bins, ability to adapt to the environment and to react to stimuli, ability of replicating, and housing ( the cell membrane ). 

“The complexity of the simplest known type of cell is so great that it is impossible to accept that such an object could have been thrown together suddenly by some kind of freakish, vastly improbable, event. Such an occurrence would be indistinguishable from a miracle.” 
― Michael Denton, Evolution: A Theory In Crisis

Determination of the Core of a Minimal Bacterial Gene Set
http://mmbr.asm.org/content/68/3/518.full.pdf
[size=12]Based on the conjoint analysis of several computational and experimental strategies designed to define the minimal set of protein-coding genes that are necessary to maintain a functional bacterial cell, we propose a minimal gene set composed of 206 genes. Such a gene set will be able to sustain the main vital functions of a hypothetical simplest bacterial cell.

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21. Considering humans are pretty widespread and traveled in various clans, tribes, and small communities before settling, even more, areas, and that languages have melded and dominated one another over thousands of years, im shocked 116 is all we have

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Human Language: The Homo Homolog 1

http://reasonandscience.heavenforum.org/t1334-the-origin-of-language

Editor's note: In his new book Evolution: Still a Theory in Crisis, Michael Denton not only updates the argument from his groundbreaking Evolution: A Theory in Crisis (1985) but also presents a powerful new critique of Darwinian evolution. This article is one in a series in which Dr. Denton summarizes some of the most important points of the new book. For the full story, get your copy of Evolution: Still a Theory in Crisis. For a limited time, you'll enjoy a 30 percent discount at CreateSpace by using the discount code QBDHMYJH.
Our own kind, Homo sapiens, slipped suddenly into being on the rich, game-laden African grasslands of the late Pleistocene, and spread rapidly over the next 200,000 years to every corner of the world. Here was the greatest of novelties, a new type of being -- for the first time a creator and molder of the world -- a speaking and thinking being, knowing, insightful, artistic, and religious. As well as a hunter, here was a storyteller, a mystic, a seer, and a dreamer. Nothing before in evolution had hinted at the possibility of such a novel organism. The radical nature of this mysterious happening, and the unprecedented intellectual advance it entailed, is shown graphically in the marvelous frescoes of cave art of the upper Paleolithic in Europe.
One of the most curious features of human evolution, and one that poses at the outset an intriguing and still unanswered challenge to the Darwinian and functionalist narrative, is the fact that all modern humans share the same higher intellectual capabilities. This means, incredible though it may seem, a brain capable of the intellectual feats of an Einstein, a Newton, or a Mozart must have already emerged in our last common ancestors more than 200,000 years ago. Such intellectual abilities seem absurdly powerful, beyond any conceivable utility for hunter-gatherers on that ancient savanna, and hence beyond any functionalist explanation.
As Noam Chomsky recently commented: "[Alfred Russel Wallace] recognized that mathematical capacities [for example] could not have evolved by natural selection; it's impossible because everybody's got them, and nobody's ever used them, except for some very tiny fringe of people in very recent times. Plainly they developed in some other way."1
From an evolutionary point of view, the origin of man's higher intellectual abilities is one of the greatest of all mysteries, of all facts to be explained. It would certainly seem, in light of these preliminary observations that the origin and evolution of our intellectual powers must have involved causal factors beyond natural selection.
Some of our mental abilities and emotional traits are certainly shared to some degree by other species, but language, as Chomsky comments, is without any homolog in any other species.2 Language is a Type-defining homolog, restricted to an individual species, and like other such homologs, it is not led up to by any empirically known sequence (e.g., starting with simple "grunts and gestures" and progressing though more and more complex communication systems till we reach human language). And again, no plausible hypothetical evolutionary series has ever been proposed. Thus, just as in the case of other defining novelties, the evidence is consistent with a saltational origin.
Because of the lack of homology and the lack of plausible adaptive evolutionary steps, the origin of language remains an abiding mystery. In two final articles in this series, we'll look at other aspects of this mystery.


http://creation.com/origin-of-language

The best-known linguist of the twentieth century, Noam Chomsky, though an evolutionist, has consistently maintained that there is no connection;6 and that, as Descartes (not surprisingly) insisted long before him,7 language is “species-specific”,8 and must have originated in humanity through some genetic input. To this extent, trans-speciate evolution seldom came into the picture in linguistics.

In fact, Chomsky insists that mid-century studies based on the evolution of language from apes to humans only “bring out more clearly the extent to which human language appears to be a unique phenomenon, without significant analogue in the animal world.”


http://www.apologeticspress.org/apcontent.aspx?category=9&article=1351

References:


(1) Noam Chomsky, The Science of Language: Interviews with James McGilvray (New York: Cambridge University Press, 2012), 15.
(2) Chomsky, The Science of Language, 47; Marc D. Hauser, Charles Yang, Robert C. Berwick, Ian Tattersall, Michael J. Ryan, Jeffrey Watumull, Noam Chomsky, and Richard C. Lewontin, "The Mystery of Language Evolution," Frontiers in Psychology 5, no. 401 (May 7, 2014).

1) http://www.evolutionnews.org/2016/04/human_language102580.html




22. We have evidence of smaller cities from far before 3000 bc.
23. I don't argue the world is ruled by anything, accept the laws of physics and chemistry. Independent thought would be a tough one to crack, if we even have independent thought. We don't know, we may very well be slaves to other chemical reactions we haven't come to understand yet. So far, many chemical reactions are sufficient to explain our behavior.



Logic, conscience, will, morality cannot be explained by physical or chemical interactions. 

24. I wouldn't say we are entirely self aware, but I would argue that animals are self aware. Anything that is locomotive requires to be aware of the position of oneself within space in order to survive.
25. Define free will. If you mean the will to do anything, no we can't fly command. If you mean philosophical freedom to reason and premeditate, then I would argue it is a survival and social mechanism of higher mammals.


We are the only known species with free will. So it is not necessary for survival. 



26. Already answered this in #16.
27. Our own ideas, society, culture, and preferences influence our morality.
28. Suffering matters because humans are generally empathetic beings. We can see others in pain, we know what pain feels like.
29. They dont, outside of the fact that we are humans, we want to live, and it is instinctual to carry on the specieis, that's why boners exist.
30. Considering we are a social species, societal harmony is prefered.
31. Well, the belief in the supernatural various culture to culture, person to person. We are also an investigative species. One explanation for superstition is our recognition of patterns and reliance on subconscious emotions like anxiety.
32. All the natural world we see. You are asking an impossible question, as only someone who knows of the world's limits can know this answer, which proves difficult as one cannot know such limits of an entirety.
33. We cant, have to die to find out. Since you aren't dead, you cannot say there is or is not.
34. Considering we agree most humans are superstitious, you have the explanation for church growth, that said, people are also tribal and put a lot of focus on identity and cultural competition. You notice, we have many more different sects of abrahamic religion than from 2000bc.
35. Yes, the bible is fiction as it does not represent events we can verify aecheologocally or anthropologically.






[size=18]Is the Bible Historically Accurate?

http://reasonandscience.heavenforum.org/t1974-is-the-bible-historically-accurate

 There are 3 essential tests that researchers use to ascertain historical reliability. The Bible stands up strongly to these tests, if not more strongly than any other historical document recorded:

Internal Test: Examining linguistic, cultural, and literary context can clear away apparent contradictions in the Bible. For example, some claim that the genealogies of Christ are contradictory. Not so: Matthew lists Joseph’s family line, and Luke lists Mary’s.

External Test: Nelson Glueck, a Jewish archaeologist says, “… it may be stated categorically that no archaeological discovery has ever controverted a biblical reference. Scores of archaeological findings have been made which confirm in clear outline or exact detail statements in the Bible.”

Bibliographic Test: Bibliographic Test: The document must contain eyewitness accounts, there must be a short amount of time between copy and original, and several copies must be made. Pass. Even many non-Christian historians who were not sympathetic to Christianity such as Flavius Josephus, Thallus and Phlegon lend support to Biblical facts.

The Bible’s Power and Influence
In some countries today, the Bible is forbidden. Bringing a Bible into Saudi Arabia, for example, or North Korea, or China, or Libya, or Burma — along with many other countries — can result in expulsion for the westerner or arrest and torture if you’re native to the country. It wasn’t that long ago that the Bible was banned in communist Eastern Europe, too; a good friend of mine was involved in Bible smuggling into places like Romania and Hungary during the 1970s and 80s and can tell hair-raising stories of near arrests and fortunate escapes.
Banned in many countries, yet desperately sought by persecuted Christians. The best selling, most widely studied piece of literature, whose influence is unquestionable, whatever you think of the book. Much of our art, law, philosophy, music and literature have drawn upon the Bible.
Yet this potency and influence aside, many people today want to ignore, rubbish, or reject the Bible. “How can you trust the Bible?” sceptics often ask. “New Atheist” writers like Richard Dawkins regularly attack the Bible, calling those who believe in it, “died in the wool faith-heads”.
Three Initial Thoughts
So how might we answer the sceptic? How can Christians show that is rational and reasonable to trust the Bible and take seriously what it says? There are numerous ways one might approach this question but this evening, I want to focus on a historical approach, as that’s my own academic background. But before that, let me start by making three general comments.
First, when somebody says “why trust the Bible?” I sometimes respond “why not trust the Bible?” One can only really doubt something if one has something more solid to believe in. Unless you merely want to be a sceptic. Whilst that’s very fashionable, it’s hard to be a consistent sceptic. Why not be sceptical about your scepticism?
Second, lots of people have bought into popular assumptions and myths about the Bible. So if somebody suggests the Bible is unreliable, ask them to be specific. How exactly? If they claim it’s full of myths, ask them which one they had in mind? Encourage them to read the Bible for themselves before passing judgement on it.
Third, there’s a lot of chronological snobbery about these days. Just because something is old or ancient, doesn’t make it false. Indeed, ancient-icity doesn’t tell us anything about whether something is true or false. Something can be ancient and true. Likewise something can be bang up to date and false.


The Internal Evidence for the Historicity of the New Testament

THE POPULAR HANDBOOK OF ARCHAEOLOGY AND THE BIBLE, pg.142

In addition to the strong external evidence for the reliability of the Gospels, there is also very good internal evidence. In fact, if one knew nothing about the Bible or Christianity but discovered a New Testament in an antique book sale, he could get a strong sense of its credibility just by reading it. Here are several reasons why:

1. The writers did not try to harmonize their accounts, which shows they were not in collusion but were independent witnesses 
2. The New Testament retained texts that placed Jesus in a bad light. Someone trying to prove that Jesus was God would not have done this.
3. The writers also included difficult passages in the text (which a fraudulent author would not have done).
4. They wrote self-incriminating stories (fraudulent authors do not invent bad stories about themselves).
5. They distinguished Jesus’ words from their own (showing they were reporting, not creating, His words).
6. They did not deny their testimony under persecution or the threat of death (which weeds out the insincere).

The cumulative weight of the multiple and independent lines of testimony is overwhelming support for the historicity of the New Testament. No other book in the world has anything close to this much evidence for its authenticity.
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