I said I would continue to post but things got busy so it has been a while. I thought I would post an excerpt from “Signature in the Cell” that goes to my previous posts on DNA coding for protein synthesis while DNA synthesis is not possible without those proteins. Dr. Meyer’s book is about 600 pages and goes in depth on this aspect of information coding of DNA. Without some bakcground in biochemistry, cell physiology, or molecular biology, a few sections of the book may take a slower pace to understand but overall it is not a difficult book. As I have studied more in depth molecular biology (I have now worked in molecular biology for 9 years), I find that the strongest case for ID, in my field, is DNA. Since DNA is required to form the multitude of proteins that are also required to create, transcribe, and translate DNA, we have a major loop problem for origins of DNA and functional proteins required in living organisms.
Past scientists like Newton, Kepler, Boyle, and others found the argument for ID in fields such as physics. Newton noted his belief in intelligence behind the planetary/space systems in his most well-known work; Philosophiæ Naturalis Principia Mathematica

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Excerpt below is from “Signature in the Cell: DNA Evidence for Intelligent Design” (Harper Collins), Stephen C. Meyer, Ph.D., University of Cambridge, Philosophy of Science

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“These and other developments in molecular biology since the 1960s have shown that the information-processing system of the cell depends on a “tightly integrated” system of components—indeed, a system of systems. Both the transcription and translation systems depend upon numerous proteins, many of which are jointly necessary for protein synthesis to occur at all. Yet all of these proteins are made by this very process. Proteins involved in transcription such as RNA polymerases, for example, are built from instructions carried on an RNA transcript. Translation of the RNA transcript depends upon other specialized enzymes such as synthetases, yet the information to build these enzymes is translated during the translation process that synthetases themselves facilitate.

Biochemist David Goodsell describes the problem, “The key molecular process that makes modern life possible is protein synthesis, since proteins are used in nearly every aspect of living. The synthesis of proteins requires a tightly integrated sequence of reactions, most of which are themselves performed by proteins.” 41 Or as Jacques Monod noted in 1971: “The code is meaningless unless translated. The modern cell’s translating machinery consists of at least fifty macromolecular components which are themselves coded in DNA: the code cannot be translated otherwise than by products of translation.” 42 (Scientists now know that translation actually requires more than a hundred proteins.) 43

The integrated complexity of the cell’s information-processing system has prompted some profound reflection. As Lewontin asks, “What makes the proteins that are necessary to make the protein?” 44 As David Goodsell puts it, this “is one of the unanswered riddles of biochemistry: which came first, proteins or protein synthesis? If proteins are needed to make proteins, how did the whole thing get started?” 45 The end result of protein synthesis is required before it can begin.

The interdependence of proteins and nucleic acids raises many obvious “chicken and egg” dilemmas—dilemmas that origin-of-life theorists before the 1960s neither anticipated nor addressed. The cell needs proteins to process and express the information in DNA in order to build proteins. But the construction of DNA molecules (during the process of DNA replication) also requires proteins. So which came first, the chicken (nucleic acids) or the egg (proteins)? If proteins must have arisen first, then how did they do so, since all extant cells construct proteins from the assembly instructions in DNA. How did either arise without the other?

As the late British philosopher Sir Karl Popper mused, “What makes the origin of life and the genetic code a disturbing riddle is this: the code cannot be translated except by using certain products of its translation. This constitutes a really baffling circle: a vicious circle it seems, for any attempt to form a model, or a theory, of the genesis of the genetic code.” 46 Even the simplest living things operate as complex systems of multiple interdependent parts. Yet how this feature of life could have arisen is, as Jacques Monod put it, “exceedingly difficult to imagine.” 47

Complexity argues against ID as simplicity is a hallmark of both intelligence and design.

Complexity does not equate to an inefficient design. We can look at highly complex systems that are designed and manufactured by humans. Just look around at machinery. I would be interested to see sources for the idea that only simple systems are designed and complex systems are random as I have never read research stating that conclusion. Observation alone would seem to refute that idea. The Large Hadron Collider is very complex, yet it was designed and built by intelligence.

When we look at just proteins, it may not be apparent the specificity that is needed for amino acid sequences to be biologically active. We are not just able to put amino acids in a sequence. We need only L forms. All amino acid bonds must be peptide bonds. The proteins must fold into the correct three dimensional pattern and they must be in the correct sequence not only for the correct folding but to react at the correct sites.

Probabilities have been calculated for just a single biologically active protein which is of short length to form by chance (which would be needed without DNA coding). Calculations have also been done for the smallest number of proteins to form for the most simple single celled organism.

These are not just six sigma events but wildly improbable. Nothing is impossible but with the advances in molecular biology in the last few decades, it is not scientifically valid to discount the probabilities of evena single organic protein forming by chance, let alone the hundreds needed for a single celled organism.

I agree that simple explanations are more likely correct yet I do not see the random formation of hundreds of proteins forming in the same geographical location that randomly happen to function in a complementary system to be the simple answer.

We would also need to figure the probability of these proteins at a later time having random encoding DNA produced that by chance create this same sequences from L forms, with peptide bonds, in the correct order (with allowable small variations). We also must have the many cofactors, minerals, vitamins, energy source molecules (like ATP) also present.

The advances in molecular biology and the mathematicians who have calculated the odds of chance have led many origin researchers to question the chance hypothesis. I am not alone and I am not nearly as intelligent as the scientists whose papers and books I have read. I have studied statistics and work with it daily in the laboratory. I also understand biochemistry and molecular so I lost the ability to stick with the random chance theory of life formation. That theory appears to be more of a “we do not know” answer and not based on any scientific principles.

Some people have even jumped to seeding by alien species, especially due to the limited time we had on Earth until the first life appeared. To me that is well beyond any simple answer and brings up an entirely non-scientific explanation.

From Meyer’s book again, this is a conclusion after a long chapter on the scientists and mathematicians working on the probability aspects:

“Axe’s experimental findings suggest that Hoyle’s guesses were pretty good. If we assume that a minimally complex cell needs at least 250 proteins of, on average, 150 amino acids and that the probability of producing just one such protein is 1 in 10164 as calculated above, then the probability of producing all the necessary proteins needed to service a minimally complex cell is 1 in 10164 multiplied by itself 250 times, or 1 in 1041,000. This kind of number allows a great amount of quibbling about the accuracy of various estimates without altering the conclusion. The probability of producing the proteins necessary to build a minimally complex cell—or the genetic information necessary to produce those proteins—by chance is unimaginably small. Conclusion Axe’s work confirmed the intuitions of an older generation origin-of-life researchers and other scientists—such as Harold Morowitz, Fred Hoyle, Chandra Wickramasinghe, Alexander Cairns-Smith, Ilya Prigogine, Hubert Yockey, Christian de Duve, Robert Shapiro, and Francis Crick (after 1980) 20—who were deeply skeptical about the chance hypothesis. Many of these scientists had performed their own calculations in which they assumed extremely favorable prebiotic conditions, more time than was actually available on the early earth, and maximally fast reaction rates between the chemical constituents of proteins, DNA, and RNA. Invariably, such calculations have fueled greater skepticism about the chance hypothesis, especially since origin-of-life researchers also recognize that DNA and proteins possess functionally specified, rather than just Shannon, information.”

I thought I would quickly revisit some subjects mentioned earlier in the thread since it has been a while and I have studied them more in depth. The two areas are the bible code and the young Earth theory. After all I have read, I cannot agree with either of them.

The bible code does not make sense as a code would require a single extant original reference from antiquity (or a perfect copy we could verify) in ancient Hebrew yet there are many variations of manuscripts that it would be impossible to know which is original, if any.

The young Earth proponents have some good arguments on geology and dating problems (there are many problems with isotope and other dating techniques). However, they are too strictly literal, in my opinion, in their interpretations while studying biblical scholarship in Hebrew, Greek, and Aramaic show that much of the bible is not strictly literal and many times is written in a particular way in order to convey a specific meaning or theological point . Also, this view requires someone to assume that the Bible was written to convey science, which it was not. Readers of the text had their own worldview and their own ideas. Nothing in the text required science to understand and it can easily be shown that some of the ideas were written with current (flawed) science of the time. Just one of these is Paul and the head covering passages, which relate to Roman understanding of physiology based on Hippocrates. If the authors were writing to convey science, their writings would have been outdated within a generation as scientific knowledge is continually advancing. If it were to speak to our current knowledge or any future knowledge of the physical world, it would have made no sense to the audience when written. The Bible is a spiritual book and not a material treatise of physics. I have read books on readings of Genesis that use a functional meaning and not a material meaning for creation as well as books on genealogical gaps that would throw any dating based on those genealogies out the window. Since there are many disagreements among scholars on interpretations, even in the ancient manuscript languages, it is very hard to dogmatically stick to a single view if it is refuted by scientific evidence. That is not to say the science is settled or that the views might not change, they usually do. Anyone who states a science is settled has a poor grasp on scientific inquiry.

When science shows evidence for any field, especially if there are multiple proofs, it seems best to support the evidence. Historical sciences are notorious for having a lack of evidence as opposed to empirical science so it makes it more difficult to find proofs but circumstantial evidence supporting a theory can help. If valid evidence interferes with ones interpretation of the Bible, it could just be that the interpretation is incorrect. I have found that church members have just as hard a time with biblical evidence that contradicts their views as non-church people do with scientific views that go against what they have been taught. One example: A few months ago I was discussing scriptural evidence for astronomical data correlating to a specific past date in Revelation with someone at church. It went against their dogma that this passage was a future event so I pointed out textual evidence based on original languages as well as astronomical software that fixed the date of the alignments. When confronted with actual evidence for my viewpoint, the person was exasperated and just walked-off, unable to handle the data. Any discussion in a field of study should be based on evidence and if the evidence is not substantial, then questioning a view is valid. If we disregard someones viewpoint, we should be willing to support that with evidence. If they wish to sway our thinking, they should be able to give us evidence to help change our view.

My view on theories of evolution are based on the research I have studied over the past 3 decades (I have only been a Christian for 5 years). They are based on my knowledge of biochemistry, molecular biology, physics and some geology. My original questioning of the validity started in the 80’s in my geology course. If I find good evidence for cross species evolution, I have no problem with it as I have no problem with God creating life in that way. I just need biological evidence that makes sense.

So far, my main point of contention is the specified coding in DNA, RNA, and proteins. Origin researchers who have studied each area have discounted chance as it is statistically impossible due to the functional sequences and information encoded in the molecules while there is no differential binding of nucleic acids to support a self organizing answer. That leaves either a protein, RNA, or DNA as the originating molecule and each of these have many problems that researchers have been unable to explain. The research is interesting but it is unlikely in any scenarios I have studied. Even researchers understand their dilemma.

Then we have the problem of the theories needing not only a differing atmosphere from anything we have known on Earth (where the proteins, RNA, DNA would not be degraded) but a hypothesized “prebiotic soup” or the biotic molecules would not have been able to form, just as they cannot form currently. Neither of these states have evidence of existing in the past and are merely theoretical.

“The nitrogen content of early Pre-Cambrian organic matter is relatively low (less than .015%). From this we can be reasonably certain that: there never was any substantial amount of ‘primitive soup’ on earth when Pre-Cambrian sediments were formed; if such a soup ever existed it was only for a brief period of time.”

- Geochemist James Brooks, “Origins of Life”, (1985) 118

More researchers quotes:

“To invoke statistical concepts, probability and complexity to account for the origin and the continuance of life is not felicitous or sufficient. As the complexity of a molecular aggregate increases, and indeed very complex arrangements and interrelationships of molecules are necessary for the simplest living unit, the probability of its existence under the disruptive and random influence of physico-chemical forces decreases; the probability that it will continue to function in a certain way, for example, to absorb and to repair, will be even lower; and the probability that it will reproduce, still lower. Statistical considerations, probability, complexity, etc., followed to their logical implications suggest that the origin and continuance of life is not controlled by such principles. An admission of this is the use of a period of practically infinite time to obtain the derived result. Using such logic, however, we can prove anything…. When in statistical processes, the probability is so low that for practical purposes infinite time must elapse for the occurrence of an event, statistical explanation is not helpful.”

- Senior research biologist at the National Institutes of Health P. T. Mora, “Urge and Molecular Biology.” Nature 199 (1963): 212–19.

“An honest man, armed with all the knowledge available to us now, could only state that in some sense, the origin of life appears at the moment to be almost a miracle, so many are the conditions which would have had to have been satisfied to get it going.”

- Francis Crick, “Life Itself”, (1980): 88.

Dose on research efforts:

“...led to a better perception of the immensity of the problem of the origin of life on earth rather than to its solution. At present, all discussions on principle theories and experiments in the field either end in a stalemate or a confession of ignorance.”

- German Biochemist Klause Dose, “The Origin of Life”, (1988)

Good design uses the minimum complexity necessary. Not to put words in Sporkboy's mouth, but that seems to be the intent of his post, and good common sense.
Examples of how biology is not by design but rather by evolution are outrageously numerous, and some have been given in this thread already. The refutation of those examples seems to be "but humans don't know the purpose of the added complexity", even though evolution seems to explain it nicely. Occam's Razor and all that.

Yes, I get the simplicity idea but complexity abounds in human manufacturing, whether we see it as being simple or not (or perhaps as simple as a complex design can be). A computer system is fairly complex and relies on many parts, including software, to work. Are we to assume that a computer was not designed by intelligence because it is complex? Perhaps the computer was designed as simple as possible, yet it is still a complex machine.

The issue is not that biology, proteins, or DNA are complex, but that no origin of life researchers can explain how they could have been formed by themselves since they are interdependent. DNA codes for the proteins while the proteins cannot be manufactured without DNA or RNA. This is why the chance hypothesis alone is no longer used. Although cellular physiology appears complex to most people, it can also be seen as simple in that it functions as is needed, just like the computer system. Inter-related parts functioning together as a system, which do not function apart.

I understand what you are saying. First life is something that we don't understand yet.
History abounds with things that we as humans did not understand and therefore were assigned to the supernatural.

There seem to be 3 types of thinking in regards to things that we don't understand:
1. Magic, Supernatural, the gods.
2. Science, natural origin that we don't understand yet, but search for a natural explanation.
3. Who cares... What's on TV ?

History is chockerblock full of examples of religions claiming ultimate knowledge about all sorts of things, only to have to retreat as science explains the mysteries. Men and women have been burnt at the stake for daring to have an opinion or explanation that is at odds with the dour old fellows in the flowing robes and bejeweled fingers...
Giordano Bruno is one of my favorites... I bet he was a real corker in life. He dared to say (amongst other things) that the little specks of light in the night sky were distant suns, just like our own, with planets in orbit around them. After he was sentenced to public execution by being hung upside down and burning, the religious authorities had an iron nail driven through his tongue and into his jaw bone so that he could not speak to the gathering crowds.

The response by religion is almost always the same... "Religions are run by imperfect men. Now we know better" or some such apology. Religious people today do not accept that their religion is the same as of those sweet fellows who ordered Mr Bruno to hang upside down and burn to death over a big pile of oil-soaked wood... "Mine is different. I wouldn't have done that."
It rings hollow to me, because religions en masse have been directly responsible for some unbelievable atrocities. A response to that last charge is "so have atheists."

All this is not meant to be a ringing indictment of religion, but to explain why I fall into the 2nd category in my list of 3, above.
There are a few great mysteries left to science...

All experience is an arch wherethro 'gleams that untravell'd world whose margins fade forever and forever....

I agree with much of what you said Mike. My premise is not to prove or disprove atheism or theism. Your original idea of this thread was due to someone attacking Pence in another thread because he did not agree with evolution and that person stated Pence not believing in evolution went against science. I have tried to list arguments which show why some scientists have valid reasoning to discount evolution. I have also listed many scientists who agree, Dr. Meyer being one who does not go into the religious realm but just states how DNA and the cell functions have encoded specific information, much as computer information systems do. His arguments are scientifically sound, whether they are proven to be true or false in the future. To state that if a person does not believe in evolution because they do not understand science is patently false. That does not mean anyone has to be of the same opinion. It also does not mean that we all have to hold the same beliefs as far as theism or atheism. I would not say that evolution does not have valid points, as a scientist who used to believe in the theory, I know it does. The issue is there are good arguments on both sides and for someone to try to say otherwise just shows that they have not studied both sides and do not understand the information encoded in DNA or molecular/cell physiology. I understand that molecular, biochem and cell phys are not easy and that most people have not studied any of them so it is not surprising that people do not read the research.

I have personal experiences for my religious views that are beyond a scientific analysis but that does not mean I must disregard science. If I were to disregard science and the scientific method, my job would be fairly difficult. My views on both need to mesh or I must change my views on one or the other. I am always looking for other views, which is why I was interested when you asked about starting this thread. I often change my views based on good arguments people make but my personal experiences hold a lot of weight in my beliefs. Although my personal experiences may be interesting, I do not go into them here but have no problem in PM if anyone is interested. Our worldview is shaped by our experiences as well as what we have been taught. If my 40 years of studying in scientific fields has taught me anything, it is that science always changes and we must keep our minds open to all possibilities. No science is ever settled, no matter how much anyone tries to say otherwise. Perhaps in the future I will have other experiences that overturn what I believe and I am open to change. If you work in a scientific field, you will not do well if you let presuppositions hold you back.

The intelligent design idea is based on DNA's informational/functional encoding. ID, per se, is not a religious argument because it holds out no prospects of answering any questions about theology. Similarly, quantum physics does not argue about how observation can collapse energy into matter, it is just a fact that we do not understand. Observation creates matter from energy, yet it tells us nothing about the mechanism. Science then moves into a philosophical discussion.

I am not stating that specified information encoded in DNA is a proof for any religion, just that there is a good case for intelligent design as one possibility. That is the case stated in Dr. Meyer's book, which he lays out exhaustively based on both past and current origin of life research using scientific methods. Functional specificity based on a quaternary, as opposed to computer binary, coding of nucleic acids is the main problem origin researchers have run into with the cell and it's DNA/protein/RNA systems. Another is the inter-related systems of the cell, as discussed earlier (creation/replication/transcription/amplification of ATP, proteins, RNA, DNA, etc). The systems of the cell work in similar ways to a computer information system. As of this time, no specified information has been shown to be randomly formed, it is based on intelligence creating the information.

Excerpt on computer vs cellular information systems:

"In any case, the cell’s information-processing system has three key elements: (1) digital storage and encoding of information, (2) machinery for processing that information to produce a functional outcome, and (3) encoding of higher-order (hierarchically arranged) regulatory information. These three key elements for expressing biological information are also found in computer-based information-processing systems. They too (1) encode information digitally, (2) process information with machinery, and (3) use hierarchically organized information to regulate the expression of other information.

These three elements provide a good example of what software designers and other engineers call a design pattern.11 A design pattern is a general way of solving a design problem. A design pattern distills a functional logic that can be applied and modified in different contexts to solve different but related engineering problems. DNA and the cell’s information-processing system exemplify many design patterns. At the highest level, the way DNA and its information-processing machinery encodes and processes digital information represents a solution to a general design problem: how to store information and transmit it across a communication channel in order to produce a functional outcome...

We see in the cell’s use of nucleotide bases as digital characters a functional motif that we know well from our own information technology. Recall Richard Dawkins’s observation that “the machine code of the genes is uncannily computer-like” or Bill Gates’s observation that “DNA is like a computer program.” We also recognize a design pattern in the way the cell stores, transmits, and processes information. Recall Hubert Yockey’s observation that the “genetic code is constructed to confront and solve the problems of communication and recording by the same principles found…in modern communication and computer codes.”12 We also recognize a functional pattern in the way the cell uses digital characters to construct three-dimensional mechanical parts. Recall the discussion in Chapter 5 of the airline manufacturing industry’s use of CAD-CAM (Computer Assisted Design and Manufacture). And scientists familiar with the logic of software design can recognize many other more specialized design patterns and strategies in the subsystems of the cell’s information-processing system...

My colleague told me that he recognized many of these specific design patterns and strategies at work in the cell. He expressed his awe at the “sophistication of its design logic” and its resemblance to that used in the software industry. He said the cell often employs a functional logic that mirrors our own, but exceeds it in the elegance of its execution. “It’s like we are looking at 8.0 or 9.0 versions of design strategies that we have just begun to implement. When I see how the cell processes information,” he said, “it gives me an eerie feeling that someone else figured this out before we got here.”

Meyer, Stephen C. - Signature in the Cell: DNA and the Evidence for Intelligent Design. HarperCollins.

I better get to sleep, hopefully I am not too tired to make a little sense.

Miller Urey experiment. Amino acids (and more) assembled spontaneously. Proteins are compound built up of amino acid compounds. No DNA needed.

No magic needed.

Add enough time and a bewildering array of proteins assemble.

Not hard to imagine after a few millions of years what can follow.

Just because we haven't figured everything out yet doesn't mean it automatically gets filed into the "well God created it Bin". That's where the research tends to get stifled. science has proven many times that things God created or writings in the bible that people take as the truth is in fact not true.

Glutathione is built from three amino acids and is biologically active.

It's easy to calculate the probablistic improbability of a thing if the correct mechanisms are unknown. Once the process/mechanism becomes known the calculations switch and the thing becomes impossible NOT to occur.

Seriously, how hard can it be for three amino acids to form a simple protein in a million years?

Jumping into the game trying to explain a cell and cellular function is silly. Start building a few protiens. Who knows the precursor forms to cyanobacteria might have been prionic in nature. Prions are interesting in many ways.

"Observation can collapse energy into matter" is so utterly wrong and clearly marks a fundamental misunderstanding of quantum theory I don't even know where to begun.

Everything I've read in this thread regarding quantum theory is similarly inflicted with such misunderstanding. I expect it as most of my collegues and even many professors are similarly confused.

Understanding the difference between a model and the system under scrutiny is critical. It is quite easy to make the fatal mistake of assigning inferences of the model into the system.

For example the wavefunction belongs to the model but not to the system. This point is key so ponder it well.

LiL protiens are biologically active and are TWO amino acids.

http://www.yalescientific.org/2015/11/t ... functions/

The size of the laboratory and the time frame that it operated in are both immense beyond human ability to comprehend.
It has always seemed odd to me that people use the "can't replicate life in the laboratory" argument (not that you have Murray.)
So the current "chicken or the egg" that is pointed out by Murray several times doesn't preclude simpler life from having developed, it just means that our current knowledge does not include a known path from simpler to current life.
I am not a biologist, so my attempts at explaining my thoughts on this are for sure going to be amateurish to the guys who work with this stuff all the time. Sorry.

Consider a phase change as an allegory to ... Hmm, that's not a good one.

I am going to pull out a few biology books to refresh my old memory of how mono-cellular critters absorb RNA and DNA from things that they "eat", effectively evolving on an instant basis.
I think it is likely that life evolved from naturally occurring organic stuff in tidal swamps like Sporkboy alludes to, then as a couple of those simpler critters married each other and turned into a far more robust (albeit complicated) organism, that more robust or aggressive combination went on to completely dominate the food sources.

Back to the size of the laboratory... How many atoms or molecules are in a Mole? Avogadro's Number is 6.02x10^23 602,000,000,000,000,000,000,000 - ish. Each one of those zeros represents an increase by a factor of 10. The human mind can't comprehend such an astronomically (haha) number, and this is the number of water molecules in 18 grams, or 18 mL
I did a search for a good description of how big this number is...
http://blog.ed.ted.com/2013/10/23/how-b ... e-exactly/

I love the kinds of descriptions like this from that site -

They are imperfect, but fun to imagine. Picture being in a small airplane and "feeling" the immensity of the volume just in the air around you... and realize how tiny that space is.

Avogadro's Number, 6.02x10^23 is the number of water molecules in 3.5 teaspoons of water.
Funny thing is, we didn't have just the Earth and all of its water and minerals for this laboratory... There are lots of chunks of Mars that made it to Earth in the early years of the solar system.

So there are some numbers to chew on to see just how bigly the laboratory was... Immense beyond comprehension.
The time frame is lengthy in a similar way, but with an added twist. We can't conceptualize, or "feel" 1 million years, let alone 500 million or a billion years. Comparisons like that of the molecular numbers in Avogadro's Number to time similarly confuse our mammalian brains. We're just not built to understand such numbers. (I sorry, brethren, I know that I repeat some topics.)
I take a random result for the search "Rate of Chemical Reaction" , http://www.dummies.com/education/scienc ... reactions/

The video is kind of dry, but he eventually gets to how quickly wet reactions can take place.

If we put these three factors together and our inability to grok the significance of each of them (incomprehensible number of reactants, time frame of reactions, rate of reactions) it becomes pretty understandable why some people take the position that a certain chemical combination is impossible to occur spontaneously. We just can't grok the scope of that chemical laboratory, The Earth.
How many people try to grok the number of molecules in 3.5 teaspoons of water?

What was the Miller-Urey experiment?