GalvestonTommy

Can you explain in technical terms (but not so technical that a layman can't understand) what were the chemicals and their reactions that got the whole thing of life started, life from non-life? The term precursor is kind of vague, sort of like some of Dr. Szostak's explanations on the first self reproducing organisms. You arrived at an enormous figure for available resources but what were they? While Dr. Szostak gave very enlightened speculations, he admits that the answer is yet to be discovered.

I realized after posting my smart aleck response that you meant precursors. I think Dr. Szostak's videos tried to explain just what the non-living chemicals could have been that got together and formed the first living organism(s). My posted quotes on May 17 from his videos show that he believes modern lab scientists are still not close to pinpointing the exact chemicals and mechanisms involved. (Those videos were listed on Moontanman's post of Jan. 26). [By the way, I did read (or at least browse) through this entire thread recently. Some earlier posts referred to other posts by a number. Where do I find the post number?] Of course I know that with what has been recently discovered, scientists have been working on this only for the past century or less. This is a relatively minute time span compared to the calculated eons that nature has had. It's that deep-time-of-the-gaps explanation again, given enough time any thing can happen. One last thing while talking about abiogenesis, I would be interested in knowing something about the background of some of the fellow posters. As mentioned, in addition to the last 8+ years studying biochemistry, etc., I have a degree in architecture, about 50 years in engineering type projects, some teaching in college, author of a textbook on a computer language which is a derivation of the lisp language (primary language used in artificial intelligence programs), co-author of a textbook on a major graphic and cadd software. Would any of you be willing to post any particulars that you might say stir your interest in this subject? Not trying to be too nosy, just interested.

Which came first, abiogenesis or bacteria?

How scientific is it to say that abiogenesis is the answer to abiogenesis?

As mentioned in an earlier post my research has included the following college textbooks and other sources: Keith L. Moore, et. al., The Developing Human; Benjamin A. Pierce, Genetics, Fourth Edition; Garrett & Grisham, Biochemistry; Patton & Thibodeau, Anatomy & Physiology; Futuyma, Evolution; Kenneth R. Miller, at least 7 books by Richard Dawkins, Matt Ridley, dozens of other books and hundreds of abstracts, articles, websites and other media. I studied the parts of the college textbooks that pertained to abiogenesis and evolution, which included topics on DNA, RNA and other cellular components, meiosis, chromatid crossover, mutations and adaptation, characteristics and traits, controlling factors, other than genes, include enzymes, signaling pathways and, in some cases, cell membranes and microtubules. I researched the various genes involved in certain features of the human body such as collagen, type I, alpha 1 (COL1A1), bone morphogenetic protein 4 (BMP4), the ANKH inorganic pyrophosphate transport regulator (ANKH) gene, the alkaline phosphatase, liver/bone/kidney (ALPL) gene, and msh homeobox (Msx) Homeobox genes, to mention a few. To repeat, I’ve studied dozens of other books and hundreds of abstracts, articles, websites and other media. I haven’t been “on the fence” forever. I’ve only been seriously studying these topics for about 8 years, hoping to understand the science behind the theories of evolution and abiogenesis. I viewed (twice) Dr. Jack Szostak’s three videos on “The Origin of Cellular Life on Earth” and the 29 (or so) videos of AronRa concerning “The Systematic Classification of Life”. Dr. Szostak stated in the first video (at 40.07 min.): “…this brings us back to the question of what was the first genetic material. Was it RNA in fact? Or is RNA so complicated or its building blocks so hard to make that life more likely began with something simpler, something easier to make, maybe something more stable that could accumulate like DNA, for example. This is an area of active debate and investigation. We really don’t know the answer to this question. But lots of people are doing experiments and trying to work out chemical pathways leading up to RNA….” Also in Dr. Szostak’s first video (at 44.42 min): “But, unfortunately, despite many advances over the years, we’re still far from having an RNA molecule that can completely catalyze the copying of its own sequence. So what we’ve decided to do is to actually again step back and try to look at the underlying chemistry and see if there might be ways of adjusting or playing (with) the chemistry of RNA polymerization that would simplify this problem. Ideally perhaps we will be able to find a complete chemical process that will drive RNA replication. That’s a very difficult task. Leslie Orgell and his colleagues worked on that for many years, got part way to a solution but were never able to have complete cycles of replication, so if we could get to that point then we would be back to being able to assemble this kind of model system, a model protocell composed of a membrane, compartment boundry, and replicating genetic material on the inside.” Also in Dr. Szostak’s third video (at 11.11 min): “...there's still many gaps in our understanding of how we would make pure concentrated starting material, There were some steps leading up to activated nucleotides that are far from clear. So there's a lot of work to be done. But I think this new chemistry has really advanced to field a lot. So, lets skip those missing link steps for the time being and assume that we can make activated nucleotides. Also in Dr. Szostak’s third video (at 20.15 min): "Unfortunately despite that challenge to the chemistry community, few people have addressed the problem and there is still no example of the chemical replication of any informational polymers. This is a major challenge." I don’t disagree with Dr. Tour. He doesn’t say that there is no evidence of abiogenesis but he says “We are nowhere near solving this problem.” There is a difference. Some of the most critical evidence just hasn’t been uncovered or proved as yet and it doesn’t look like it soon in coming. So, it gets back to what many have posted that it's the only possibility that today's science can come up with, solid evidence or no solid evidence

I stand corrected. I should have been talking about "The appearance of life on earth...", abiogenesis, not evolution.

And all this time I thought I was sorta nice, not a hard, unreasonable, illogical and unintelligent task master. But, as you said: "we still lack evidence." That kinda goes along with Tour's statement: "The appearance of life on earth is a mystery. We are nowhere near solving this problem." This is with ignoring mythical supernatural and paranormal propaganda. It's only considering the scientific approach. When better scientific evidence arises that supports the theory of evolution, it would definitely gain many adherents.

A good example of how words are defined is found in J. Edgar Hoover's Masters of Deceit (1958) where he tells of different definitions of the word "peace". In negotiations between the West and the USSR. The West's definition of peace was that each sovereign nation could determine their own type of government without outside interference. The USSR's definition was that peace was the absence of everything except communism in the world. So, while a rose is still a rose, the implication is that there is consensus of what a rose is before another name is applied. Random by any other name is still random; accident, chance, what have you. In this case there seems to be no consensus of what random is. It's like not being able to agree what is meant by the word "rose." To me, the whole process of "descent with modification" has enough randomness to it by the fact that a beneficial modification must be a rare event when you consider the size of a gene (if the modification is a mutation) like BMP4 and how it came into a useful arrangement of nucleotides. It contains over 9000 bases. There are many arrangements that will not work compared to the arrangements that will. I don't know the odds because I don't know which will not work. One arrangement that does work, of course, is the one that currently exists in organisms that have this gene. This argument applies mainly to evolution, but I think there is a similarity to understanding abiogenesis. As a lifelong doubter (questions keep nagging at me for reasons I cannot explain) I'm still seeking the scientific explanation I can understand.

"predetermined" sounds suspiciously like "predestined" or like all of existence (say a 747) was bound to happen from the beginning of molecular collisions. This is a rather limited definition of the idea of randomness. The insurance salesman finally convinced the old farmer to buy a policy. Before getting him to sign, he asked, “Would you like to add a double indemnity clause?”. The farmer replied, “A double what?” The insurance salesman said, “That is if you die by accident, the policy will pay double.” “Why sure I want that,” the farmer said, “If I die, it shore won’t be a-purpose.” The farmer’s view was that anything that wasn’t on purpose (by design) was an accident. Of course, the insurance company had a list of non-accident and non-on-purpose causes that mainly involved what they referred to as natural causes. In the life science fields, an accident is referred to as a random occurrence, without design and not attributed to natural laws. Some scientists like to minimize random events by stating that natural selection is not random and therefore the process of descent with modification is not random. See Douglas J. Futuyma, Evolution; ISBN 0-87893-187-2 (2005) page 534; “…natural selection is a deterministic, not a random, process. The random processes of evolution—mutation and genetic drift—do not result in the evolution of complexity, as far as we know.” Having one non-random event in the “descent with modification” process is like having just one strong link in an otherwise very weak chain of events. Delving into the theory of descent with modification will show that it is predominantly random (by accident) in spite of one phase of it (natural selection) be something less than completely random. I'm still trying to learn the scientific interpretations of words like random and phrases like deep time.

Again, Tour's video presents his scientific opinion regarding abiogenesis. He does not present it from a creationist's point of view nor does he give his opinion on evolution. In "An Open Letter to my Colleagues" he states: "We synthetic chemists should state the obvious. The appearance of life on earth is a mystery. We are nowhere near solving this problem. The proposals offered thus far to explain life’s origin make no scientific sense." He seems to disagree with the deep-time-of-the-gaps opinion that anything can happen if given enough time and that if abiogenesis cannot be achieved in the controlled environment of a laboratory then the odds of it happening in nature are insurmountable. He just states that we aren't close to solving the problem. I stated that I have not been able, so far, to erase some of the doubts I have regarding both abiogenesis and evolution. As far as Tour's credentials, see the following: Tour has over 640 research publications and over 120 patents, with an H-index = 129 (107 by ISI Web of Science) and i10 index = 538 with total citations over 77,000 (Google Scholar). He was inducted into the National Academy of Inventors in 2015. Tour was named among “The 50 Most Influential Scientists in the World Today” by TheBestSchools.org in 2014; listed in “The World’s Most Influential Scientific Minds” by Thomson Reuters ScienceWatch.com in 2014; and recipient of the Trotter Prize in “Information, Complexity and Inference” in 2014; and was the Lady Davis Visiting Professor, Hebrew University, June, 2014. Tour was named “Scientist of the Year” by R&D Magazine, 2013. He was awarded the George R. Brown Award for Superior Teaching, 2012, Rice University; won the ACS Nano Lectureship Award from the American Chemical Society, 2012; ws the Lady Davis Visiting Professor, Hebrew University, June, 2011 and was elected Fellow of the American Association for the Advancement of Science (AAAS), 2009. Tour was ranked one of the Top 10 chemists in the world over the past decade, by a Thomson Reuters citations per publication index survey, 2009; won the Distinguished Alumni Award, Purdue University, 2009 and the Houston Technology Center’s Nanotechnology Award in 2009. He won the Feynman Prize in Experimental Nanotechnology in 2008, the NASA Space Act Award in 2008 for his development of carbon nanotube reinforced elastomers and the Arthur C. Cope Scholar Award from the American Chemical Society for his achievements in organic chemistry in 2007. Tour was the recipient of the George R. Brown Award for Superior Teaching in 2007. He also won the Small Times magazine’s Innovator of the Year Award in 2006, the Nanotech Briefs Nano 50 Innovator Award in 2006, the Alan Berman Research Publication Award, Department of the Navy in 2006, the Southern Chemist of the Year Award from the American Chemical Society in 2005 and The Honda Innovation Award for Nanocars in 2005. Tour’s paper on Nanocars was the most highly accessed journal article of all American Chemical Society articles in 2005, and it was listed by LiveScience as the second most influential paper in all of science in 2005. Tour has won several other national awards including the National Science Foundation Presidential Young Investigator Award in Polymer Chemistry and the Office of Naval Research Young Investigator Award in Polymer Chemistry. Tour is the founder and principal of NanoJtech Consultants, LLC, performing technology assessments for the prospective investor. Tour is also a founder of Weebit (silicon oxide electronic memory), Dotz (graphene quantum dots from coal), Tubz (graphene nanopillar electrodes for energy storage devices), Acelerox (antioxidant particles for mitigating oxidative stress during trauma and autoimmune diseases) and Avid Chemotherapeutics (drug delivery for cancer chemotherapy). He has served as a visiting scholar at Harvard University, on the Chemical Reviews Editorial Advisory Board, the Governor’s Mathematics and Science Advisory Board for South Carolina, the Defense Science Study Group through the Institute for Defense Analyses, the Defense Science Board Chem/Nano Study Section, the Department of Commerce Emerging Technology and Research Advisory Committee and the MD Anderson Cancer Research Center’s Competitive Grant Renewal Board. He has been active in consulting on several national defense-related topics, in addition to numerous other professional committees and panels.

I'm not saying it must be wrong. As you might guess my name is Thomas. I'm a natural doubter. As a youngster, my mother said a visitor once asked her why she let met dismantle the new toy I just received. She said I always did that to see how it worked and then put it back together and enjoyed playing with it. I want to see how evolution works. I'm not saying it doesn't, but explanations with so many "I believes" and "might have been's" bring out the doubter in me. After studying, not just reading, at least 7 of Dawkins' books, I came away with the conclusion that there was a whole lot of speculation and not enough solid evidence to erase my doubts. His video on the evolution of the eye was interesting also, but was such an oversimplification that it left me with more questions than answers. My forum ID might also lead one to jump to the conclusion that I live in Galveston. I was born there, but moved away in 1953 when I was 14. Jumping to conclusions without adequate information is also an easy trap to fall into, I've found. I've done it myself. I'm not saying the modification came from the parents, only that it can be inherited by descendants

I can't. It's beyond my understanding.

Not really. That is why I asked the question: " how many generations will a population of organisms continue to exist (with perhaps a partial jawbone evolving into a complete jawbone) while modifications to the separate genes, gene sets and/or hereditary units accumulate until all of those necessary are in place so that the complete jawbone can be “selected” by natural selection?" Your response included an "I believe" and several "might have beens". That is why I'm not really picturing it happening, whether by a sudden jump or during many eons. Until more solid proofs of what you say "might have been" are unearthed, I will keep asking.Our divergent opinions on the possibilities of the mechanisms of evolution being a sure thing are like the difference between "guilty until proven innocent" and "innocent until proven guilty". Just a joke, please don't take that seriously. Perhaps we can just agree to disagree at this point. I hope I can continue this after a couple of weeks. If not, thanks for letting me participate.

As mentioned in my post of Thursday at 11:46, I have studied the subject. I posted a list of some of the sources. The Selfish Gene was one of the first I read when I began research 8 years ago. I understand that my 5 steps are not the only way that the theory of evolution is supposed to work, they are perhaps an oversimplification, but I believe that the other proposed or additional processes involved still have to answer my query. I just outlined what I thought was the most predominant process, descent with modification along with natural selection. I'm going to stand my ground with step 5. Are you telling me that if one of the genes, gene sets or other heritable factors that define one of the necessary characteristics of the jawbone is missing or faulty, that the jawbone will emerge in a population of organisms that has no jawbones?

For evolution to work as advertised the following must happen: 1. Something in an organism must be modified to make it different from its parents. 2. The modification must be caused by something that can be inherited by descendants. 3. The modification must be beneficial to the organism. 4. The benefit derived from the modification must provide an advantage to the organism such that natural selection will cause descendants to increase in numbers in the population. 5. If multiple modifications are required in order for the change in the organism to be beneficial then all of those required modifications must be present in the organism at the same time for the change to occur. Requirements 1 thru 4 above occur constantly throughout biological history. In most cases the benefits are derived from one or no more than two or three modifications. The modifications are primarily adaptations of traits of characteristics of already existing features; bird beaks, tortoise shells, pea pods, etc. Requirement 5 above (simultaneous accumulation of multiple modifications) has not been addressed fully by science. And, it is necessary for all of the required genes, gene sets and/or hereditary units to all be present simultaneously for all the expressed characteristics that are needed by a feature for that feature to come into existence and be suitable for natural selection. So the question is, how many generations will a population of organisms continue to exist (with perhaps a partial jawbone evolving into a complete jawbone) while modifications to the separate genes, gene sets and/or hereditary units accumulate until all of those necessary are in place so that the complete jawbone can be “selected” by natural selection? I think it is down to irreducible simplicity. Do the odds and deep time favor this happening? Am I being unscientific in asking this? If so, I'll sign off. That is why I told them I didn't want to involve creationism. As I said earlier, creationism is a matter of faith.

Isn't that what science is all about, questioning itself if it is on the right track. It seems like some areas are untouchable, even from a scientific approach. If some aspects of evolution prove to be in question that doesn't automatically make creationism valid. I believe that the right track is to keep questioning and not make certain concepts out of bounds. As you stated "Nothing is ever officially labeled 'truth'." It appears evolutionists want to label evolution "truth". It's a sort of "cake and eat" it approach. I'll be okay with a satisfactory explanation to the query I posed. Because they are members of the creationist community, I told them I appreciated their comments but if my approach was to be valid it needed to stand apart from creationism.

In my opinion, gravitational force fits in with a truth that came out with Newton's third law of motion. Also, electrical energy that we all use (along with its properties) fits in with my idea of truth. The truth is, if I fall off a ladder and land on a live wire on the ground, I don't expect anything good to come out of it. But I guess that is not very scientific. Eye color is only one characteristic of the eye, or any other feature that exhibits color. It's like Darwin coming to his conclusions by observing the change in the size/shape characteristic of the beaks of finches or the size/shape of tortoise shells. One characteristic along with its controlling factors does not cause an eye, beak, tortoise shell or jawbone to come into being. It requires a multitude of characteristics, which in turn requires there being a multitude of genes, gene sets or other heritable factors in place. How and when did the bird beak become selectable, not just its size/shape? I KNOW that science is on the right track, especially medical science. I (and millions like me) would not be alive today if were not for medicines and treatments discovered by hard working scientists. I go into a risky esophagectomy this coming Wednesday with the knowledge that my chances are greatly increased because of the advances in medical science. So on a personal basis I do think science is on the right track. Ive presented my ideas to about 6 PhD's about the need for controlling factors of multiple characteristics to be simultaneously present for a particular body feature to come into being. I was told " Your approach is fresh and so far as I am aware is unique." Otherwise I would probably not be pursuing this approach. I hardly expect any prizes or recognition if the approach is looked a seriously, but do believe it is a valid question. Your exchange of thoughts about this is greatly appreciated.

I definitely would encourage all the field and lab work that will, hopefully and eventually, uncover the facts. The biggest problem I see in a lot of previous findings is in the interpretation of those findings. History has proven that occasionally some deductions have been erroneous, especially before the 20th century. It's those deductions, erroneous or not, that have caused the biggest arguments. So, keep digging and testing and deducing (whether right or wrong). It's what science is all about. Eventually the truth will come out. I'm just mentally digging into the process by which even a simple feature like the jawbone can evolve. I hope that complies with scientific principles. I'm aware of reptilian jawbones having multiple bones that appear in humans as ear parts. I'm also aware that the jawbone starts out as multiple parts that become fused in the same manner as the skull does. Maybe I should have used our opposing thumb, but again it is made up of multiple bones that don't fuse. Or maybe the humerus. Just looking for a simple feature as an example whose function is selectable. That is why I used the jawbone as an example to pose my query. It is functional, it is selectable, and it is simple compared to those other parts.

I wasn't referring to the ancient vertebrates in that statement " Now all vertebrates, excepting maybe hagfish and lampreys, have jawbones." The idea that lots of vertebrate ancestors had no jaw begs a different set of questions about the jawbone evolving down multiple lines that I'm not concerned with. No, more like irreducible simplicity. Michael Behe defined irreducible complexity as "... a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning." The jawbone is a single part. We can even leave out the dentary in this discussion to keep it as simple as possible. The jawbone is the simplest feature that I can think of that lends itself to functions like eating and communicating that give the vertebrate an advantage that make it (the jawbone) selectable by natural selection. The same questions might apply to the distal phalanx of the little toe but its functionality is less critical to selectivity. My query involves the number of characteristics that every feature or body part, the jawbone and little toe bones alike, require to just become what they are. For example in the size/shape characteristic, even though the jawbone conforms to the general location and configuration of Meckel’s cartilage, other parameters must be determined such as length, width, depth, thickness, special bends, offsets, holes, cavities, protrusions, curvatures and all other aspects necessary to define the final form. This requires a gene or gene set. And then another gene or gene set is required to determine the material of the jawbone. And another gene or gene set determines the position and so fourth for each of the many separate characteristics of the jawbone or any other feature. There are no "interacting parts", just one. Even if the wing started out as something else that "something else" must have required a similar set of characteristics that were determined by genes, gene sets or other controlling factors.

Okay.

Do I detect prejudice? Hopefully no fantasy, just the facts. My understanding of the theory of evolution that I think is universally accepted is that it primarily involves descent with modification and natural selection. I know that genetic drift and other processes are mentioned also. I'll use the jawbone (simpler than heart, brain, lung, etc.) as an example. And for purposes of this discussion, I'll use the term characteristics for things like material or color. And I'll use the term traits for things like calcium phosphate for the material characteristic and red or brown for the color characteristic. Going back far enough in time we are told there was an ancestor that had no jawbone, an invertebrate, say. Now all vertebrates, excepting maybe hagfish and lampreys, have jawbones. I understand that for each characteristic there is/are genes or other controlling factors that determine that there is that characteristic and what traits will be exhibited; Bone morphogenetic protein 4 or BMP4 is reported to be associated with the size/shape characteristic of the jawbone due to the fact that certain mutations that might occur in BMP4 cause malformation of the jawbone. Another gene is collagen, type 1, alpha 1 (COL1A1) that when mutated, causes abnormalities in the jawbone. The material characteristic is affected adversely if the ANKH or ALPH gene is mutated. For the position characteristic, msh homeobox (Msx) Homeobox genes are thought to be essential for normal craniofacial development. While bone may have color, it would not be considered a characteristic (like in hair and skin color) because the color of bone is only a non-variable aspect of its material makeup. In addition to size/shape, material, position, and color there are other characteristics like connectivity, polarity (left and right), orientation, surface texture, extracellular makeup, quantity, and developmental process to mention a few. It appears that all of the characteristics of a feature like the jawbone (beak if it is a bird) must be in place for the jawbone or beak to be of benefit to the vertebrate. And each controlling factor must not have a detrimental mutation or the feature could be rendered unusable to a point that would be hazardous to the organism. I.e., the genes and other controlling factors must be in place and in sufficiently good order. My question is; is it logical to assume that all of the necessary characteristics (and therefore all of the genes and controlling factors) must be in place before a feature is of benefit to the organism in order to be selectable by natural selection? Or, will these factors show up periodically throughout time until eventually a jawbone will appear?

Whew! I guess I'd better let that dog go back to sleep. I do have another question, however. It has to do more with how features or body parts like the heart or jawbone evolve in the first place rather than the previous question that asked about the genetic instructions that controlling factors follow once a feature has evolved. Is this appropriate venue or thread to pose such a question?

My question has more to do with expected complexity, like the shape of a hand. Sometimes the first thing a mother of a newborn child does is count the baby's fingers and toes. If she and the father are normal, she expects (and hopes) her baby will inherit certain expected complexities with minor normal variations, but not a different number of digits. Although I knew a fellow engineer who had 6 digits on each on his extremities. He showed me the scars of the operation to remove the extra little finger on each hand but he still had 12 toes. He claimed to be living evidence of the theory of evolution. I'm not sure if I got the answer I was looking for in the first place, that scientists haven't yet been able to explain the plan that controlling factors go by to produce the expected complexities we are born with. I'm not implying intelligent design with this question nor creationism. I'm only trying to point out one of the countless bits of knowledge that has eluded us so far. Do I understand that you agree that details of the genetic instructions have not yet been fully discovered? It was really a simple query, I thought.

Can you tell me where in the genes are the instructions for, as you put it in an earlier post, determine the "shape of a hand or an eye"? Shapes and sizes of body parts are only one or their characteristics. Others include location, materials, polarity, connectivity, orientation, color (for some body parts like hair, skin and eyes).