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Everything posted by lucaspa

  1. I was not. The problem is that "purpose" has been mistakenly linked with action by an intelligent agent. Like "design" has been mistakenly linked with action by an intelligent agent. The point here is that natural selection is an unintelligent method to get design. Aristotle listed 4 types of causes. His example was a chameleon changing color bright green on a leaf to dull-gray on a twig. 1. Formal cause: Generalization of the conditions under which the change takes place. In this case the formal cause would be the chameleon moving from the leaf to the twig. 2. Material cause: the substance in skin that changes color. This gets us to the biochemistry of the skin cells and chemicals in them that are responsible for the color change. 3. Efficient cause. This is the transition of leaf to twig and the associated change in reflected light of the leaf vs the twig. 4. Final cause or teleological cause. This is that the chameleon is escaping detection by predators. But notice that this is not conscious. The chameleon does not know it is escapting detection by predators. Nor did the chameleon "plan" to do this. But natural selection did "plan" it this way. Natural selection is, in the Aristotlean view, a teleological cause event tho it is not intelligent. And that is the whole point of natural selection. It is the teleological cause instead of an intelligent agent who had to "design" and manufacture the chameleon so that it avoided predators. Merged post follows: Consecutive posts merged But it does. If natural selection does not do the designing, then what does? Natural selection is a two step process: 1. Variation 2. Selection When you say "natural selection does not cause variation" that is true, but irrelevant. In order for the entity "natural selection" to exist, there must be variation. The source of that variation is immaterial. It can be sexual recombination, mutation, changes in syntax in computer code (in the case of genetic algorithms) etc. Natural selection will still happen. That is the reductionist definition of "changes in allele frequency through time". But that is NOT the essence of natural selection. After all, genetic drift will have some organisms reproducing more successfully and will dominate. Look at Darwin (why is it that so many "evolutionists" have never read Origin of Species?): " But if variations useful to any organic being do occur, assuredly individuals thus characterized will have the best chance of being preserved in the struggle for life;" It's not about just "reproduce more successfully", but why they reproduce more successfully: the variations are a better design ("useful to any organic being") than the other variations. Again, there is no "long term" purpose. But there is a short term purpose. "Diversity" is not the criteria for a changing environment. As you noted, the overall parameters of the population change. Unless that is "random", then that change must be to some purpose. What's the purpose? That the individuals survive in that environment. Look above to my discussion of the types of causes. The "purpose" of a chameleon changing color is to avoid predators. The purpose of your eyes is to detect light. The purpose of your ears is to detect sound. The purpose of cytochrome c is to transfer electrons to oxygen and, in the process, make ATP. Biological organisms are full of purpose. How did it get there? Natural selection. Do NOT run away from "design" or "purpose". Embrace them. Natural selection provides the explanation for how those designs for particular purposes arose. Discard that and say there are no designs or purposes in biological organisms and you deny reality.
  2. Actually, no. Remember, this is a loss of air pressure -- being put in a vacuum. The animals go thru the torture of decompression, with bursting blood vessels, bulging eyes, etc. All very painful. Humane suffocation is carbon dioxide inhalation. Put an animal (usually a rat or mouse) in a chamber and then flood it with CO2. The animal peacefully goes to sleep and then stops breathing. And this is one of the approved methods of euthanasia for animal research. Merged post follows: Consecutive posts merged Remember the experiments the Nazis did on Jews that were "gunna get fried anyway"? That's where this logic ultimately leads. It also leads to the result Larry Niven discussed in several of his short stories: if medical benefits come from prisoners condemned for death, there won't be enough of these and it becomes very easy to extend the death penalty to more and more crimes to make sure there are enough prisoners for testing. Remember, right now rapists and child molesters cannot get the death penalty. So you are already advocating extending the death penalty to these crimes. We all have heard, especially in rape cases, where DNA evidence has overturned the conviction of several "rapists". You would have those individuals executed when, in fact, they were innocent. Do you really want that on your conscience? I think we are all agreed that using animals for painful tests -- such as the Draize test -- for cosmetics is wrong. But medical testing is different. Even if you are using prisoners, most prisoners do not have melanoma, or tuberculosis, or cardiac arrythmias, etc. Would you inject prisoners with melanoma cells? Deliberately infect them with tuberculosis bacteria? If that is the case, how are you different from the Nazis? Merged post follows: Consecutive posts merged Basically, that is the rule applied to all animal research, with a few minor exceptions. If you would give a human a pain reliever, then you must do the same for an animal. If you would perform sterile surgery with anesthesia on a human, then you must perform essentially the same surgery and anesthesia on the animal. The exceptions come when such pain relief would compromise the data. Remember, the ultimate purpose of the animal research is to obtain data that will ultimately lead to a better understanding of disease or physiology in humans. So, altho we might feel constrained to give a human pain relief (never mind the data), if such pain relief would make it impossible to get the data from the animal, we are using animal as a route to get data we can't get from humans. One example is neurological data from the brains of rats. The normal methods of euthanasia are either 1) carbon dioxide inhalation or 2) pentobarbital injection. Both are painless but both take a long time and result in the destruction of short term neurotransmitters in the brain. So if you are studying models of Parkinson's or other brain disorders in rats, you are allowed to guillotine the rat. That death is so quick that it preserves the neurotransmitters you need to study.
  3. Notice that there were no citations to back this claim. There were other quotes you should also have looked at. For instance: "It has long been known that an intact cortex is required for the full extent of suffering. In his studies on the neurology of noiception, Woolf (1983) removed the cortex of rats to “obviate” the problem of suffering from pain. Even now, it is not well-understood how higher association areas in the brain interpret subcorticol input. " You are trying to make an Argument from Authority here. What matters is the data and, reading the presentation carefully, the data does not back the claims with the certainty the authors are claiming. Merged post follows: Consecutive posts merged That isn't what the presentation states. The presentation says that these species have the anatomical areas associated with pain, fear, and terror in humans. BUT, the data from the papers cited are not able to tell whether the animal feels fear or terror! I found this interesting from the presentation: "The present consensus is that the PFC mediates executive functions which include advanced higher mental processes, such as directing attention, accessing various memory systems, coordinating sensory and motor information, and modulating emotional states (Krasnegor, et al 1997). In humans, the prefrontal cortex must be intact in order to experience the emotional sensation associated with pain (Freeman and Watts, 1950). However, neurobiologists long believed that the PFC is a recent evolutionary acquisition and is unusually large in the human brain. Recent advances in the study of prefrontal cortex find no justification for these beliefs. Jerison (1997) conducted a formal analysis of similarities and differences between species and provides evidence that the PFC is an ancient part of the mammalian brain, is put together in all mammals pretty much the same way, and it’s functions are basically similar. The percentages of frontal cortex in relation to the rest of the brain are 29% in humans, 17% in chimps, 7% in the dog, and 3% in the cat (Broadman, 1912, Fuster, 1980). Although cats have less PFC compared to dogs, we would argue against any suggestion that cats suffer less from pain than dogs, or that rats suffer less than cats. It is likely that the cat has sufficient frontal cortex circuitry to have the minimum required amount to fully suffer. " It does appear that the PFC is unusually large in humans. Notice that there is no data on comparison of pain between cats and dogs. Instead, the authors make the unwarranted inference that cats have sufficient PFC to "fully suffer". They need data to back that claim. There is no such things as "highly evolved". Amoebas are just as 'highly evolved' as humans. The question is whether the brains of cattle and pigs can experience "dread, terror" as humans do. No data. And the paper does not provide any. Again, the question would be: are nervous systems the ONLY way that an organism can feel pain? You assume the answer is "yes". But it's an assumption, not one based on data. What you are doing is projecting human emotions on cows and pigs when you say "suffers when it is killed for slaughter". I would argue from an evolutionary standpoint that this is not the case. Both cows and pigs are prey in nature. Individuals are "slaughtered" all the time by predators. Would an ability to "suffer" aid or hinder survival under these circumstances. I would argue that the ability to feel "terror" or "suffer" would be deleterious. What happens to humans experiencing "terror"? They tend to freeze and be unable to act. Such behavior would make an individual prey easier to catch. Therefore the ability to anticipate "suffering" or feeling "terror" would be eliminated by evolution. Hominids might have evolved such feelings only after extensive tool use when humans became predators instead of prey.
  4. That is not quite correct. Pain is a complex neurological reaction, with both impulses of the sensory nerves and interpretation of impulses in the brain. As you noted below, if you are concentrating on something else. you don't "feel" pain. Enough adrenaline in a human will block "feeling" pain. Humans, as noted, get used to "chronic" pain and don't "feel" it anymore. Or at least don't feel it at the intensity of someone encountering that sensory input for the first time. Also, humans feel pain when there are no nerves being stimulated. This is a common phenomenon following traumatic amputation of a limb -- called phantom limb pain. Interestingly, phantom limb pain is not present when the amputation is a voluntary decision in reaction to chronic pain. It is very difficult to tell when animals are in pain. I haved performed many surgeries on rats and witnessed many procedures on rats that humans would regard as painful, yet the rats exhibit no pain-related behaviors. Do they "feel" the pain? I can't tell. Are the nerves stimulated? Maybe. Does their brain process the stimulation as pain? I don't know. We mostly know pain in humans due to speech -- we tell each other we are in pain. In some cases of severe pain, there are behaviors: screaming, writhing, etc. But some people don't display those behaviors with injuries where other people do. Merged post follows: Consecutive posts merged Those are the 2 possibilities, aren't they? 1. Behavior to noxious stimuli is not evidence of pain. 2. Plants do not feel pain. You can argue in favor of #2 by saying that plants do not have nerves. However, are nerves the only way "pain" can be transmitted? So #2 isn't as solid a conclusion as you seem to believe. Humans have behavior to noxious stimuli that, by means of speech, we know is pain. How can you conclude that similar behavior in other species is absolutely not evidence of pain? The uncertainty in the whole situation is why IACUC rules follow human standards: if a human reports pain from a similar procedure, then it is assumed the animal will feel similar pain and require analgesics. That may be on the conservative side, but IACUC has decided to err on the conservative side.
  5. You can define "naughty" only in regard to pets. And then only in regard to behavior that people define as objectionable. By its own standards, is a dog or a lab rat being "naughty" when it bites someone? No. Often it is only defending itself to a perceived threat or acting like a meat-eater -- which dogs are. So I appreciate the effort at compromise, but it won't work. As the regulations stand now, it is illegal to use dogs or cats obtained from a shelter for research. ALL research animals must be purchased from a licensed vendor. So unwanted dogs and cats cannot be used for research, but instead are put to death in a hypobaric chamber -- which means they suffocate to death.
  6. 100 amino acids ~ 10,000 MW. Insulin and other proteins are shorter than that. Also, many of the chains of dimeric, trimeric, etc. proteins are that length. I think what you meant was "longer chains" instead of "higher yield". The average weight of proteins obtained by dry heating amino acids is ~ 60,000 MW, which is also about the average weight of proteins by DNA directed protein synthesis.
  7. Why aren't those published studies listed at the website? Why don't you list them for us? Studies in the peer-reviewed scientific literature, please. What is the "proof"? I've never seen any papers quantifying the number of stem cells released. Also remember that there are 6 million red blood cells per milliliter in adult blood. Adults have > 5 liters of blood, or over 5,000 milliliters. So the increase doesn't amount to the number of red blood cells in 1 milliliter. When I treated a 3 mm defect in rabbit cartilage with adult stem cells, I had more than 60 million adult stem cells at the site. That's 10 times more than you say is released and will be in the entire body. Most stem cells (>80%) injected into the blood are captured in the lungs. So even your 6 million, only 1.2 million circulate twice. Now, let me ask you this? WHICH stem cells are released? According to studies in the literature, there are at least FIVE distinct types of adult stem cells in marrow: 1. Hematopoietic stem cells. 2. Chondro-osteogenic stem cells. 3. Mesenchymal stem cells. 4. Multipotent Adult Progenitor Cells. 5. Multipotent Adult Stem Cells. 6. Orlic's stem cells (similar to hematopoietic stem cells but said to be different). Finally, do you have any idea what you mean by adult stem cells "are more stable than embryonic stem cells"? Stable how?
  8. Kids can't be in enough pain to justify giving them morphine? You must be kidding. I can remember being in tremendous pain from appendicitis when I was 8 and 9 and hoping for morphine. How about kids who have had their legs blown off by landmines? No morphine? You are cruel.
  9. We don't know it is tail chasing. When Dawkins proposed this argument toward the end of The Blind Watchmaker, it was in response to a specific argument that "complexity cannot arise by chance, it must have an intelligent creator". That specific claim leads you into an infinite regress. BUT, there is no need to make that claim. NONE of the hypotheses for First Cause have a cause. ALL of them could be open to the argument you are using if that argument were valid. In fact, if we would use that argument -- you can't accept an answer for a cause unless you know the cause of the cause -- then all science immediately stops. IF it turns out that deity created the universe, THEN we look for a cause for deity. It is exactly the same as the situation for ekpyrotic: IF it turns out that there is a 5 D 'brane in which 4 D 'branes float, THEN it is time to ask "where did the 5 D 'brane come from?" Yes, they could be arbitrary. It could be pure chance that the universe has these parameters. However, many of the parameters are such that life could not exist. For instance, if the strong nuclear force were different, only hydrogen would be possible. No one can imagine a scenario where you can have life with only 1 element. That is essentially what I was saying: the strong AP is an error in logic. The universe is not required to have these parameters. If it did not, we simply would not be here to wonder about it. Basically, it is invalid to use the strong AP as "proof" of the existence of deity. However, that the universe has these parameters instead of some other parameters begs an explanation. The various multiverse theories are one attempt at an explanation: if there are an infinite number of universes, then one of them by chance will have the parameters of this one. We happen to be in this one. Another attempt at an explanation -- another hypothesis -- is that the universe is created and these parameters were chosen. NEITHER hypothesis has been disproven. Both are on the table.
  10. Individual atoms are not alive. By "atoms" we mean things like a single carbon atom or a single helium atom. You do know that atoms combine to form molecules, right? Hydrogen does not exist as a single atom in nature, but as a molecule of two hydrogen atoms. Life is chemistry. That's what the whole field of biochemistry is about: looking at the chemistry that makes up living organisms. Life is an entity that has all 4 of the following characteristics: 1. Metabolism (anabolism and catabolism) 2. Growth 3. Response to stimuli 4. Reproduction. Fire has all but anabolism, therefore it is not alive. Modern life is a group of many types of molecules: proteins, nucleic acids, sugars, lipids, porphyrins, etc. in many different combinations. For instance, many proteins are glycoproteins, which mean they have some molecules of sugar attached. Many of the molecules are polymers. That is, they are long strings of smaller molecules. Proteins are polymers of amino acids. Amino acids in turn are molecules composed of carbon, nitrogen, hydrogen, and oxygen. These atoms can be arranged in many different combinations. There are thousands of possible amino acids, but proteins in modern cells use 20 different amino acids. Biochemistry. There are entire huge textbooks on the subject. I suggest Lenninger's Biochemistry. It is more readable than many others. The subdiscipline of chemistry dealing with how life arises from non-living chemicals is called abiogenesis. Much of abiogenesis deals with a specific aspect of life: directed protein synthesis. This is how DNA/RNA codes for individual proteins arose. There are several ways that you can get life arising from non-life. Here is just one of them: http://www.theharbinger.org/articles/rel_sci/fox.html http://www.siu.edu/~protocell/ Basically, you start with amino acids. These are formed by a number of chemical reactions from methane, carbon dioxide, nitrogen, cyanide, etc. If proteins are either dry heated or heated at underwater hydrothermal vents, they form proteins. If water is added to the dry heated proteins (like in a tidal pool) or the water in the hydrothermal vent cools (as it moves away from the volcanic vent), the proteins spontaneously form cells the size of bacteria. Each cell contains roughly 10^9 - 10^12 protein molecules. That's 1 billion to 1 trillion protein molecules. Remember, 1 mole of any compound contains 6.022 x 10^23 molecules. That's a huge number of molecules. So even a small cell is going to have a lot of protein molecules in it. (BTW, the number comes from calculations and estimates of the number of protein molecules in a liver cell: http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mcb.section.199) Each of those proteins has A biological activity. It may be structural or it may be enzymatic, or both. Together, they have enough biological activity for the cell to be alive: it has both anabolism and catabolism, grows (by absorbing more proteins and making new ones), responds to stimuli (has an action potential like a nerve cell), and reproduces (by both budding and fission like bacteria). Thus, the cells are alive. Does that answer your question about number and type of molecules for life?
  11. The articles did not say that. Did you read them? In particular, look at this one: http://dsc.discovery.com/news/2009/01/15/mars-methane-life.html "Whatever the source [biological or geological], methane on Mars should stick around for about 300 years, all things being equal. Instead, Mumma and his team, who published their findings in this week's issue of Science, found that over parts of Mars the methane is disappearing in a span of time as short as one year. ""We really can't tell if it's biological or geochemical at this time," Mumma added. "On Earth, it can be produced by either mechanism." "The definitive way to determine the methane's origins is to analyze its isotopes. Methane produced from biological sources on Earth has distinctively different isotopic ratios than methane generated by geochemical processes." " A new effort is underway to search for other gases that, like methane, are tied to biological processes on Earth. Targeted compounds include ethane, propane and hydrocarbons. " Basically, this science news article has the required tentativeness. The continued influx of methane to Mar's atmosphere may indicate life. Right now, there are no observable geochemical processes -- like volcanoes -- that can account for the methane.
  12. If you were a raisin in the bread, some of the raisins would be moving toward you even tho the bread were expanding. That isn't the case with the universe. No matter which direction we look, galaxies beyond our local group are all moving away from us. The universe doesn't have a "centre" as you are using the term. And, if all were collapsing from a maximum expansion, those at the "edge" of the maximum expansion would look like they are moving towards us. They would be blue-shifted, not red-shifted. I suggest you read the Scientific American article "Misconceptions about the Big Bang". Merged post follows: Consecutive posts merged For expansion, it doesn't matter whether they are moving away from us or we moving away from them, or both. In any of these scenarios, the universe must be expanding. As it happens, every galaxy (beyond the local group) is moving away from every other galaxy. They would all see a red shift from every galaxy beyond their own local group. (Within our own local group of galaxies, there are a few that are moving towards our galaxy and show a blue shift.) Merged post follows: Consecutive posts merged Because only that option was consistent with the data. Since many of the physicists who accepted the expansion were either agnostics or atheists, they would not have been swayed by any appeal to deity. Remember that the preceding accepted theory was Steady State, where supposedly "God's work" just remained static. Theists were content with that. As several people pointed out, if the universe were collapsing we would be seeing blue shifts, not red shifts.
  13. lucaspa

    Being open minded

    Let's test that. You are saying that physicists don't change "beliefs" or theories. But physics has changed theories lots of times! 1. Physicists changed from Newtonian gravity to Einstein's General Relativity. 2. Physicists changed from classical mechanics to quantum mechanics. 3. Physicists changed from Steady State universe to Big Bang and an expanding universe. 4. Several physicists and groups of physicists are looking at different theories of quantum gravity: string theory, loop quantum gravity, etc. All these are just major events in the 20th century. All falsify the claim.
  14. This is very big now. The cells are called "induced pluripotent stem cells" or IPS for short. There are a huge number of laboratories doing this now and investigating the use of IPS cells for regenerative medicine. Do a PubMed search on "induced, pluripotent, stem, cells" and you will get a lot of articles. If you want the original methods paper on how to do this, I have the PDF file and can attach it. There is a hitch, however. At least one of the genes transduced into the skin cells to turn them into embryonic stem cells is an oncogene -- a gene associated with cancers. So there is concern that the IPS cells might become cancerous if implanted into a human. Merged post follows: Consecutive posts merged The mitochondria replicates separately from the cell. During mitosis the cytoplasm simply splits up the mitochondria that are in it. Embryonic stem cells have 3 major problems: 1. If implanted en masse in a body, they form a type of tumor called a "teratoma". 2. Because they do not come from the individual being treated, the ES cells can cause an immune rejection response. 3. They differentiate willy-nilly into all the phenotypes. That's why they make a teratoma in vivo. Adult stem cells have several advantages: 1. They can come from your own body, thus no immune rejection. 2. They seem to modulate the immune response and it looks like we can use adult stem cells from another person to treat you. 3. They do not form teratomas when implanted en masse, so you can use them for large defects in tissue, like defects in cartilage in osteoarthritis. 4. They remain undifferentiated until they receive a specific signal to differentiate. Thus, once we find specific differentiation signals, we can differentiate the cells outside the body to form a tissue (such as a bone) and then implant the completed tissue. 5. There are no ethical concerns about adult stem cells.
  15. There are machines that can now synthesize quite large proteins by adding one amino acid at a time to a growing chain. Older machines were limited to smaller peptides, but the newer ones can get more than 100 amino acid proteins. Of course, if you dry heat amino acids they will polymerize and make proteins -- many of them exceeding 100,000 MW. This has been done in a number of labs.
  16. Because every animal species kills other species for their benefit. Why aren't we? We test on Have you considered why the proportions are like this? We use rodents the most because 1) they are mammals and 2) they are relatively inexpensive. I think you have overrepresented the fish, amphibians, and reptiles. I notice there are no insects listed, but they are also animals. In fact, this list is only vertebrate animals. So it seems like you care only about vertebrates, not all animals. As we get to dogs, cats, rabbits (small mammals), large mammals, and primates, the cost to use those animals (purchase and housing costs) increases a lot. Notice that, if we really did this based only on closeness to us, we would use primates 99% of the time. Because, until recently, we had no other way to determine if those products were safe for humans. Now, however, cultured human fibroblasts are used. Irrelevant. However, I do call your attention to the drugs and surgical prodecures used by vets. Those animals did benefit from animal research, didn't they? To eliminate all the possible drugs that are harmful to humans. You forget that a lot of the animal testing is for safety. If the drug is harmful to a rat, then it is probably harmful to a person, also. That's a bad non-sequitor. Also apples and oranges. Yes, living creatures are part of the "supplies" for an experiment, but are far more useful than a pipecleaner or glitter. Rather, they are as useful as a pipet, pipet aid, cell culture media, cell culture plates, electrophoresis plates, etc. You've got to compare animals with the other supplies used in experiments, not with things that are not used in experiments. Please document them. In particular, please document the way I can replace animal experiments in looking at new treatments for non-union fractures or degenerative disc disease. That is my current research, and I'm required to list any possible alternatives to animals in the IACUC forms. If you have such an alternative and really want to stop animal research, then you need to tell me which of those "400 ways" will replace animal experiments in my area. Now you raised another point -- abuse. If you mean that any use of animals = abuse, then history shows that medical progress cannot be achieved without using animals. If abuse = inflicting pain without without the appropriate pain medication, then yes, most medical progress (except neurobiology) can be achieved without abuse. Think again. Merged post follows: Consecutive posts mergedMy lab technician brought up an interesting point (he was commenting on my doing IACUC forms): People will allow the most inhumane killing of mice and rats in their homes, but want lots of restrictions on how to treat them in research. I wonder if any of the people advocating "animal rights" allows mice and rats to live in and freely roam in their houses or whether they set out traps and poisons to kill them. If animals have "rights" in regard to research and can't be killed in the course of research, then how can animal rights advocates allow the killing of mice and rats that set up housekeeping in the homes of people?
  17. Which university are you attending? Abiogenesis is viewed as being almost certain. There is, however, quite a wide range of theories on how abiogensis can happen. There is the Protein First theory, Fox's protocells, RNA World, and the Hypercycle theory. There is little funding and few funding sources for abiogenesis research. NIH does not fund it (concentrating mostly on research related to understanding life that already exists). That rules out the major funding of biological research in the USA. NASA used to fund abiogenesis research, but NASA's research budget has been severely cut over the last decade or so. There is some funding thru I see Gerald Joyce had an article in a recent issue of Science showing a system of 2 RNA molecules that catalyzed each other's synthesis. But if you go to PubMed and enter "RNA, world" as your search term, you are going to get over 20 articles published just this year on that abiogenesis theory. Merged post follows: Consecutive posts merged Scrappy, once again you are confusing "directed protein synthesis" with abiogenesis. Directed protein synthesis is where you have genes that code for specific proteins. No one is saying you get that by "poof". You need to abandon that strawman. We've given you one paper that outlines a route from the RNA world of RNA acting as enzymes to build proteins to directed protein synthesis. In doing a PubMed search for Seraph on RNA world I just came across two recent papers proposing a different route to directed protein synthesis: http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=17540026 Look at this one carefully. It discusses how the "digital code" arose. Not "poof", but very slowly. Here's the second one: "1: Orig Life Evol Biosph. 2009 May 26. [Epub ahead of print] A Specific Scenario for the Origin of Life and the Genetic Code Based on Peptide/Oligonucleotide Interdependence. Griffith RW. Department of Biology, University of Massachusetts Dartmouth, North Dartmouth, Massachusetts, 02747, USA, rgriffith@umassd.edu. Among various scenarios that attempt to explain how life arose, the RNA world is currently the most widely accepted scientific hypothesis among biologists. However, the RNA world is logistically implausible and doesn't explain how translation arose and DNA became incorporated into living systems. Here I propose an alternative hypothesis for life's origin based on cooperation between simple nucleic acids, peptides and lipids. Organic matter that accumulated on the prebiotic Earth segregated into phases in the ocean based on density and solubility. Synthesis of complex organic monomers and polymerization reactions occurred within a surface hydrophilic layer and at its aqueous and atmospheric interfaces. Replication of nucleic acids and ranslation of peptides began at the emulsified interface between hydrophobic and aqueous layers. At the core of the protobiont was a family of short nucleic acids bearing arginine's codon and anticodon that added this amino acid to pre-formed peptides. In turn, the survival and replication of nucleic acid was aided by the peptides. The arginine-enriched peptides served to sequester and transfer phosphate bond energy and acted as cohesive agents, aggregating nucleic acids and keeping them at the interface."
  18. This has nothing to do with "the mainstream perspective"! This is DATA. Observation. That observation is independent of the theory it is testing. Photons don't have mass whether General Relativity is true or not. You seem to be under the impression that data changes when we change theories. NO! Objects accelerate under the force of gravity on earth at 32 ft/sec^2 under Newton's theory of gravity and Einstein's. They must accelerate at that rate under your theory, too. First, please explain what you think are the "mainstream answers to the cause of mass and gravity". Then explain how they are not "compatible". This isn't "Higgs theory" but instead is the Standard Model of particles. What you are talking about is how particles get mass in guage theory! First you need to understand and be correct about the current theories before you can even start on alternatives. Otherwise your "alternatives" are nothing more than strawmen. The LHC is trying to find the "Higgs particle". And yes, if they can't find it it will cause a rethink. But your "anticipation" can already be tested against known data, and it fails that test. ROFL! That has been the history of physics! Atoms that we can't detect that cause the behavior of gasses that we can. Electrons we can't detect that cause the behavior of electricity. Quarks that cause the behavior of protons and electrons, and now strings and 'branes. Listen carefully: It's not that I am rejecting your idea because it is new, but because data we already have falsifies it! IOW, I am treating it just like any other scientific theory, including my own. I regularly falsify my own theories about stem cells and tissue regeneration. I've just falsified my theory that bone regeneration by adult stem cells in a bone defect will be by endochondral ossification. At the one week time point, where I should have seen cartilage (if my theory was correct), I didn't find any. Theory falsified. It won't negate the data we have. It can't. I understand why. You don't want your "theory" to be wrong. You have become emotionally involved with it. You can't do that if you really want to do science. As you said, "science is tentative", including your theory. You don't consider your own theory to be tentative, just other people's. So instead of admitting it's falsified, or even working at it to the point where you can test it yourself against known data, you make up these excuses. I'm truly sorry for that, but it's your problem and you'll have to deal with it. Of course it can be quantified. It must to be of any use. As I told you, we already know what an energy quantum must be. But for you, you can at least get a series of possible values by calculating what the quantum has to be for 1) a mass to have an acceleration of 32 ft/sec^2 on earth, 2) the electron to orbit the proton in a hydrogen atom, 3) a photon to deviate around the sun to displace the stars behind it to the observed positions. If your theory won't account for those effects we observe, it's worthless, no matter how much you think it unites mass and gravity. You mistake "mainstream ideas" for data! You must deal with the observations that people have already made. For instance, Planck quantized energy. If you are going to quantize it further (and 10-34 joules is very small, then multiples of that new quanta are going to have to equal Planck's figures. Because that is the observation. Or we realize you are making ad hoc hypotheses to avoid falsification. Remember, you said photons must have mass. Well, how much mass do they have to have to deflect around the sun the way Einstein saw? Is that mass within the detectable limits of experiments to detect mass in a photon? I'm saying "yes" because those detectable limits are so very low that we can detect masses well below that of a neutrino. But you won't even do the math to find out, just make character attacks that I will only accept the "mainstream". Frack no! I'm testing your theory just like the "mainstream" was tested. It's just that your theory doesn't survive testing. No, I don't. Nor do I. It's not a question of accept GR or take your theory. I can find shortcomings in both. Unless your idea can be put into mathematics so that we can see if it yields the observations we already have (and makes predictions of observations we should only see if your idea is correct), then your "possible" is worthless. There are literally millions of ways we can imagine to "couple mass and gravity". What matters is testing those to see if they are correct or not. You don't care about that part. You only want to imagine something and then declare it correct and avoid testing. The second sentence is where you are off the rails. The known data always applies. The data isn't what it is because of the theory we think is correct. Data doesn't change when we change theories. "Facts are the world's data. Theories are structures of ideas that explain and interpret facts. Facts don't go away when scientists debate rival theories to explain them. Einstein's theory of gravitation replaced Newton's in this century, but apples didn't suspend themselves in midair, pending the outcome." SJ Gould, Science and Creationism, ed. by Ashley Montagu, 1984. The data showing photons have no mass doesn't change. The fact of the displacement of light by the sun doesn't change whether we have your theory or Einstein's. What you are doing is a major crime in science: rejecting data because it doesn't match with your theory. No, they are quantum increments of energy. It is actually a physical quantum. That's why they are "constants". All levels of energy we observe are multiples of the Planck constant. Now, you perhaps think there is a level below that and that the Planck constant is a multiple of it, but you can't deny that the Planck constant is a quantum. You disputed equivalence. However, consider the Planck constant. That gives you a precise unit of energy that you can plug into the equation for E and then solve for m. The precies unit of energy of which all mass is composes would be Planck constant divided by the speed of light squared. I don't have unlimited time. I skipped that to get to the falsification. Yes, you are. What is the mass of a photon necessary to give the displacement of seen? What is the mass of a photon necessary to account for changes in motion of an electron when it drops a level inthe atom as it emits that photon. C'mon, you have change in position, the mass of the electron, so you should be able to calculate the mass of the photon in your theory. I don't have to. We are testing this theory to see if it is correct or not. To say this theory is incorrect does not require that I have a correct theory. Why would it?
  19. Medicine: Much to learn, long hours during training (college, med school, residency), salary $100,000 + when done. Could be long hours depending on sub-specialty. Environmental science: not quite so long in training and hours will be less. Salary much less, probably not above $70,000 with Ph.D. Not familiar enough with the other 2 to comment.
  20. lucaspa

    global warming

    Cetus, many birds are insectivores and we want them to eat a lot of insects! Some eat fruit and spread the seeds as they go thru their digestive tract, so we don't want them to eat less because that would result in fewer trees. Ecosystems are complicated balances and disrupting them by having birds eat less is going to have a lot of negative consequences that far outweigh any reduction in CO2 that might result. Also, getting a few plants to grow faster isn't going to eliminate enough CO2 to matter. The bit extra isn't going to compensate for all the plants killed as the Amazonian rainforest is cut down. So no, cutting CO2 down is going to help the world a lot more.
  21. Sigh. Sometimes you guys get a bit too nitpicky. The OP was clearly referring to G1 phase. paul clearly was confused about the relationship between chromosome and DNA molecules. If he knows that one chromosome = one DNA molecule, then paul (when he comes to learning S phase) will clearly realize that copying the chromosome will mean that there are 2 DNA molecules at that point. And, in the mitchondria, one chromosome = 1 DNA molecule there, too. So when paul gets to mitochondrial DNA, he will be able to work it out. Please, try to understand what the question is asking and then answer it in the simplest terms that are still sufficient. That will be a lot more help than going into unnecessary details. Try to focus on the needs of the questioner and not either showing off how much you know or scoring "points" off me when I don't give every possible permutation.
  22. I thought I was crystal clear: I am talking equations and quantification. That's what Einstein had. Supposely you "have been building my ideas over several years on various forums" but you don't have the equations and quantification for known data? Boy, have you wasted not only your time but everyone else's! No offence, but you have. It must be done by you. Learn the math! It's a theory. Hypotheses/theories are statements about the physical universe. You are making statements about the physical universe: photons have mass; space is not curved, etc. There is no hierarchy of certainty as you go from idea to hypothesis to theory. Each of those can be 1) untested, 2) falsified, or 3) supported. What Klaynos and I are doing is testing your theory against known data. That data, so far, is falsifying the theory. Not the way to test your ideas. What you want to do is deduce consequences from your ideas and then test those consequences against known data in an attempt to show your idea to be wrong. You need to be your harshest critic. Try your best to show that your theory is wrong. That's how theories/ideas are tested in science. As an idea it still has to do this. After all, that is how we are testing the idea: to see how well it predicts (accounts for) the known data of gravitation effects. Until your theory can do this, it's nothing. Sorry, but energy has already been quantized. Have you ever heard of Planck's Constant? Energy is quantized at 6.63 * 10E-34 Js. However, this has not allowed anyone to quantize gravity. Been done. Ever hear of E = mc^2? Now, I'm going to skip over your contradictory discussion about the rocket. Remember when I said you test your theory against existing data in an attempt to falsify it? What mass do photons have? And give me a precise number! After all, if you have been working on your theory for several years, you should at least have gotten that far. However, as Klaynos has noted, all the experimental evidence says photons are massless. There is no way that we would not have detected mass in them. Your theory has a false consequence: therefore your theory is falsified. Sorry, but get used to it. We're done.
  23. Nice nitpicking. "An object that does not emit light of its own has a color due to the wavelengths of light it reflects." Merged post follows: Consecutive posts merged Welcome to ad hoc hypotheses! Ad hoc hypotheses are formulated to save hypotheses from falsification, which is what you are doing here, isn't it? The key to whether an ad hoc hypothesis is valid is whether it can be tested independently of the hypothesis it is designed to save. Can any of your hypotheses be tested independently? Well, we could use a microscope to see a very small IPU. But notice that unicorns are horse-sized creatures. Basically, Sisyphus, any scientific theory can be made unfalsifiable by the use of ad hoc hypotheses. So you have to be very careful about using them to avoid "throwing in the towel". Better to throw in the towel. Merged post follows: Consecutive posts merged In this case, yes. "invisible" and "pink" are depicted as essential parts of the entity. If it was not essential, then why specify pink? So, if you disprove the essential parts, then you've disproven that particular entity. What you are doing is proposing a different entity: a Unicorn. Now you have an example of "a rose by any other name ..." If I say "glupforg has one proton and one electron" but you say "no, hydrogen has one proton and one electron", are we really saying different things? Have I really made a point by saying "glupforg" instead of "hydrogen"? You have "flying sphagetti monster" and "unicorn" have the same properties as "intelligent designer" or "deity". It's still an intelligent entity with the power to create a universe with the parameters we see. By whatever name you call it -- "intelligent entity", "deity", "flying sphagetti monster", "Yahweh", etc.,-- yes, it remains on the table as a possibility. Merged post follows: Consecutive posts merged First, I'm not using "designer" here for complexity. If you've read a number of my posts, complexity arises from the processes of physics, chemistry, and evolution. As I said, deity cannot be used as a hypothesis for direct action except for these two questions. Second, first cause is a legitimate scientific question. What is the initial Cause that started the chain of cause and effect we see in the universe? The idea that our universe has always existed has been falsified. You need a cause for it. This isn't the same as the earth. As Swansout and others have pointed out, the overwhelming majority of values for the parameters give a homogenous universe where life cannot exist i.e. the universe is only hydrogen or only photons. Reference, please? Sigh. This is the argument I already gave! "The universe is not required to have the constants it does. If it had different constants, we simply would not be here to observe it." This is why SAP is bad logic and cannot be used as proof of deity or an intelligent designer. Read carefully, that the constants are what they are allows the hypothesis of an intelligent entity (let's not use "designer" because that confuses this with Intelligent Design theory, and we aren't talking about that) making the universe. Until we can falsify that hypothesis, it stays on the table like all the other hypotheses we can't falsify, i.e. multiple universes. Merged post follows: Consecutive posts merged I have found reference in physics papers to the AP as stated. You didn't describe how the SAP I stated was altered. First, I don't see how the AP is being used here to contradict the SM. Instead, we have an observation that the universe exists of matter. That's different than the fine-tuned constants. Second, what you have here is 1) falsification of the SM and 2) ad hoc hypotheses to try to save the SM. The observation is CP violation in SM doesn't produce enough asymmetry to have a universe of matter: http://physicsworld.com/cws/article/print/61 So, how do we "save" the SM? You give 2 ad hoc hypotheses to do so: 1. The universe started with more matter and the standard hot BB theory is wrong. 2. Extend the SM so that neutrinos have mass. Both should be independently testable. However, there's a third ad hoc hypothesis: matter/antimatter didn't all annihilate each other and there are pockets of anti-matter out there: http://www.newscientist.com/article/dn16780-antimatter-mysteries-1-where-is-all-the-antimatter.html
  24. No, the definition of life does NOT include crystals and sea foam. Remember, all four characteristics have to be present. Crystals grow, but they don't respond to stimuli or have metabolism. Sea foam reproduces and responds to stimuli, but doesn't have metabolism. Fire grows, reproduces, responds to stimuli, and has catabolism. But it doesn't have metabolism. Only biological life, so far, has all four. What you have done is attach an unnecessary characteristic to "life" -- hereditary tools. In particular, you demand that life " carries digital information forward from generation to generation." That isn't necessary to be alive. The protocells have heredity and carry information from generation to generation. You have never countered the arguments and data concerning this. LOL! You are still hung up on what I said you were: modern life. Thanks for proving my point. Also showing that you aren't really listening to what people are saying. All modern life has directed protein synthesis. But that doesn't mean that all life must. And I just did show you a form of life that doesn't require genetics! The protocells. American Scientist is a completely different publication than Scientific American! No wonder I couldn't find it looking at Scientific American, you got the magazine wrong. What are "chemical analogues" to you? But actually, the article did mention it: "Shelley Copley at the University of Colorado at Boulder has been sorting out the intermediate chemistry leading to the current nucleic acid–protein system of genetic coding, with an eye toward resolving the chicken-and-egg problem. These experiments represent a major paradigm shift from the top-down control envisioned in RNA World scenarios. Rather than supposing that a few large RNA molecules control the adaptation of a passive small-molecule reaction network, Copley supposes that whole networks of intermediate molecules support each other on the path toward complexity. In this experimental setting, networks of small and randomly synthesized amino acids and single RNA units aid each others’ formation, assembly into strings and evolution of catalytic capacity. Both types of molecules grow long together. Complexity, adaptation and control are distributed in such networks, rather than concentrated in one molecular species or reaction type. Distributed control is likely to be a central paradigm in the development of Metabolism First as a viable theory. We eagerly anticipate more experimental efforts like these to explore the many facets of small-molecule system organization." Notice the bold. What you call "digital information" is directed protein synthesis. Instead of having this "poof" into existence, Copley is looking at proteins and RNA formed by chemical reactions. The formation of proteins is exactly what the protocells is all about. Proteins are formed from single amino acids by heating. You don't get "small proteins", but large ones. The proteins then make RNA. The RNA in turn then helps to make proteins. The protocells are living cells, not "chemical analogues". For one thing, the protocells are composed of chemicals, not "analogues". No, far from "poof". First you have the protocells making RNA. Now you have the RNA for the RNA World Hypothesis. Second, you have the observation that proteins with preponderance of particular amino acids associate with RNA/DNA with a preponderance of particular bases. That's the start of the type of association you need for directed protein synthesis. Then you have the observation that ribosomes with just RNA can make proteins. From that you move to particular RNAs covalently binding particular amino acids. That's transfer RNA. NOW you have a "digital genetic alphabet". Many, many steps in between. I wish he'd sent me one. But I found it on my own. Other people have. There is an extensive literature proposing the eukaryotes came first and that prokaryotes were derived from them as the introns were excised. That's exactly what happens with the protocells. Because each protocell is formed from quintillions of proteins, each has at least some proteins with all the catalytic properties of a metabolic network. Or several metabolic networks. Those networks would not be efficient as those in modern cells (product of 3.8 billion years of evolution), but the evidence is that the metabolic networks necessary for life do exist within the protocells. After all, there is the metabolic network to make proteins and another to make nucleic acids. This is just one of the cool things about the protocells: they provide, ready-made in just two steps, the metabolism and metabolic networks of life. What you really mean by "digital information" is that a particular RNA molecule with a particular anti-codon (3 bases), always binds to a particular amino acid. This RNA molecule with the amino acid attached (tRNA) then binds to the 3 complementary bases on a messenger RNA molecule. Let's discuss the Poole et. al. article because it gives a pathway for this to happen.
  25. Irrelevant right now. We don't know if there is an intelligent agent as designer. If and when we find that there is one, then is the time to ask that question. Think of it this way: when scientists were trying to determine if the entity called Big Bang actually existed/happened, asking "what caused the Big Bang?' was irrelevant. We didn't know (and still don't) but that has no effect on whether Big Bang exists or not. Merged post follows: Consecutive posts merged Which is not the definition? The SAP or the AP? And what definition is used "in your field"? AP is, if anything, in the field of physics. I don't see how it could be ignored. The universe is data. If the proposed hypothesis does not produce the universe that exists, then it can't be right. Falsified by existing data. How exactly does the Standard Model fail the AP? From what I have read, the constants are arbitrary in the Standard Model. IOW, there is nothing in the Standard Model to dictate what the constants are. This is an alternatively logically correct way to phrase the AP. Notice that the SAP says the universe itself MUST have the constants. That is, there is no other choice but that the universe has the constants. This version is correct in that, for us to exist, the constants must be what they are. This changes the "must" from the universe itself to our existence, which is correct.
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