lucaspa

Let me reinforce Paralith: the organism does NOT "decide". Instead, however "poor" in overall quality the first mutation that gave rhodopsin was, having rhodopsin was better than not having it at all. Under those conditions, the equations of Mendelian inheritance are very clear: the allele will spread from generation to generation such that EVERYONE in the population will have it. The math says that this can't be stopped short of a major disaster to the population that kills (for other reasons) every individual that has the allele. That is a false premise. Even being able to detect light vs dark would help a single celled organism: it helps keep the organism near the surface instead of going too deep where there is not going to be any food. Just "go to the light". Yes, we have mutations. Many of them are beneficial. But no, the scale did NOT have to be "enormous". Each step can be quite small. I highly recommend Richard Dawkins Climbing Mt. Improbable because he looks at this specific example: evolution of eyes. Another false premise. It is NOT "across the board". It is in ONE species. However, because the individuals in that species do well, eventually all species are going to be descended from that species by "descent with modification". Species that did not evolve eyes in environments where they would be advantageous are going to go extinct.

First, let's get rid of that idea of "learn". And stop applying evolution to a single "organism" Evolution happens to populations. I can't emphasize that enough. The individual doesn't have any conscious input into evolution. An individual is either lucky or unlucky enough to be born with the alleles (forms of genes) it is born with. If those alleles give it an advantage in the struggle for existence, the individual will do find and have lots of offspring. If not, too bad. An individual did not "learn" that it can see. Instead, a lucky individual had a mutation in a protein that conferred the ability to detect light. "In the land of the blind, the one-eyed man is king". That ability gave an advantage of this individual over all the other individuals of its species. Over a period of generations, every individual was descended from the lucky one and had the ability to detect light. Adaptations come about thru natural selection. Again, the cell did NOT "think to create". There is no input or conscious decision on the part of the individual in natural selection. The advantage is obvious: an individual that can sense light and its surroundings, however dimly, can avoid danger or find food better than an individual without the ability. With eyes the answer is known. The protein that detects light is rhodopsin, which makes up the light sensitive spot on the single-celled Paramecium. The gene Pax-6 regulate the production of rhodopsin and has evolved to direct the evolution of the eye by controlling the expression of the genes that code for the construction of the eye. Sight gives no advantage to plants. After all, they can't avoid herbivores (predators). They also make their own food. Animals have to get food from others. Natural selection is a means of cutting down odds. It does so by breaking up the formation of an organ into many, many steps and then ensuring that those steps will happen because only by having the step can the individual be the "winner" in the struggle for existence. Here is a simplified example of how natural selection -- cumulative selection -- cuts down odds: You have a 1 in 1024 chance of correctly winning 10 coin tosses in a row. But I can guarantee you I can find someone who can do so. How? Simple, use cumulative selection in the form of a single elimination tournament. I start with 1024 people and pair them up. Then each pair tosses a coin. The 512 winners are selected to go to the next round. Again they are paired and do a coin toss; the 256 winners are selected to go to the next round. Repeat this 7 more times. Now you have 2 people who have won 9 coin tosses in a row. The winner of this round has won 10 coin tosses in a row. And it is a certainty that such a person will be found with this method. We have taken odds of 1 in 1024 and converted that into virtual certainty. Now, I don't know which individual will win the tosses, but it is certain that one of them will, given the algorithm of the competition. Evolution by natural selection is a competition algorithm, more complex but analogous to the single elimination tournament algorithm. The theory is natural selection. Here is Darwin's summary of it: "If, during the long course of ages and under varying conditions of life, organic beings vary at all in the several parts of their organization, and I think this cannot be disputed; if there be, owing to the high geometric powers of increase of each species, at some age, season, or year, a severe struggle for life, and this certainly cannot be disputed; then, considering the infinite complexity of the relations of all organic beings to each other and to their conditions of existence, causing an infinite diversity in structure, constitution, and habits, to be advantageous to them, I think it would be a most extraordinary fact if no variation ever had occurred useful to each beings welfare, in the same way as so many variations have occured useful to man. 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; and from the strong principle of inheritance they will will tend to produce offspring similarly characterized. This principle of preservation, I have called, for the sake of brevity, Natural Selection." [Origin, p 127 6th ed.]

No problem. One of the failings of forums is that we can't see you or hear your voice. If I had been able to do either, I probably would have guessed that you weren't all there. As it is, a reader has to take you as serious and meaning exactly what you say. Then respond as tho you were.

Yep. Which is why there are the 4 scenarios. Based on different educated guesses on what the fertility rate (and mortality rate!) is going to be in the future. Don't forget mortality rate. Say we develop cheap tissue engineering and find a cure for cancer. What happens to the mortality rate? It plummets. We have a lot more total people because they simply aren't dying anymore, so the population projections are hosed. This would be one case where SkepticLance's (nonskeptical) optimism in technology would really screw up his optimism. Ironic, isn't it?

Apoptosis and susceptibility to the immune system are two different but related things. The similiarity is that both the ability to avoid apoptosis and susceptibility to the immune system are due to abnormal proteins. Cells are constantly processing parts of their proteins and putting parts of them out on the cell's membrane for the immune system to "see". A cancer cell has abnormal proteins, therefore the immune system recognizes it as "not self" and kills it. The new treatment does not "increase the immune response in cancerous cells" but instead increases the body's immune response to the abnormal proteins produced by cancerous cells. Some of cancer cells are removed from the patient the complexes on the surface of the cancer cells that react with immune cells are then used to "train" the patient's immune cells -- again outside the body. The immune cells are then put back into the patient and go after the cancer cells. Or sometimes the patient's cancer cells are used to train immune cells to make antibodies to the cancer cells, and then the antibodies are injected into the patient.

No, not "everyone" gets cancer. As you noted, even if we include people who got cancer but were cured surgically, still over 1/2 of people die without every having cancer. However, as age increases the odds that a cell will have genetic defects that give it both the ability to avoid apoptosis AND be able to avoid being killed by the immune system increases.

The data says this is true. Nearly all abnormal cells either 1) die by apoptosis or 2) are killed by natural killer cells of the immune system. Cancers arise from the, very, rare cell that has changes that abort apoptosis AND keep it from being killed by the immune system. All you need do is do a PubMed search on "immunity, cancer" and "apoptosis, cancer" to see the huge literature documenting what I've said. It's not a matter of "belief", but of knowing what the data is. Current thinking is trending toward the idea that cancer cells are adult stem cells that have lost growth control. Stem cells already have an unlimited ability to proliferate. Their proliferation instead is stopped. Block that "turn off proliferation" control and you already have both characteristics of cancer cells: they are undifferentiated and have no growth control. Then "all" the cell needs is a way to keep the immune system from killing it.

Actually, that's NOT the Razor. William of Ockham actually meant that, when describing a phenomenon, include no unnecessary entities. In Ockham's time, people said "an object moves because of an impetus". Ockham argued that "moves" means simply locations in space at different times. Therefore, "because of an impetus" is unnecessary. All we should say is "an object moves". The idea that the simplest solution is the correct one is actually the position William of Ockham argued against. People of the time noted that in reflection, the angle of reflection = the angle of incidence. They reasoned from that that, in refraction, the angle of refraction should = 1/2 the angle of incidence, because that was the next "simplest". Ockham thought that reasoning was stupid. There was no a priori reason to think that. The angle of refraction, instead, had to be established by measurement. See John Losee's Introduction to the Philosophy of Science for a fuller discussion of this. The idea that the simplest solution is the correct one comes from Newton. And it's wrong. There are many better examples of how wrong the Razor or Parsimony is in biology. Basically signal transduction and transcription control have thrown out Parsimony and they invent more complicated systems all the time. Why? Because the "less simple" systems eventually turn out to be correct. I'll give you another real world scenario, this one involving controlled experiments. In 1962 Marshall Urist discovered that implantation of demineralized bone matrix (DBM) under the skin of a rat or rabbit would cause bone to form at that site -- a site where bone would normally NEVER form. He established, by controlled experiments, that the responsible agent was a protein. The Razor would say that there was only ONE protein -- that would be the simplest solution. Therefore over a dozen laboratories over the next 35 years tried to purify THE protein. All failed. They always ended up with at least 3 peptides. Finally, Wang and colleagues at Genetics Institute threw out the Razor and stopped trying to purify "the" protein. Instead, they cloned cDNA from every protein in the partially purified mixture. A brute force, non-simple approach. Turns out that there were five proteins, each of which would induce bone formation. The proteins were dimers of 2 identical peptide chains held together by disulfide bonds. They were called bone morphogentic proteins (BMPs) and were given numbers. It turns out that the naturally occuring BMP in bones is a heterodimer of BMP-2 and 7. Again, not the simplest. E.coli, if you try to modify parsimony like you did: "Occam's razor still holds true... scientists just don't know the whole story. It's difficult to make an accurate hypothesis is you're not aware of all the variables." you basically reduce it to a tautology: The simplest answer is correct because, however complicated it is, it won't work if it is simpler. That may "save" Ockham's Razor, but it does so by making it useless.

Why should I do this? YOU are the one that needed the info. All I have to do is refer to my molecular biology textbook or walk down the hall and talk to my colleague who does this routinely.

Sorry, but you missed it too. These are NOT "averages of many calculations". They are ONE calculation based on ONE scenario. We have 4 projections because there are 4 scenarios. There is no averaging being done here. We have 4 separate calculations. It's worse than that. The "middle case" that gave the 9 billion is based on the assumption that the fertility rate will change in the 45 years from 2005 to 2050. It's not an "average fertility rate" -- that implies measurement -- but instead picks a fertility rate for each year from 2005 to 2050. Since those years are in the future, there is no measurement. It's an assumption. As you noted, reality doesn't have to match the assumption. But SkepticLance is "assuming" that the assumption is correct when he states that population will stablize as tho it were a fact. You can't have a "fact" based on the assumption of an assumption. Facts are observations.

Interesting coming from someone who has 3 times made agreement look like argument. The rest of us are not as sure that this is the "fact" that you think it is. The changes are based on a lot of human factors that are not required to conform to the reasonable or logical scientific position. I urge you to be more cautious about your assertions on the future. Again, there is an upper limit to productivity. The laws of physics and biology ensure that. You don't seem to consider that fact. We may not have reached the limits of technology in regards to food production, but there are such limits. No, it's not called "the error factor". The error factor comes from inherent differences in different measurements of the same thing. Take a ruler and measure a line 10 times, and you get 10 different measurements. The difference in those measurements is the error factor. Look below before replying, because that is NOT what is happening here. No, it's not. Read the article. It is a single calculation based on a single set of assumptions. It is NOT "the 'most probable' figure". You are thinking above about the difference in several measurements and making a bell shaped curve. You think 9 billion is the middle of the curve and 11 billion is off to the right. That's not what is happening. Instead, the team takes different sets of assumptions about fertility, death rates, migration(when looking at regions), and then does a calculation extrapolating propulation. You didn't even read the quote I gave, SkepticLance! It's right there: "To project population until 2050, the United Nations Population Division applies assumptions regarding future trends in fertility, mortality, and migration. Because future trends cannot be known with certainty, a number of projection variants are produced." Pay attention! Look at the DATA, stop ignoring it and saying something complete contrary to what is being done. What you are doing is really poor science, so poor it is not science at all. Now do you see how wrong you are? NONE of the projections are "more probable" than any other. Not based on the number. The only way one can be more probable is that the assumptions are more probable. And this is not the case. "Medium" doesn't mean "more probable". It means just that: between the lower and higher assumptions. That's all. But there is no way to tell which of the assumptions are more probable. If anything, the more probable assumption is that birth rates are going to stay the same! That assumption involves no change in the overall behavior of humans. And, of course, that assumption gives you the highest population numbers.

Good second thought. Molecular biologists tend to view DNA coded polypeptides -- of whatever length -- as proteins. Polypeptides not coded by DNA tend to get the polypeptide designation. I haven't ever heard of "oligoprotein". That makes no sense. It should be "oligopeptide", analogous to "oligonucleotide". Biochemists don't make that distinction. Glutathione, a tripeptide synthesized in the cytoplasm and a major antioxidant, is referred to as a "protein" all the time. When Fox and others made polypeptides by thermal polymerization of amino acids, they called them "thermal proteins" as a concession to the many people who viewed "proteins" as referring only to polypeptides coded by DNA.

Neither. Nerves enter muscles at multiple points along the body of the muscle, where the muscle cells are. Both the origin and insertion (and both are "musculotendinous junctions") are mostly fibroblasts, not myofibers (muscle cells). Any decent anatomy book will show this.

No, protocells are frightfully easy to come by. There are so many varied conditions in which thermal proteins and protocells can form: a wide variety of atmospheres, amino acids, temperatures, etc. The 2 most relevant for abiogenesis research are: 1. Tidal pools. Have a solution of amino acids in a tidal pool that is evaporated by the sun. The result are proteins. Have the tide come back in and the result is protocells. 2. Hydrothermal vents. Amino acids are made at hydrothermal vents under today's conditions, and those same conditions will make the amino acids into proteins and then into protocells. So abiogenesis is occuring today at hydrothermal vents!

Yes. RNA. RNA in most cells not used as the primary hereditary material. But in many viruses and some unicellular organisms it is. Define "works". Most RNA World guys are looking for an RNA that catalyzes its own replication. That's what they mean by "works". There are many, many RNAs that act as enzymes for one reaction or another. The simplest is only 3 bases long and catalyzes the hydrolysis of U from an RNA chain. You don't need lipids to get a cell membrane. Even in modern cells, 60% of the cell membrane is protein. As you saw in the protocell article, proteins will make the entire cell membrane just fine.

Despite some of the definitive claims in the thread, this is matter of hot debate in abiogenesis circles. The most recent Scientific American has an article by Shapiro arguing against RNA first and arguing for cell first (Metabolism First). I personally favor cell first by making cells from thermal proteins: http://www.theharbinger.org/articles/rel_sci/fox.html

The common detergent is 0.1% Triton X-100. You use antibodies to identify the protein once it is made and do immunohistochemistry on dead cells.

And the cells are usually dead when this happens. Immunohistochemistry is done either for surface proteins, in which case the cell can remain living, or for intracellular proteins. If intracellular, the cell is dead either by freezing or fixing and means are used to poke holes in the cell membrane. Detergents are one method. In my lab, we fix in methanol, remove the methanol, and then dry the cells. This results in fractures in the cell membrane thru which the antibodies can move.

We call smaller polypeptides proteins. The distinction between "polypeptide" and "protein" is artificial. Proteins are polypeptides and polypeptides are proteins. The terms are interchangeable. No, proteins are NOT responsible for ALL biological functions. In addition to E. coli's excellent example of ribosomes (which can make proteins using only RNA without proteins), lipids form a bilayer and a membrane without any protein involvement. Hyaluronic acid is a glycosaminoglycan and is mostly responsible for the slipperiness of joint fluid (like in the knee). Most mutations do NOT result in any disease or change in the protein. A mutation of one amino acid CAN result in change of function of the protein. BUT, in most cases it does NOT and in the cases it does, very few of those lead to diseases. BTW, in areas where malaria is endemic, sickle cell trait is a benefit. Being heterozygous for sickle cell is a benefit. Being homozygous for normal hemoglobin results in getting malaria and dying. Being homozygous for sickle cell hemoglobin results in sickle cell anemia and dying. Sickle cell trait is a classic example in natural selection of selection for the heterozygote. BTW, in case anyone does not understand the terms used, such as heterozygote, glycosaminoglycan, etc, be sure to ask.

In addition to CharonY, avoid heat above 50° C. That will denature the protein. Avoid strong acids and bases, keep them about pH 7.0 Avoid denaturing solutions such as 4 M GdnHCl or 6 M urea. Also avoid ammonium chloride solutions as they will precipitate proteins. Summary: try as much as possible to keep proteins in physiological solutions at ~ pH 7.0 and less than or equal to 37° C. If you are going to store them for a long time, lyophilize them (freeze-dry) and store at -80°C. You can also store them in solution at -20° or -80° for shorter periods of time (about a year or 2) as long as the freezer is not frost-free (self-defrosting). The defrost cycle heats things up and can thaw the protein. As CharonY said, avoid repeated freeze-thaw cycles as this will denature the protein.

1. There are many more than 20 amino acids. It's just that there are 20 that are coded by DNA to be in proteins. There are some other amino acids that show up as intermediates in metabolism. 2. No, amino acids are not "everything in a biological system". Amino acids are the constituents of proteins. DNA/RNA are composed of nucleic acids. Nucleic acids are, in turn, compounds of nitrogenous ringed bases (such as adenine), ribose (a sugar), and phosphate. DNA is deoxyribose, which is ribose without an OH group. Glycogen is a chain of glucose -- a sugar. Glycosaminoglycans are chains of sugars. There are different glycosaminoglycans composed of different sugars. Lipids are long chain hydrocarbons and form about 50% of cell membranes. They are also the basis of the molecules that make up the mylenated sheath around nerves. Does this help?

Again, you are not reading what is written but changing the terms. IOW, you are making strawmen. This is getting annoying. I also said in the post: " We need to think about the consumer side -- the number of humans -- instead of only the technology side. If we can't stabilize the population ..." What you are saying is that the population will stabilize. IOW, you are saying exactly what I did: that the problem must be approached from the consumer side! The addition you are making to my point -- not contradiction -- is that the problem may be solved on the consumer side. MC's point was that we can't using existing methods. Pay attention to the bold. There are 2 different claims here: 1. Yours: we can sustainably feed 9 billion people by some form of technology/practices. 2. MC's: we cannot sustainably feed 9 billion people by current technology/practices. Those are not mutually exclusive and, if fact, you have tacitly agreed to MC's claim by stating that we need to expand the practice of particular technologies. You never agreed that current practices could sustainably feed 9 billion people, but instead pointed out different technologies you believe could do the job. Now, a note on your "data". I found the UN webpage and looked at the assumptions behind the posted table showing a convergence of population to about 9 billion: "To project population until 2050, the United Nations Population Division applies assumptions regarding future trends in fertility, mortality, and migration. Because future trends cannot be known with certainty, a number of projection variants are produced. This note presents the assumptions underlying the derivation of demographic indicators for the period starting in 2005 and ending in 2050. The 2006 Revision includes seven projection variants and three AIDS scenarios. The seven variants are: low, medium, high, constant-fertility, instant-replacement-fertility, constant-mortality, and zero-migration. The World Population Prospects Highlights focus on the medium variant of the 2006 Revision, and results from the first four variants are available on-line and traditionally published in volume I of World Population Prospects (forthcoming). The full set of results for all variants and scenarios are available only on CD-ROM." "Medium-fertility assumptions: Total fertility in all countries is assumed to converge eventually toward a level of 1.85 children per woman. However, not all countries reach this level during the projection period, that is, by 2045-2050. The basic principle of fertility projection is the same for all countries, but projection procedures are slightly different depending on whether countries had a total fertility above or below 1.85 children per woman in 2005-2010." You looked only at the "Medium Variant" table at http://esa.un.org/unpp/index.asp?panel=1 to get your stabilization at 9 billion. And "medium variant" assumes that fertility rates drop. BUT, if you look at all the variants at http://esa.un.org/unpp/p2k0data.asp, a very different picture emerges. If you look at "high variant", then population in 2050 is 10.7 billion and increasing. But even this assumes a drop in fertility. If, instead, you look at the "constant fertility" variant, where fertility rates stay the same as they are today, then population in 2050 is 11.8 billion and rising. So, your optimism is based on some very optimistic assumptions. If we don't make any assumptions about drops in fertility but simply take the data we have and extrapolate it, then we are looking at nearly 12 billion people by 2050 and no stabilization in sight!

Theoretically, this is correct. However how many males do you know that have NO "reproductive success"? Yet none of them have saved anyone. In a thought experiment, this should be correct. In the real world of population genetics, I have severe doubts it applies.

There's two problems here: 1. evolution works on populations, not on individuals. 2. What do you mean by "improve it [out behavior]"? Define "improve". Do you see that you are outside of science here when you start making moral judgements about which behaviors are "better" and which "worse"? Evolution provides an explanation why we choose to save one of the kids without thinking about it. Evolution does NOT say we "should" save the kid. In fact, in evolutionary terms the decision to risk your life to save ANY of the people is the wrong decision now. Since none of those people are your relatives, you are risking your alleles for no possible gain. The correct evolutionary decision now is to simply watch. Not entirely true. Observation gives us a lot of information about "human nature". It may not be scientifically codified as we know it, but that does not mean people were in "total ignorance" about it. And we still enforce morals by indoctrination. We indoctrinate our children to share, play "nice", not to lie, be polite, etc. We punish them (use force, even if the force is mild such as a "time out") if they do not adhere to our moral code. I think you have made the Naturalistic Fallacy. This fallacy states that what "is" in nature is what "ought" to be in human society. That is not true. Yes, evolution explains why we try to save one of the people, but wouldn't you argue that we ought to try to save one of those? Since that no longer makes sense in evolutionary terms, you have to find another reason outside of science to justify the decision to risk your life for another's. Easy. What we ought to do is not necessarily what "is" in nature. Also, anyone can distort the scientific knowledge. Remember, Spencer, Virchow and others distorted the scientific knowledge of evolution to make Social Darwinism and make a moral code that justified war! Not "omniscient science" in terms of the ENTIRE universe. But they are based on established theories and hypotheses in the LIMITED part of the universe that applies to them. You are confusing the entire universe and that we don't have "perfect" knowledge about ALL of it to saying we don't have knowledge about part of the universe. Ironically, that is the same argument used by creationists against science. Creationists argue that, since we don't know about ALL the universe, we don't know enough about life on earth to say that evolution happened. You consider religion a "folly". Isn't it then a folly to use one of the fallacious arguments of one sect of religion?

Philosophy and science are different disciplines and usually look at different aspects of human existence. I would disagree that philosophy ends up "being almost just inconsequent mental masturbation". It can do that, and some of philosophy is that way. However, the same charge can be leveled at parts of science. In any scientific sense, No Boundary and quantum splitting are useless. They start from imaginary assumptions. In fact, ALL of science starts from "imaginary assumptions" in that hypotheses are statements derived from human imagination. Science then tests those hypotheses to see if they are right or wrong. But then, philosophers check their hypotheses, too. Science is successful because it is very limited and because it uses only a subset of evidence: intersubjective. It is the intersubjectivity that causes you to say "reliable evidence". What you state as "solid facts" is another limitation of science: it deals only with the physical universe. Philosophy deals with abstract ideas. True. But if you don't have the entire picture, you must take lots of care in how you "make use of this knowledge". You have 2 different things here: 1. The knowledge itself. 2. Making use of the knowledge. Let's take one example of incomplete knowledge bringing human tragedy. Science knew how to make atom bombs. It did NOT know about the residual effects of radiation released from those bombs. Therefore tens of thousands of US military personnel were exposed to atomic bomb blasts as part of their training in the late 1940s and early 1950s. As a result, these people had very high rates of cancer later in life. So, I would urge lots of caution in "making use of the knowlege" of evolution in terms of human behavior.