Darwinsbulldog

I am just wondering why this post is in the ethics section.

Even the concepts of good and bad genes have problems. What is a bad gene in one environment may be favorable in another. Consider:- "All vertebrates need haemoglobin". This seems to ring true, until you find exceptions. Like ice fish. They can survive without haemo because cold water holds more dissolved gases than warm water. Therefore more oxygen is available to them. Haemo also makes the blood thicker, and this is not a good thing in the cold. So they have evolved anti-freeze proteins as well. Anti=freeze proteins would not do hot springs bacteria much good, and their enzymes only switch on at high temperatures, so for them, and enzyme with a lower temp range would be deleterious.

A difficult thing to answer really. The sheer diversity of life suggests that no one way of living is the perfect one. Do you remain small and generalist, and therefore only do averagely well in times of [relative] environmental stasis, but can have a better chance of surviving a mass extinction---or do you specialize which gives immediate benefits, but may mark you for extinction [again probably] when the shit hits the fan??

With modern international air and sea travel, the gene pool is getting thoroughly mixed. I don't see a speciation event in our near future unless a population colonizes Mars or somewhere, then it could happen fast. I would like to be optimistic and say that racism is on the decline. However there is also religious segregation, but perhaps that is in decline too. There has been a little evolution-stuff like lactose tolerance which has occurred in historical times. Mainly amoung people who domesticate herds and drink milk of course.

Yes, it is the same Paley. It is true the young Darwin was very taken with Paley's argument. It is after all, a persuasive one if you make the mistake of accepting the premise of the argument. Darwin's travels, and his later research caused him to re-think. "Evolutionists" existed well before Darwin's time, and arguably go back to Classical Greece with folks like Democritus. The main problem with the evolutionary argument was the idea of a natural mechanism that would explain how evolution could work without a supernatural agent such as God. It is interesting that you jump to specualtions about my intellectual powers, or lack of them. In fact I admire Paley's arguments in the context of what was known at the time of Darwin. David Hume for example, came very close to cracking the problem. Daniel C. Dennett called Darwin's insight a "Strange Inversion of reasoning":- Dennett, D. (2009). "Darwin's “strange inversion of reasoning”." Proceedings of the National Academy of Sciences 106(Supplement 1): 10061-10065. http://www.pnas.org/content/106/suppl.1/10061.full Science is often counter-intuitive, and so it does not help if one starts from a firm belief, and then tries to prove it.

I agree that ad-homs lower the tone of the debate, are insulting, and irrelevant to the discussions. However, ad bacterium may be suitable for those who demonstrate that level of cognition.

Science does not prove anything. A successful scientific theory is one that is robustly supported by the evidence, and nothing [to date] to contradict it. Philosophers may highen awareness that science is not perfect....eg David Hume on the problems of induction or whatever. That is all good, a cautionary tale to keep us sharp and skeptical. One can so easily fall in love with one's own theory-which is why we have peer review. As for facts, they are much the same. Evolution is a fact. Until Haldane's genuine fossil bunnies start hopping out of preCambrian rock, it will stil be a fact. The value of science is the destructive testing of it's ideas, and while it may not be perfect, it is a far superior system to some of the others on offer. Like God, exists, now let's set out to prove it? Religion fails as a system of knowledge because of this "confirmation bias". Religion makes smart people think dumb thoughts and more modest intellects psychotic. Take Pascal. A smart guy. Now think about Pascal's wager. It does not take a genius or philosophy PhD to find holes in his case. Or William Paley's. Or go modern, to someone like Kenneth B. Miller, who posits that god can interact at the quantum level. Or Francisco Ayala, who thinks god works through evolution. Both untestable assertions from folks who are trained in methodological naturalism. And yet, those god of the gaps arguments keep re-appearing, not because new evidence of god has arrived, but due to faith that god exists. Real scientists are "evidence sluts"-their opinion is where the evidence is, not where they want it to be. If religious propositions were so self-evidently true, then they should survive destructive testing. They don't. But there not just propositions, they are touted as facts by the faithful. Hence the intellectual bankruptcy of NOMA. Sorry for the digress, but comapring non-facts and non-theory with real facts and real theory puts both into sharp relief. Pseudosciences are the same as religion, they make the same mistakes. But non-explanations like pseudo-science and religion as memes replicate faster than memes [like science] that require thought and effort and honesty.

Hi everyone, I'm Rob. I am Environmental science [Murdoch Uni] and Arts Graduate [uni of Western Australia]. Main interests these days evolutionary theory in particular and biology and science in general. Also interested in the philosophy of science, but not much of a fan of post-modernist interpretations of things, especially of the radical type. What else, I'm an old fart. I get a certain puerile enjoyment out of de-bunking creationism and pseudosciences. I was a Moderator on the old RDF forum site before it folded, and can now be found at places like RatSkeps, the AFA forum, Talk Rational and the like. I am an atheist, because I think it is the only way that one can try to be a full-time "methodological rationalist" without being inconsistent and experiencing cognitive dissonance. Not that I am claiming to be a perfect rationalist-I am a human being, not a robot. But I find that the more one exercises one's rational skepticism, the easier it gets, and hopefully, one makes fewer mistakes. Certainly, many contradictions disappeared when I became an atheist. The God Hypothesis is a hard one to subject to destructive testing, given that there are so many moving goalposts. Even more strange that some claim god as an absolute fact. It seems to me that if one claims that god is real, then one is claiming omniscience, for only with total knowledge could you absolutely claim the existence or non-existence of god. Therefore any belief that god exists must be surely irrational. For who amongst us humans is omniscient? Good to meet you all.

Higher energy states.

This is a very interesting question, because it is obvious that we humans are both products of blind evolution and yet have the ability to model the future. So unless we want to go down the path of using a supernatural cause [which is unscientific anyway] we are left with natural causation somehow producing a self-aware species such as ourselves. This gives the illusion of a self-forfilling prophesy! So, if we take the Dawkins idea of genes building bodies to protect themselves so that they can replicate, then we have the essence of the answer. Replicates are seldom perfect copies, and thus there is variation. Variation is subject to natural selection and so we get organisms acquiring information about their environment. [but not, at least initially, understanding]. Thus a bear born with thick fur in a cold country "knows" something about it's environment. [All the "bald" bears, we presume, would suffer reduced survival and reproduction compared to the hairy bear.] But let's backtrack to the original putative proto-cell. Some sort of sensation-response network needs to be set up. This is done by chemical signaling. A cell membrane polypeptide might respond to -say- acidic conditions. As too much acid [or perhaps too little] would kill the cell, any variations in the polypeptide that improved it's pH detection capability would be favoured by selection. So would any linkage between this "key and lock system" with a protein that produces a response. Survival might be further enhanced by putting a "decision" phase between detection and response. Perhaps a chain of molecules that allowed various "options", or a flexible response, perhaps by the liking of different biochemical "detection" and response molecules. With the evolution of multicellularity, different cells could first adhere together, and then differentiate in function. Chains/networks of cells that depolarised their membranes in response to physical stimulii would evolve into nerves. Nerves give "real-time" information about the environment, as well as inherited information as I outlined in the bear example. As nerves congregated into ganglia and eventually brains, the integration and processing of different senses gave the organism even more real time information about it's environment. Such a sophisticated sensory and processing network would eventually lead not just to a good model of external [and of course internal] environmental states, but any "spare" processing ability could produce or predict possible or likely future environmental states. This is because brains can store historical information, and thus the organism will be aware of history [it's own and the external] , and in particular, recurrent patterns or cycles. For example, the seasons or day and night. We can thus easily imagine that consciousness could emerge from this process. Thus over the eons, genes learnt to build bodies that could see into the future, even though they themselves have no idea what they are doing. Of course, organisms can do fine without intelligence, but sensory organs do appear to be universal, and sight is present in about 95% of animals species. Spiders and sharks are not known for their intellectual prowess, and yet they proser very well, so I do not want to give the impression that intelligence was inevitable, just a viable way of making a living among many. Plants do very well without animal senses or brains, although they do sense their environment chemically and sense light without vision. Thus their is a tiny grain of truth in creationists creotards, but for a different reason than the ones they postulate. If there is no supernatural creator, then the whole process must be natural. What I have outlined above is highly speculative, and many details are not confirmed or even known. But given the efficacy of organic evolution-the fact of evolution, it seems likely that both chemical evolution [abiogenesis] and the evolution of consiousness requires no intervention of gods at all, but are entirely products of nature. ================================================================ Any question about morphology will probably involve an answer in terms of Hox gene activity and expression. In the case of sexual dimorphism therefore, we can expect that any morphological differences between the sexes would involve an interaction of Hox and sex determining genes to produce differential outcomes in the embryos in each sex. In humans for example, the organismal bauplan is female, and the downstream gene expression of the master sex determination SRY gene seems to be modifying parts of the bauplan for male morphology and functionality. These are only proximate rather than ultimate answers, but perhaps a few papers will shed more light on the subject. This paper, by Sandie M. Degnan, Bernard M. Degnan (2006) "THE ORIGIN OF THE PELAGOBENTHIC METAZOAN LIFE CYCLE: WHATS SEX GOT TO DO WITH IT? [Oxford University press] shows how sex itself may have evolved:- Source:- http://elibrary.ru/i...asp?id=10215273 This next source specifies an example of the connection between SRY and Hox:- Barmina, O. and A. Kopp (2007). "Sex-specific expression of a HOX gene associated with rapid morphological evolution." Developmental Biology 311(2): 277-286. Source [full paper downloadable] at:- http://www.eve.ucdav...Kopp%202007.pdf This paper outlines the process in fruit flies:- Ng, C. and A. Kopp (2008). "Sex Combs are Important for Male Mating Success in <i>Drosophila melanogaster</i&gt." Behavior Genetics 38(2): 195-201. SOURCE AVAILABLE AT:- http://www.eve.ucdav...Kopp%202008.pdf So from these examples, we can see how sex determining genes and Hox Gene Clusters [Gene Regulatory Networks] can interact to produce sexual dimorphic traits. ---- Here is another paper:- http://www.ncbi.nlm....les/PMC2597198/ Williams, T. M., J. E. Selegue, et al. (2008). "The Regulation and Evolution of a Genetic Switch Controlling Sexually Dimorphic Traits in Drosophila." 134(4): 610-623.

Lots of females having sex, but without males! [Where is the downside???]

An excellent resource on animal vision is:- Land, M. F. N., Nilsson, D.E. (2002). "ANIMAL EYES". Oxford, Oxford University Press. Needless to say, a google scholar search with the names of these two authors will produce a rich selection of papers on vision, as they are regarded as leaders in the filed. There are also lots of journal articles about vision, colour vision, and so on...eg Awata, H., M. Wakakuwa, et al. (2009). "Evolution of color vision in pierid butterflies: blue opsin duplication, ommatidial heterogeneity and eye regionalization in Colias erate." Journal of Comparative Physiology A: Neuroethology, Sensory, Neural, and Behavioral Physiology 195(4): 401-408. Yokoyama, R. and S. Yokoyama (1990). "ISOLATION DNA SEQUENCE AND EVOLUTION OF A COLOR VISUAL PIGMENT GENE OF THE BLIND CAVE FISH ASTYANAX-FASCIATUS." Vision Research 30(6): 807-815. As you can see, blind cave fish are an interest of mine. So perhaps I should add some variety:- Kevan, P., M. Giurfa, et al. (1996). "Why are there so many and so few white flowers?" Trends in Plant Science 1(8): 280-284. Insects can see into the ultraviolet, and so what appears to us as a plain white flower looks very different to a bee or whatever. As the human-ape-monkey clades are primarily aboreal, we have good colour vision to distinguish fruits etc, but lousy smell compared to dogs. Dogs have great olfactory senses but their vision is not as good. We can only distinguish about 200-250 smells whereas dogs can distinguish millions. In both cases, loss of function was accompanied by [or rather due to] loss of genes.

Some resources about the evidence for evolution:- Coyne, J. A. (2009). Why Evolution is True. Oxford, Oxford University Press. Carroll, S. B. (2005). Endless Forms Most Beautiful:The New Science Of Evo-Devo and the Making Of The Animal Kingdom. London, Phoenix. Dawkins, R. (1996). Climbing Mount Improbable. London, Viking. (see also his book "The Greatest Show on Earth". Also, any books or papers at all by a chap named Charles Robert Darwin. http://darwin-online.org.uk/ Any google scholar search will turn up enough material to keep anyone going for a 1000 lifetimes. If one wants to know experimental techniques for evolutionary biology, then consult books like:- Garland, T. R., Michael (2009). EXPERIMENTAL EVOLUTION: concepts, methods, and applications of selection experiments. Berkeley, University of California Press. A great general text is:- FREEMAN, S. H., & Herron, Jon C. (2007). "EVOLUTIONARY ANALYSIS". New Jersey, Pearson, Prentice-Hall. and for the more mathematically minded:- Nowak, M. A. (2006). EVOLUTIONARY DYNAMICS: Exploring The equations of Life. London, Harvard University Press.

1. Biochemistry- not just humans, but every organism has complex biochemical pathways. They work, but they have every indication of the blind "design" by Natural selection. 2. Gene Regulatory Networks- again, they work [of course], but they show complexities and redundancies all over the place. Basically, the Hox cluster genes have been duplicated via polyploidy and some other mistakes. Cis -regulation [local, often just upstream], trans -regulation-is distal [like on another chromosome] . Positive and negative feedback loops, and stuff like repressors who repress more repressors. A designer would just have repressors and promoters. GRN's resemble complex circuit diagrams designed by a drunken idiot. Nevertheless, the logic works, and everything [usually ] happens at the right time and the right place in the embryo. The work on Hox has given insight into how limb loss, limb gain and novelization occurs. How whales lost their legs, and gained flippers. How flight structures evolved in insects, reptiles, mammals and birds.

Carroll, S. B. (2005). Endless Forms Most Beautiful:The New Science Of Evo-Devo and the Making Of The Animal Kingdom. London, Phoenix. This popular book by Carroll has some references on the topic. He has also published [with others:- Carroll, S. B. (2005). "FROM DNA TO DIVERSITY: Molecular Genetics and The Evolution Of Animal Design". Oxford, Blackwell.