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Unforced Variations: May 2013

Filed under: — group @ 3 May 2013

This month’s open thread.


551 Responses to “Unforced Variations: May 2013”

  1. 251
    chris says:

    David Housholder @241,

    I notice on your webpage that you made a hackneyed cherrypick of Eisenhower’s “leaving office” speech which was an insightful call for moderation and balance in addressing the position of the US in a complex and fractious world. These sentences of his speech are germane to the subject of this thread:

    “Another factor in maintaining balance involves the element of time. As we peer into society’s future, we – you and I, and our government – must avoid the impulse to live only for today, plundering for, for our own ease and convenience, the precious resources of tomorrow. We cannot mo..tgage the material assets of our grandchildren without asking the loss also of their political and spiritual heritage. We want democracy to survive for all generations to come, not to become the insolvent phantom of tomorrow.”

    D. W. Eisenhower, January 17 1961

  2. 252

    #241–David, it gives me grave concern when you describe a WSJ op ed as a “study.” That’s normally a term reserved for an actual piece of peer-reviewed research published in the professional literature.

    The Schmitt/Happer piece is nothing more than propaganda, tossing around some basics of plant physiology as though they were newly-minted discoveries–and suggesting, indirectly, that they are far more significant than is actually the case. For a real “study” on these topics, a fairly cursory Google search turns up:

    http://jxb.oxfordjournals.org/content/55/407/2365.short

    “Drought is one of the greatest limitations to crop expansion outside the present-day agricultural areas. It will become increasingly important in regions of the globe where, in the past, the problem was negligible, due to the recognized changes in global climate. Today the concern is with improving cultural practices and crop genotypes for drought-prone areas; therefore, understanding the mechanisms behind drought resistance and the efficient use of water by the plants is fundamental for the achievement of those goals. In this paper, the major constraints to carbon assimilation and the metabolic regulations that play a role in plant responses to water deficits, acting in isolation or in conjunction with other stresses, is reviewed.”

  3. 253
    Steve Fish says:

    Re- Evolution and probability

    Whitman, et al. 1998, estimated that there are 5 X 10^30 prokaryotes (bacteria) on earth. Following this fact and the average mutation rate for bacteria, a whole new gene that can produce a different protein will arise every few minutes. Because bacteria can exchange genetic material in a form of sex without reproduction, called horizontal genetic transfer (HGT) via plasmids and some other vectors, the worldwide buildup of new genetic material can be pretty fast. This is why disease can quickly become resistant to new antibiotics and why the indiscriminant use of antibiotics for both humans and in agriculture can create a big problem. This mechanism was responsible for the large library of genetic information that was required for eukaryotes and we multicellular organisms to evolve.

    In sexual species, transfer of genetic material is via sex (with reproduction) and genes are spread horizontally within a species in this way. Unlike older wisdom, most mutations are not negative, instead most are neutral and because they are not weeded out, they build up within a species genome. All of this new genetic material and its duplication and horizontal transfer results in a buildup of raw data for the creation of novel proteins when a further point mutations create something useful. Horizontal transfer of genes and neutral mutation are mechanisms that greatly increase the productivity of the evolutionary process. How can the probability of this process be calculated?

    Actually, trying to calculate the probability of a current outcome from this complicated process is not only wrong, it is lying with statistics. After the fact, the probability is 100%. For example, considering all of the states of muscle fibers, bones, neurons, and their molecular components, an estimate of the probability of my walking across the room to pour a cup of coffee is astronomical. How did I just do that?

    Whitman et al. – http://www.pnas.org/content/95/12/6578.full
    Plasmids – http://en.wikipedia.org/wiki/Plasmid

    Steve

  4. 254
    Patrick says:

    @241 Sorry. Excuse me for not being clear. If you want to make a theological homily about fundamental freedom, or be a pop libertarian radio personality (lots of rights–like speech–but without responsibility),or teach bible–then leave out the climate science, planetary physics, and plant biology. It’s irresponsible to spin it the way you do. Potshots at science, and distortions of it, in no way aid the theological case.

  5. 255
    Pete Dunkelberg says:

    Simon,
    > “…it’s unlikely there can be anything comparable [to us geniuses] elsewhere in the universe, regardless of the availability of suitable planets.”
    > (Hint: it would be like tossing 80 heads in a row).

    This type of thinking is sometimes described as painting the bullseye around the arrow. First you shoot an arrow at the side of a barn, then you paint the target around the arrow.

    There are several million plant and animal species on earth. Every one of them is the descendent of a long line of winners. Indeed, so is each individual beetle. How could it be otherwise?

    The exact arrangement of molecules in a thimble of air is astronomically improbable. It hardly follows that there is nothing else comparable. And from the fact that each species and individual must have descended from a long line of winners, it hardly follows that there are not numerous paths to intelligence.

    > “Evolution branches. Never combines”.

    Actually, hybridization is a common enough route to speciation. But that’s neither here not there for your argument. Once you “get it” about painting the bullseye around the arrow, you’ll have taken a good step toward clear thinking.

  6. 256
    simon abingdon says:

    #249 Phil Scadden

    The phrase I used was “evolution of thinking”. Did you think I meant “intelligence”? Did you notice the “if”?

  7. 257
    simon abingdon says:

    #255 Pete Dunkelberg

    At #150 I wrote “The number of stars in the universe has been estimated on the low side of 10^24 which approximates to 2^80. If our own example of intelligent life has had to survive more than 80 potentially negative bifurcations in its Earthly evolution since abiogenesis over maybe 4 billion years ago (that’s an average of just 1 every 50 million years) then it’s unlikely there can be anything comparable elsewhere in the universe, regardless of the availability of suitable planets”.

    At #194 I wrote “If tossing 80 heads in a row is more likely than the evolution of thinking then there are not enough stars for it to happen”.

    In both these anodyne posts my conjectures are conditional. The sense of neither is changed if “our own example of intelligent life” and “thinking” are each replaced by “any specific trait”. Your parenthetic “[to us geniuses]” is superfluous and unwarranted.

  8. 258
    Patrick says:

    @253 Brilliant. Thanks for the links. I’m reading it all. I note: “We are grateful to our colleagues, whose understanding, generosity, and sense of humor made this project possible.” Scientists!

  9. 259
    Phil Scadden says:

    “Thinking” means what? There is evidence grey parrots can do logical reasoning – is that thinking? I did notice “if” but I thought you implied that this was reasonable. Furthermore, your probability estimate didnt seem to be taking account of time. Suppose humans got wiped – suppose primates got wiped. Do you think it unlikely that say another bullion years of evolution wouldnt throw up a different sentient being? Quite a lot raw material still around.

  10. 260
    prokaryotes says:

    Re Steve, interesting in regards to climate change and prokaryotic content

    “Environmental change during the PETM drives formation of gigantic biogenic magnetite

    The development of a thick suboxic zone with high iron bioavailability – a product of dramatic changes in weathering and sedimentation patterns driven by severe global warming – may have resulted in diversification of magnetite-forming organisms, likely including eukaryotes.” http://www.landesmuseum.at/pdf_frei_remote/BerichteGeolBundesanstalt_78_0040-0041.pdf

    And

    “Faivre & Schüler (2008) estimated that, in some locations on Earth, up to 10% of the iron contained within sediment may be contributed by magnetotactic bacteria. Recently, Haltia-Hovi and colleagues suggested that fossil magnetosome concentrations could be used as a climate indicator (Haltia-Hovi et al. 2010). Magnetosome production was influenced by changes in the bacteria’s natural habitat (e.g., organic matter), which is directly controlled by climate.

    As we begin to understand Earth’s magnetotactic bacteria and the mechanism by which these organisms synthesize iron oxides and sulfides, we may also be able to answer whether the magnetite observed in the Martian meteorite ALH84001 (or others) may be biotic in origin as well. Such insight might help us understand the origin of life on Earth and elsewhere in the universe.” http://www.nature.com/scitable/knowledge/library/bacteria-that-synthesize-nano-sized-compasses-to-15669190

    It appears to me that “The large population size and rapid growth of prokaryotes provides an enormous capacity for genetic diversity.” you mentioned above, will go up considerably with what we can observe with more aquatic dead zones, as water temperature rises, less oxygen dissolves.

    “Water temperature is one of the most important characteristics of an aquatic system, affecting:

    Dissolved oxygen levels. The solubility of oxygen decreases as water temperature increases.
    Chemical processes. Temperature affects the solubility and reaction rates of chemicals. In general, the rate of chemical reactions increases with increasing water temperature.
    Biological processes. Temperature affects metabolism, growth, and reproduction.
    Species composition of the aquatic ecosystem. Many aquatic species can survive only within a limited temperature range.
    Water density and stratification. Water is most dense at 4ºC. Differences in water temperature and density between layers of water in a lake leads to stratification and seasonal turnover.
    Environmental cues for life-history stages. Changes in water temperature may act as a signal for aquatic insects to emerge or for fish to spawn.” http://www.ramp-alberta.org/river/water+sediment+quality/chemical/temperature+and+dissolved+oxygen.aspx

  11. 261
    David Miller says:

    Simon, your comment about evolution only branching and never combining is just silly.

    Hint: when one species branches out, it sometimes comes home to roost. Polar bears are supposed to have mated with land bears many years ago when lack of ice forced them onto land.

    But, really, just look in a mirror. Neanderthals and H Sapiens split apart long ago, but when competing for food and territory in modern day Europe they interbred. Today we all carry some Neanderthal genes.

    I’m not a biologist, particularly not an evolutionary biologist, but I don’t doubt I could find you many more such examples without looking very hard.

  12. 262
    ozajh says:

    Pete Best #229,

    My layman’s understanding is that there is an annual cycle of about 6ppm between early May (the peak) and September/October (the trough), due to carbon take-up by plants. Since the Northern hemisphere has more vegetation than the Southern hemisphere, it dominates this cycle (the peak occurs during the Northern spring and the trough occurs at the very start of the Southern spring).

    The recent breach of 400ppm has occurred right at the 2013 peak, so we can expect the level to drop back to about 394 or so later in the year. NEXT year, however, we will cross 400ppm for a couple of months, and at current rates of increase 2016 onwards (and just conceivably 2015) will see 400ppm at Mauna Loa for the entire year.

  13. 263
    simon abingdon says:

    #246 Patrick

    Thank you for your interesting post and particularly to the link to http://en.wikipedia.org/wiki/Cladistics

    (I quote)

    Cladistics, either generally or in specific applications, has been criticized from its beginnings.

    Decisions as to whether particular character states are homologous have been challenged as involving circular reasoning and subjective judgements.

    Being homologous (“the same organ in different animals under every variety of form and function”) is evaluated strictly in an evolutionary context. That is, organs in two species are homologous only if the same was present in their last common ancestor. Organs as disparate as a bat’s wing, a seal’s flipper, a cat’s limb and a human arm have a common underlying anatomy which was present in their last common ancestor and so therefore are homologous as forelimbs.

    (endquote)

    Patrick you say “Cladistics has thrown a lot of light on what has been called independent evolution of similar traits or character states”.

    The keyword here is “similar”. Similar does not mean identical (homologous). While homoplasy may be a (loosely-defined) trait shared because of convergence, it cannot be “the same organ in different animals under every variety of form and function”.

    It seems to me to be a mistake to think otherwise.

  14. 264
    deconvoluter says:

    “Doubt is their product” is a phrase used by Oreskes concerning contrarian propaganda. At its most honest, this involves highlighting every conceivable uncertainty in the science.

    There is also an alternative contrarian tactic exemplified by the WSJ article and that is to step into a complicated subject, where the experts are a bit unsure of the future. An essay is produced full of fake optimism and presented with such confidence that it sounds attractive to the layman because all the complications and uncertainties have been removed and it is easy to read and remember.

    Where can the reader go to get reliable advice about the effects of
    CO2, warming and water stress on food production?

    The first answer is the AR4 working group 2.

    There is also the suggestion given by Kevin McKinney in #252

    For a real “study” on these topics, a fairly cursory Google search turns up..:

    I’m wondering whether RC can be persuaded to invite one or more experts to write some up to date summaries of this large subject?

  15. 265
    prokaryotes says:

    Here is another threat outlined, from Nitrous oxide uptake and a connection to these

    Magnetotactic Bacteria

    Prokaryotes that exhibit magnetotaxis, collectively known as the magnetotactic bacteria, are those whose direction of motility is influenced by the Earth’s geomagnetic and externally applied magnetic fields. These ubiquitous, aquatic microorganisms represent a morphologically, phylogenetically, and physiologically diverse group that biomineralize unique organelles called magnetosomes that are responsible for the cells’ magnetotactic behavior.

    Almost all cultured species exhibit nitrogenase activity and thus fix atmospheric nitrogen and many denitrify. Magnetotactic bacteria thus show a great potential for iron, nitrogen, sulfur, and carbon cycling in natural environments.

    Genetic determinants for magnetosome synthesis, the mam and mms genes, are organized as clusters in the genomes of all magnetotactic bacteria examined. These clusters are in close proximity to each other within the genomes and are surrounded by genomic features that suggest that magnetosome genes are organized as a magnetosome gene island that might be transmitted to many different bacteria through horizontal gene transfer. Through the development of genetic systems in some magnetotactic bacteria, the functions of several magnetosome membrane proteins in the biomineralization of the magnetite magnetosome chain have been demonstrated although the roles of most remain unknown.
    Bacterial magnetosomes have novel physical and magnetic properties and also geological significance and have been used in a large number of commercial and medical applications. http://link.springer.com/referenceworkentry/10.1007%2F978-3-642-30141-4_74

    Nitrous oxide molecules stay in the atmosphere for an average of 120 years before being removed by a sink or destroyed through chemical reactions. The impact of 1 pound of N2O on warming the atmosphere is over 300 times that of 1 pound of carbon dioxide. Globally, about 40% of total N2O emissions come from human activities. Nitrous oxide is emitted from agriculture, transportation, and industry activities http://epa.gov/climatechange/ghgemissions/gases/n2o.html

    Nitrous Oxide Emitting Aquatic ‘Dead Zones’ Contributing To Climate Change

    The increased frequency and intensity of oxygen-deprived “dead zones” along the world’s coasts can negatively impact environmental conditions in far more than just local waters. In the March 12 edition of the journal Science, University of Maryland Center for Environmental Science oceanographer Dr. Lou Codispoti explains that the increased amount of nitrous oxide (N2O) produced in low-oxygen (hypoxic) waters can elevate concentrations in the atmosphere, further exacerbating the impacts of global warming and contributing to ozone “holes” that cause an increase in our exposure to harmful UV radiation.

    When suboxic waters (oxygen essentially absent) occur at depths of less than 300 feet, the combination of high respiration rates, and the peculiarities of a process called denitrification can cause N2O production rates to be 10,000 times higher than the average for the open ocean. The future of marine N2O production depends critically on what will happen to the roughly ten percent of the ocean volume that is hypoxic and suboxic. http://www.underwatertimes.com/news.php?article_id=85403791012

    This means that there is another source of Greenhouse Gases, contributing to feedback cycles, which has not yet been discussed.

  16. 266
    SecularAnimist says:

    A while back, Phil Scadden wrote: “However, who says that … intelligence can only be like human?”

    I replied (#199): “A suprising number of people, including some scientists, seem to have a problem recognizing the intelligence of non-human animals right here on Earth.”

    Just recently Phil Scadden wrote: ” ‘Thinking’ means what? There is evidence grey parrots can do logical reasoning – is that thinking?”

    How can “logical reasoning” not be “thinking”? Just because it’s a non-human animal doing it?

    In at least one case (Dr. Irene Pepperberg’s work with the parrot Alex, an African Grey Parrot learned to communicate intelligently and interactively in spoken English, including the ability to understand and communicate abstract concepts like size, shape, color, same and different.

    Numerous other studies have demonstrated that a variety of non-human animals (mostly but not exclusively mammals and birds) have advanced, sophisticated cognitive and communicative capabilities — including the ability to count, the ability to anticipate the consequences of their actions, and to anticipate the actions of others, to solve problems, and to plan.

    Yet there remains a stubborn resistance among some people to accepting that non-human animals can “think” or “reason”.

    As for intelligent extraterrestrial life, I wonder whether humans will even recognize it if we see it.

  17. 267
    simon abingdon says:

    #257 simon abingdon postscript to:
    #255 Pete Dunkelberg “once you ‘get it’ about painting the bullseye around the arrow, you’ll have taken a good step toward clear thinking”

    I have pondered your metaphor of the random arrow’s destination and the retrospectively painted target but I have failed so far to “get it” so the fulfilment of your prediction has for me yet to be realised.

    I am assuming that your arrow represents the random undirected unfolding of an evolutionary pathway and your retrospectively painted target the post hoc inevitability of its culmination. But the position I am inviting you to consider is that the appearance of Homo sapiens remains an event of extreme unlikelihood. I do not portray it as an outcome inevitable from the outset. You are the one painting the target, or so it seems to me. I’m surely missing something.

  18. 268
    chris says:

    @257 simon,

    “In both these anodyne posts my conjectures are conditional. The sense of neither is changed if “our own example of intelligent life” and “thinking” are each replaced by “any specific trait”.”

    Nope. You’re still using a semantic argument. It depends what you mean by “specific”. A more logical and meaningful way of addressing this is to recognize the distinction between “specific” and “generic”.

    We resolved this earlier in the thread of course. Your “elephants” and “giraffes” and Paul D’s “white deer”, are specific entities, which we wouldn’t expect to find elsewhere. The human eye is a specific entity that we’d be very surprised to find in beings on other planets. However we know that eyes as a generic organ have evolved independently in many forms on Earth, and we wouldn’t be surprised if beings elsewhere (should these exist) had evolved organs that respond to particular forms of electromagnetic radiation, an entity which by the way is “specific” but also has a “generic” quality in that it is a pervasive property of the entire Universe. Intelligence is likely a generic property.

  19. 269
    chris says:

    you are missing something simon (or pretending to). The evolution of Homo sapiens is unlikely; the evolution of some complex intelligent being not necessarily so.

    After all the appearance of a “simon abingdon” is astonishingly unlikely, being the product of conjoining of this particular sperm with that particular egg in the current generation, the unlikelihood similarly multiplied back through thousands and millions of generations. It’s less “80 heads in a row” and more “winning the lottery 100,000 times in a row” (there are some philosophical arguments for reducing this stupefying degree of unlikelihood).

    Clearly the specific entity of a “simon abingdon” is astonishingly unlikely. However the “generic” entity (“some bloke”) isn’t, since “blokes” pop into existence all the time. It’s only when you specifify the outcome from the outset that you generate astonishing unlikelihoods as in your sneaky statement: “I do not portray it as an outcome inevitable from the outset.” After all I doubt you’d be astonished if I dealt 52 cards from a shuffled deck. On the other hand you might perk up if I dealt a sequence that you had specified “from the outset”.

    I suspect you know all that – I doubt even hardcore creationists consider that they can still make much traction with your jaded second-hand arguments from incredulity.

  20. 270
    Hank Roberts says:

    > March 12 edition of the journal Science,
    > University of Maryland Center for Environmental Science
    > oceanographer Dr. Lou Codispoti

    Which year?

    I found this one from March 12, 2010 — is there a newer article?

    Science 12 March 2010: Vol. 327 no. 5971 pp. 1339-1340
    DOI: 10.1126/science.1184945
    Perspective
    Interesting Times for Marine N2O
    Louis A. Codispoti
    https://www.sciencemag.org/content/327/5971/1339.summary?sid=d74af249-1556-4b96-8e6c-95053658170b

  21. 271
    SecularAnimist says:

    simon abingdon wrote: “… the appearance of Homo sapiens remains an event of extreme unlikelihood …”

    So far so good.

    But where you go too far is equating “the appearance of Homo sapiens” with “the appearance of intelligent life”.

    I find myself picturing this science fiction scene:

    A huge flying sauncer lands on the National Mall in DC, just like in “The Day The Earth Stood Still”. At last, intelligent extraterrestrial life has contacted us!

    The door opens. But instead of the humanoid Klaatu, what emerges is … a swarm of ants.

  22. 272
    Ray Ladbury says:

    Simon,
    Your thinking reminds me of a cruel trick we once played on a female friend who we thought was being too particular in her criteria for a boyfriend and then lamenting the lack thereof. We asked her to list all her criteria and assigned a probability to each corresponding to the number of males who might fulfill those criteria. Of course, we came up with a vanishingly small probability that said man had ever existed in the entire history of humankind. And of course our exercise was fallacious. First, the probabilities are not all independent, but rather in most cases conditional. And of course, my friend’s criteria turned out to be a lot more flexible when “the right guy” came along.

    You are assuming that any intelligent life would have to be pretty much just like humans. I’m hoping for their sake that is not the case. It is as if we are having a game of darts. Of course the probability of hitting any one point on the wall opposite us is vanishingly small. However, unless you are as bad as I am at darts, you must hit some point on that wall. The probability space for intelligent life is likely much larger than you imagine. Of course, I’ve yet to be convinced that humans represent intelligent life.

  23. 273
    simon abingdon says:

    #268 #269 Chris

    “the distinction between “specific” and “generic”

    The ability to think (at the level of Homo sapiens) is “generic” not necessarily “specific”. Shortening the odds by replacing “specific” by “generic” in this case does not do damage to my thesis. Many organisms are able to see, to fly, and so on. Here only one has learnt to predict eclipses or understand how to split the atom.

    “The evolution of Homo sapiens is unlikely; the evolution of some complex intelligent being not necessarily so”

    Here we have only ever seen one example of complex intelligence. We have many examples of eyesight and other survival traits. Complex intelligence looks special, unusual.

    “It’s only when you specify the outcome from the outset that you generate astonishing unlikelihoods”

    Not if the outcome is expressed in general (generic) terms like the ability to control fire or possessing more than an elementary language.

    If you think parrots and dolphins, admirable as they are, exhibit intelligence in the sense of being ever able to understand Pythagoras then I disagree with you.

    But as ever it’s only opinion; we have zero evidence.

    I have said before that if incontrovertible evidence of extraterrestrial intelligence were to be found it would be the most exciting day of my life.

    Let me know when you’ve got some.

  24. 274
    simon abingdon says:

    #271 SecularAnimist

    “But where you go too far is equating “the appearance of Homo sapiens” with “the appearance of intelligent life””

    Sorry, I’m not aware of having done so.

    Instead I refer to abilities that intelligence connotes like thinking and introspection and complex communication through an elaborate language.

  25. 275
    Hank Roberts says:

    > a swarm of ants

    Black ants, here to colonize this under-used planet before their great competitors, the red ants, find it. First, clear out these pesky mammals, which never develop any real intelligence …

    I’m sure I’ve read that science fiction story somewhere.

  26. 276
    simon abingdon says:

    #272 Ray Ladbury

    Good point Ray.

  27. 277
    Jason says:

    Nice article in the NYT today. I think it is good science writing, headline writing aside.

    http://www.nytimes.com/2013/05/14/science/what-will-a-doubling-of-carbon-dioxide-mean-for-climate.html?hp

  28. 278
    simon abingdon says:

    #269 Chris

    Disregard:

    “It’s only when you specify the outcome from the outset that you generate astonishing unlikelihoods”

    Not if the outcome is expressed in general (generic) terms like the ability to control fire or possessing more than an elementary language.

    Replace with:

    “It’s only when you specify the outcome from the outset that you generate astonishing unlikelihoods as in your sneaky statement: “I do not portray it as an outcome inevitable from the outset”.

    Read that again:

    “I do not portray it as an outcome inevitable from the outset”. And that’s why the outcome is unlikely.

    It’s the guy who paints the target retrospectively who portrays it as an outcome inevitable from the outset” Not me.

    In any case why are you responding instead of Pete Dunkelberg. It was he who introduced the red herring of painting the target round the arrow and which he hasn’t yet explained.

  29. 279
    James Cross says:

    Regarding Intelligence

    You might want to take a look at this:

    http://www.alexwg.org/publications/PhysRevLett_110-168702.pdf

    Or, the layman’s version:

    http://phys.org/news/2013-04-emergence-complex-behaviors-causal-entropic.html

    The above paper attempts to derive a general theory of intelligence from basic physical processes and “describes intelligent behavior as a way to maximize the capture of possible future histories of a particular system.”

    If this is the case, then intelligence might be seen as a property built into life. DNA might be itself be the foundation capturing information and “maximizing future histories” on long time scales and what we generally think of as intelligence (planning, rational behavior, etc) as “maximizing” on a real time scales. Culture and collective knowledge extend the real time intelligence over generations.

    This would tend to lead one to believe that evolution given a reasonable stable environment for a long enough time would lead to intelligence and this intelligence might be very similar to ours at some point in its evolution.

    Of course, the intelligent outcome of evolution would probably seldom look anything like human. But it is interesting to speculate how much it might look like something we might not be surprised to find on Earth. Every organism that we know of that have higher intellectual capacities are descendants from some original member(s) of the bilateria – probably a worm. A worm is basically a digestive tract with a nerve curve running along it, a mouth with a concentration of nerve fibers at one end (a rudimentary brain), and you know what at the other end. In other words, a eating machine. All of the animals with really exceptional intelligence are highly social creatures with at least rudiments of culture.

  30. 280
    prokaryotes says:

    Re Hank Roberts #270 “… is there a newer article?” about “Nitrous Oxide Emitting Aquatic ‘Dead Zones’ Contributing To Climate Change”

    Well i found a bit more via Wikipedia (quote below) and a TED talk from Peter Ward, which context was new to me.

    Anoxic event

    Oceanic anoxic events or anoxic events occur when the Earth’s oceans become completely depleted of oxygen (O2) below the surface levels. Although anoxic events have not happened for millions of years, the geological record shows that they happened many times in the past. Anoxic events may have caused mass extinctions. These mass extinctions were so characteristic, they include some that geobiologists use as time markers in biostratigraphic dating. It is believed oceanic anoxic events are strongly linked to lapses in key oceanic current circulations, to climate warming and greenhouse gases.

    The second hypothesis suggests that oceanic anoxic events record a major change in the fertility of the oceans that resulted in an increase in organic-walled plankton (including bacteria) at the expense of calcareous plankton such as coccoliths and foraminifera.

    Such an accelerated flux of organic matter would have expanded and intensified the oxygen minimum zone, further enhancing the amount of organic carbon entering the sedimentary record. Essentially this mechanism assumes a major increase in the availability of dissolved nutrients such as nitrate, phosphate and possibly iron to the phytoplankton population living in the illuminated layers of the oceans.

    For such an increase to occur would have required an accelerated influx of land-derived nutrients coupled with vigorous upwelling, requiring major climate change on a global scale. Geochemical data from oxygen-isotope ratios in carbonate sediments and fossils, and magnesium/calcium ratios in fossils, indicate that all major oceanic anoxic events were associated with thermal maxima, making it likely that global weathering rates, and nutrient flux to the oceans, were increased during these intervals. Indeed, the reduced solubility of oxygen would lead to phosphate release, further nourishing the ocean and fuelling high productivity, hence a high oxygen demand – sustaining the event through a positive feedback.

    Here is another way of looking at oceanic anoxic events. Assume that the earth releases a huge volume of carbon dioxide during an interval of excessive volcanism; global temperatures rise due to the greenhouse effect; global weathering rates and fluvial nutrient flux increase; organic productivity in the oceans increases; organic-carbon burial in the oceans increases (OAE begins); carbon dioxide is drawn down (inverse greenhouse effect); global temperatures fall, and the ocean–atmosphere system returns to equilibrium (OAE ends).

    In this way, an oceanic anoxic event can be viewed as the Earth’s response to the injection of excess carbon dioxide into the atmosphere and hydrosphere. One test of this notion is to look at the age of large igneous provinces (LIPs), the extrusion of which would presumably have been accompanied by rapid effusion of vast quantities of volcanogenic gases such as carbon dioxide. Intriguingly, the age of three LIPs (Karoo-Ferrar flood basalt, Caribbean large igneous province, Ontong Java Plateau) correlates uncannily well with that of the major Jurassic (early Toarcian) and Cretaceous (early Aptian and Cenomanian–Turonian) oceanic anoxic events, indicating that a causal link is feasible.

    http://en.wikipedia.org/wiki/Anoxic_event

    Related video with Peter Ward
    http://climatestate.com/2013/05/13/peter-ward-earths-mass-extinction/

    Diazotrophic cyanobacteria as the major photoautotrophs during mid-Cretaceous oceanic anoxic events: Nitrogen and carbon isotopic evidence from sedimentary porphyrin http://www.sciencedirect.com/science/article/pii/S0146638007002628

  31. 281

    Complete mastery of biochemistry is a characteristic of bacteria that even we as intelligent beings are not yet capable of, Simon. Again, you are unnecessarily restricting your definition of intelligence to a nervous system when many levels of technical sophistication precede that development.

  32. 282
    Hank Roberts says:

    Peter Ward’s work has come up in discussion at RC since way back; 2005, maybe earlier. Worth re-reading; use the site search.

  33. 283
    Dave123 says:

    I don’t mean to wade into an off-topic thread…but I think there’s a lack of molecular biologists commenting on the probabilities.

    First of all, all the really hard work is at the beginning to get viable living cells. Really.

    But that hard work was greatly simplified because there weren’t “bifurcations”. Way back when, the notion of an individual conserved species wasn’t applicable. Cell-like structures exchanged material at a rapid rate. Imagine picking up butterfly chromosomes because one flew by shedding as it went. Only latter, after a lot of basic system were worked out did protecting the cell from outside genetic information become useful and event today it is observed that plasmid exchange is a mechanism for transferring immunity to antibiotics from one species of bacteria to another. One really ancient example is that mitochondria have their own DNA… but they are part of modern cells…they are simply cells that formed a commensal relationship with another type of cell and that combination was so successful it proliferated to be the core of nearly all of modern biota.

    Now all this stuff was learned after I got out of graduate school…back when kerry Mullis was still riding his surf board. But it’s very different thinking about the development of life than what Simon is proposing, and has very different odds of success. If you want to get a taste for this Smith College has a summer lab course on Molecular biology that’s a lot of fun. Took it back in 2003.

  34. 284
    doug says:

    I was lectured on here a few months ago by Ray Ladbury that a question I was asking really wasn’t climate related, but he seems to have no problem engaging in a debate about whether there is life beyond earth, on a climate blog… I wouldn’t call you out Ray, except that I’ve noticed you can be a real jerk to a lot of people. Let’s all be a little bit nicer huh? How’s that sound?

  35. 285
    Killian says:

    Re: 280 and eutrophication.

    A point I have made regarding concurrent degradation of the whole system (human activity simultaneously degrading all ecosystems) vs. cascading degradation (i.e. Minakovitch > warming > Co2) fits here.

    While the past ELE’s seem to have been the latter type, we have already begun the simultaneous degradation of the ocean system with runoff of FF-based chem fertilizers, top soil and other pollutants.

    This can seemingly only lead to an even faster cascading failures.

    Lot’s of bad news in the climate news this past week or two.

    Gotta love that climate sensitivity is as bad, or worse, than even I thought.

    :/

  36. 286

    OMG, are we still on about this undefined quasi-probabilistic hooha?

    Simon wrote quote and commented:

    “It’s the guy who paints the target retrospectively who portrays it as an outcome inevitable from the outset” Not me.

    Simon, you are ‘painting the target’ when you claim that the evolution of intelligence/abiogenesis/whatever is tremendously improbable: “Look, the arrow (or in Ray’s iteration, dart) hit that *one exact spot.* How unlikely!” Seems to me that your argument here is sign-reversed.

  37. 287
    James Cross says:

    #283

    Dave,do you have some references for that? I am not doubting it, but I am not 100% sure about it either. I would just like to read a little more about it.

    What I don’t understand is why we cannot do something like that experimentally to create a viable organism to prove it is possible.

    The problem is I see is in the notion of “cell-like structures”. That implies a membrane but you need an organism to create a membrane unless you are hypothesizing some natural, non-living membrane such as clay or lipids.

  38. 288
    simon abingdon says:

    #286 Kevin McKinney

    “Simon, you are ‘painting the target’ when you claim that the evolution of intelligence/abiogenesis/whatever is tremendously improbable”.

    Come on Kevin. My arrows (hopeful candidates for emerging extraterrestrial intelligence) all fail to reach the barn door: I’ve got no possible places to paint a retrospective target. Neither apparently has Ray as he admits at #272 (“unless you are as bad as I am at darts, you must hit some point on that wall”). Ray’s hopeful darts likewise fail and he too has nothing to paint.

  39. 289
    Steve Fish says:

    Re- Comment by James Cross — 14 May 2013 @ 7:24 AM

    If you want to know why membranes are not the main problem in biogenesis watch the David Deamer video suggested by pete best (11 May 2013 @ 5:17 AM) above.

    Steve

  40. 290
    chris says:

    simon @ 278

    Fair enough, if all you’re saying is that evolution of Homo sapiens is unlikely in the same sense that the appearance of a “simon abingdon” (as opposed to some other generic bloke) is unlikely then it’s not obvious what your point is. And one then wonders why you attempt to equate the likelihood of technologically-developed life elsewhere in the Universe with the likelihood of finding giraffes and elephants…or make a play about the apparent unlikelihood of extant homochilarity, when in fact the probability of homochirality in a carbon-based life form is high (maybe approaching 1), and we can understand a plausible mechanism for generation of the specific extant homochirality in earth life. Those seem like efforts to exaggerate unlikelihoods…

  41. 291
    Hank Roberts says:

    > James Cross
    > … I would just like to read a little more
    > … what I don’t understand

    Your own blog linked behind your name discusses this extensively.
    Please, people, opine about this further at length somewhere else?

    Please. This isn’t climate science. It’s microbiology, standard coursework, basic material you can read up on. You don’t need opinion blogged here on it.

  42. 292
    Ray Ladbury says:

    Doug,
    Fair enough. However, my interest here is not so much in the biology, but rather in the fallacious way Simon is using statistics. I would contend that this is relevant, because we see the same sorts of fallacious arguments from denialists seizing on every cold snap to proclaim the end of the global warming threat.

    I think that part of the problem here is that we are actually dealing with subjective probabilities. The ACTUAL probability of intelligent life in the Universe (depending whether or not we accept humans as intelligent life) is either zero or one. The actual probability distribution for Charney climate sensitivity at any given time is a delta function. It is our imperfect knowledge that smears it out to a (roughly) lognormal.

    However, subjective probability is not arbitrary probability. There are rules for how to interpret evidence and how to incorporate new evidence. Unless we follow those rules we are at risk of sloppy thinking and self-deception.

    My goal in coming to science-related sites is to avoid such sloppy thinking. It has not been my experience that “nice” really helps much with that.

  43. 293
    Hank Roberts says:

    PS — the origins of life folks are a large group glad to have attention.
    Follow the links to their own blogs that they keep posting and mentioning.
    Note the links they like, as presented on their blogrolls.
    The doubt-is-in-the-gaps notion covers both evolution and climate.
    Eschew.

  44. 294
    chris says:

    “What I don’t understand is why we cannot do something like that experimentally to create a viable organism to prove it is possible.”

    I think the answer is we don’t know where to start. There are lots of potential entries into bits of the puzzle. It’s easy to understand how the huge number of small molecule precursors of biomolecules arise since these can be produced in supposed prebiotic environments or found on comets. It’s easy to understand the origin of homochirality. Almost all (but not all) of the steps of the most basic biochemical cycles (the citric acid cycle which is a funamental energy producing metabolic cycle in most living systems) can be made to proceed without using enzymes. Amphiphilic molecules can associate to form crude membrane-like structures and so on. But those are just snippets of possibilities.

    You could approach this by doing a hardcore chemical synthesis of all of the components of the simplest unicellular organism. DNA is easy to synthesise, and RNA, proteins, membrane lipids etc. can all be chemically -synthesized. If one were able to combine these together to recreate the simple organism (there are good reasons why this wouldn’t actually work) you wouldn’t have learned anything about the origins of life, but merely confirmed that living beings are comprised of chemicals and their macromolecules.

    Dave123 is completely right when he says “First of all, all the really hard work is at the beginning to get viable living cells”. It’s verey difficult to know how that happened. After that evolution of complexity is conceptually

  45. 295
    Martin Vermeer says:

    Simon says #170:

    You have a problem with that logic?

    Yes. And find it amazing that you don’t. Did you really drink the creationist kool-aid that evolution is ‘random’?

  46. 296
    simon abingdon says:

    #291 Ray Ladbury

    “The ACTUAL probability of intelligent life in the Universe (depending whether or not we accept humans as intelligent life) is either zero or one”.

    So, if we “accept humans as intelligent life” the probability is one. (We knew that).

    On the other hand if we do not “accept humans as intelligent life” the probability is zero. (Non-human intelligent life does not exist).

  47. 297
    Dave123 says:

    @James Cross- I’m afraid that I don’t collect abiogensis papers…but I’ve been well aware of primordial soup experiments that produce encapsultated cell like structures. The evolutionary drivers work well here- thermodynamics causes non-polar materials to move away from water, they float to the top. Random chemistry that makes detergent like materials with polar and non polar species is also favored, if only be oxidation of lipid chain to provide partial water solubility. Since lipids float at the top near all that lovely ionizing radiation, you’ll get enough of that going on that there will be a “survival” advantage to materials that mix better with water and slip down a bit into it. There will be common species, and those species will by the same thermodynamics that promote crystal formation make certain combinations of small detergent like microcapsules more stable than others, more persistent. All of this is at huge rates per second. Microcapsules bump into each other, exchange material when thermodynamically favored. Non-polar materials will tend to accumulate in the interior of these little globules as well as less stable materials that benefit from the shelter at a molecular level. Bit by bit you can accumulate chemistry in these environments- for example to replace oxidation at the surface, a primative iron complete that promotes alkane oxidation to provide more membrane materials. Or a means of making true lipids coupling sugars with alkanes. From a chemist’s point of view the rates of reaction sustained over millions of years, the promiscuity leading to exchange and proliferation of survival factors removes a lot of the odds against abiogenisis. But where the transition occured? I don’t know. Cell membrane evolution from primordial soup, RNA/DNA origins, Amino acid origins, everything at the molecular level that goes into making life has been observed in the lab.

    Again, this is just my memories from reading Science and Journal of the Americal Chemical Society for decades…and I really should be doing something else right now.

  48. 298
    Russell says:

    It is diagnostic of the intellectual poverty of disbelief in spontaneous complexity giving rise to a large variety of organic componds that inorganic chemistry gives rise to some 4000 minerals on Earth alone.

  49. 299
    Paraquat says:

    @#150 “The number of stars in the universe has been estimated on the low side of 10^24 which approximates to 2^80. If our own example of intelligent life has had to survive more than 80 potentially negative bifurcations in its Earthly evolution since abiogenesis over maybe 4 billion years ago (that’s an average of just 1 every 50 million years) then it’s unlikely there can be anything comparable elsewhere in the universe, regardless of the availability of suitable planets”.

    Maybe. But you ought to consider the possibility that life could travel between planets, known as the theory of “panspermia.”

    http://en.wikipedia.org/wiki/Panspermia

    I admit that the theory has yet to be proved, and such proof will not be easy to obtain. But it’s a possibility to consider. At the minimum, we’ve got to get to Mars and dig around in the soil looking for evidence of current or past life. And Mars is just one small dot in the universe. The chance of sending even unmanned probes to other stars to look for life is slim indeed. So we may never have an answer.

  50. 300
    Sou says:

    Can anyone point to the origins of this Reuters article and comment on its veracity? The Reuters article is saying that sea level rise will be contained to 69cm this century and ostensibly quoting Ice2Sea as its source.

    It’s being offered up by fake skeptics as their alternative “it’s warming but it won’t be that bad” meme, presumably for people who can’t quite swallow their “we’re heading for an ice age” meme.

    I’ve looked at the Ice2Sea website and all I found was a press release about this new paper in Nature, which doesn’t exactly match up.


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