Episode 2 "Some of the Things That Molecules Do"
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3/16/2014 at 1:04:54 PM GMT
Posts: 142
Episode 2 "Some of the Things That Molecules Do"
This topic is devoted to episode 2 of Cosmos: A Spacetime Odyssey

Last edited Sunday, May 11, 2014
3/17/2014 at 11:15:18 AM GMT
Posts: 142
The storyline that connects episode 2 to episode 1 isn’t very clear to me. For whatever reason, Tyson chose to jump from cosmology to evolution.
What a dramatic story of what we know about the evolutionary development of life! The graphic wizardry continued as he showed clever simulations of various evolutionary paths from wolves to dogs and from sightless beings to complex eyes for vision. But he spent very little time spelling out how we know this narrative is really true. It seems like an imaginative fantasy. The main hint he provided was the connection of DNA among all the species. Clearly, the intent was to show what we know but not how we know it. As a consequence, I doubt if anyone would be persuaded of the validity of evolution from this program alone. There are plenty of other resources for that. 

Tyson did, unfortunately, seem to make a special effort to juxtapose his view of evolution against commonly held religious perspectives. He emphasized that evolution occurred “purely by chance” and was “entirely random.” In this usage, chance and randomness mean that the changes occur independently from the end result. Many people interpret chance and randomness to be in opposition to guidance from a supernatural designer, which may be one reason why Tyson singled out the Paleyesque view of intentional design.

The objection to Tyson that needs to be raised is not that there was no chance or randomness but that divine creation is not mutually exclusive of evolution. Chance and randomness, as the Bible tells us, can also be tools of our creator.

3/17/2014 at 3:15:44 PM GMT
Posts: 19

I had the same thoughts, especially when Tyson firmly reiterated that all mutations are always random. This is the neo-Darwinian modern synthesis which has become dogma. This has been challenged recently by data showing that some mutations in bacteria (called stress-directed mutations, SDM) are not at all random. This is still scientifically controversial, but is becoming an alternative to the standard dogma.

Of course, I wasn’t surprised that the writers went with the standard view. This show is not about reconciliation of science and faith, and so I was less bothered by the content of this episode than I was at the distorted focus on Bruno in the first episode. In fact, I almost expected a 10 minute discussion of the Scopes trial, and how evil Christians opposed Darwinism, and was relieved when that didn’t happen.

I also agree with you that the treatment of evolution was not terribly convincing, but I did think that the idea of using the artificial selection of dogs in the opening was a brilliant way to introduce the whole concept of natural selection.

As a minor note, I thought the graphics could have been used to better advantage. For example, the depiction of DNA was quite simplistic, and could have easily been raised to a higher educational level. The bases were shown as simple straight lines rather than interacting base pairs. Again, this is a minor point, but I felt it was an opportunity lost.

Last edited Monday, March 17, 2014
3/17/2014 at 3:52:49 PM GMT
Posts: 142
Sy, I'm still trying to get my arms around claims of  "...not at all random..." and it appears to me that it really refers to mutations that are influenced by the environment in some way. That's not quite the same as being determined by the end result. I think randomness is generally properly understood in this context as independent of the end result, not independent of the environment. But maybe I have misunderstood it.

Originally posted by S. Garte:
... This has been challenged recently by data showing that some mutations in bacteria (called stress-directed mutations, SDM) are not at all random. ...

3/17/2014 at 4:36:50 PM GMT
Posts: 19

You are right that SDM is influenced by the environment, but there is a connection with the end result in that the gene whose mutation can relieve the stress is specifically mutated. This seems at first glance to be counterintuitive in a biological sense, but mechanisms have been found to explain it (hypermutability of transcribed genes that are over-expressed as a result of the stress, for example).

On the other hand, Shapiro's concept of natural genetic engineering, which also postulates a strong role for the environment in the creation of genomic variations (including transposon activation, whole gene duplication and so on) is, as you suggest, independent of the end result, and requires the action of natural selection as much as any random mutation.

I think that random in a biological sense means independent of anything, including the environment. This is certainly true of neo-Darwinism, which is why the fanatical neo-Darwinists hate both SDM and Shapiro. Theologically, your point is interesting. It raises the issue of whether God, by controlling the environment, can influence the course of evolution, but that is probably the subject for a discussion elsewhere.

Last edited Monday, March 17, 2014
3/17/2014 at 9:54:14 PM GMT
Posts: 19
On another note, I was not at all impressed with the ship of the imagination going to search for life on Titan. The idea that some form of hydrocarbon based anaerobic life would form in a sea of methane (with no mention of an energy source) is highly speculative, of course. It wasn’t made sufficiently clear that this idea is pure fantasy, as opposed to the strong evidence for evolution on Earth. There are some pretty good biochemical reasons to doubt Titan as a potential location for life, but I am not sure how much actual biochemical expertise was available to the writers. And of course, Tyson, being an astronomer, loves the idea of extra-terrestrial life (much like Sagan). I predict we will hear a lot more about life elsewhere as the series continues.

Last edited Monday, March 17, 2014
3/18/2014 at 2:39:21 AM GMT
Posts: 1
randomness in evolution
Hello folks, I am poking my head in here for the first time at the polite request of my friend Randy. This discussion makes me see how much I am missing. Having near-adolescent kids, I am concentrating too much recently on the dangers of the internet, and need sometimes to be reminded of the wonderful benefits.  Forums like this have to be near the top of the list.  Still, in the days of Johnson, Boswell, and Goldsmith we'd all be discussing this in someone's living room, but here we are now in cyberland. So be it. Anyway, I would say that in nearly any introductory science program we have to put up with generalities that are violated by a few specific examples.  This is especially the case in biology where every category is violated by the realization of a continuum (a theologian should investigate the importance of this lesson).  But it is also the case in physics where general rules are violated either by mundane things like friction or in situations when things are very small or very large.  So I do not fault Tyson or anyone else for describing evolutionary change as being given scope by mutations whose existence and specific nature are independent of their outcomes, in the same way that the causes of a landslide are independent of what gets squashed or accreted downhill. It is the responsibility of each producer/writer/performer to decide how much of the complexity in life can be presented in a particular format to a particular audience in a particular amount of time. I myself teach to my introductory undergrads that mutations are random with respect to outcome, then merely mention that there are some exceptions they might learn later; whereas I teach to doctoral students the current state of knowledge of the complexity. Still, there is no known case to my knowledge where the specific mutation, as opposed to the likelihood of mutation, is driven by outcome. In other words, we might predict and discover genes that are high-mutation and genes that are low-mutation, in terms of the accuracy of copying, based on the functions of those genes and the variability of the relevant environmental features (by the way these predictions derive directly from evolutionary theory, although I admit that the framers might not have realized this). Mechanisms to assure that DNA replication is accurate are themselves products of, and thus subject to, natural selection. Of course, for point mutations we have a limited array of possibilities, and as far as I know a situation has not yet been discovered where an A can be predicted to mutate into a T in a particular environment. In other words, mutations might only have been "directed" to the extent that certain genes are more or less accurate in their replication, period (and this rarely, as far as we know).  Transposon activation might be a technical exception, but even here we cannot predict the specific change. Still, I would be among the most excited and bright-eyed readers of an article that reported the discovery of a mutation that was very specifically guided by the current environment, in order to produce a phenotypic effect that was advantageous in that environment. Such would be worthy of a Nobel prize (although unfortunately our category doesn't exist, as I am reminded repeatedly by ambitious colleagues). Such a discovery would be perfectly fine in the sense that it wouldn't cause the sky or evolutionary biology to fall, much less reasonable theological theories. One can imagine (and this could be modeled) the possibilities for natural selection to result in the increased likelihood of very specific chemical changes that produce particular mutations leading to specific phenotypic effects.

Ok, I mentioned theology, but before I go there briefly, I just want to reiterate Randy's enlightening yet humble (I am always deeply inspired by Randy's humility) suggestion that when evolutionary biologists refer to random mutation they mean random with respect to outcome. I certainly would go out on a limb to say that random in this context entirely, and I mean entirely, means random with respect to the outcome, and specifically whether the phenotypic outcome of a genetic mutation is advantageous or not. There is not an evolutionary biologist worth his or her salt who claims that randomness means independent of the environment impacting the genes. Of course mutation has to be caused by something in the microenvironment of the genes, whether it is a localized deficiency of the appropriate base during replication, a trace amount of some chemical in the cytoplasm, ultraviolet radiation causing thiamine dimers, or whatever else. This is a fledgling area of biology, and a very exciting one-- the causes of mutation-- but we will certainly continue to uncover the reasons, in terms of physical causes in the environment of the genes, why any particular gene mutates the way it does. The problem in any particular case, of course, is to explain why a singularity happened in the past, however recent. This is a problem in any sort of scientific explanation. But we all agree, including the most "fanatical neo-Darwinists" (of which I am not sure whether I ought to be considered one), that every mutation, every single mutation, has a physical cause. In fact, one aspect of the temptation to become a fanatical neo-Darwinist is the commitment, an almost religious commitment to the point of yikesitude, to the regularity and uniformity and exclusivity of physical causation.  These aren't the people invoking indeterminacy based on the uncertainty principle in quantum mechanics, much less postmodern ideas of the fundamental incompleteness of the physical universe as described by science. Fanatical neo-Darwinists are among the ones who are saying that physicalism says it all and that we should in principle be able to explain everything on this basis. I think they're wrong, but I agree with them in their faith, or a bet (for me it is just a bet) that all mutations have physical causes. Therefore the sense in which biologists use the term "random" must exclude the radical one meaning a lack of influence or cause located in the makeup or environment of the genes. For my part, I'd bet my life that any particular mutation's physical cause could be identified if we had a way to record the sequence of events.

As for theology, I am out of my depth so I can only offer my opinion that the extent to which mutations are random, in the sense of being uninfluenced by the advantage of their outcome for the bearer, has no relation to the nature or existence of God. The idea that "explained regularity" is automatic and doesn't require God, whereas the inexplicable and unexplained indicates or provides an opening for divine action, is a theology for which I have no time. I have lived with it in my (fundamentalist) family and my (evangelical) church and my (Catholic) biology teachers my whole young life and I have had thoroughly enough of it. I haven't the faintest idea why so many Christians must be anti-science in the sense of failing to understand or accept evolution, and yet at the same time so inappropriately reverent of science as to give it the power to usurp God merely by describing that something has a certain regularity. And I somewhat understand but strongly disagree with the accompanying view that God's action is more special or significant or meaningful or spiritually potent when it is accompanied by inexplicability. We should combat this tendency to invest natural explanation with the power to disenchant.  The end of that road is the terrible view that ignorance is blessed and knowledge an evil. I believe that we should conclude nothing at all about the meaning or importance of divine action on the basis of whether we can understand it physically-- nothing at all. Miracles in the Bible are exceptions precisely because the state of being exceptional functions as an object lesson for us; they are not manifestations of a split divine personality, much less a polytheistic conflict between one god wanting to do something now and some other power that is responsible for the ordinary operation of the universe. Thus even the examples of apparent divine self-contradiction appear as such solely for our benefit (and in most cases we are a vain generation for needing them). Returning to natural processes such as mutation, do we really want to see them as either divine self-contradiction or implicit polytheism?! Whether mutations are "random", and what that word means, has in my view no theological importance whatsoever. Divine action will occur, cosmic Architecture will proceed all the same, whether or not we do, or ever will, understand the mechanism.

Last edited Tuesday, March 18, 2014
3/18/2014 at 3:03:01 PM GMT
Posts: 23
Hi, Randy & company. First, I'll add a hearty 'amen' to D. Lahti's expressed disagreement with the proposition ... " that God's action is more special or significant or meaningful or spiritually potent when it is accompanied by inexplicability"

I enjoyed watching the streamed second episode of 'Cosmos' with my own sons last night. Based on the first two episodes so far, it would seem the writers either are not genuine in their mission to bring the excitement of science to a wider audience (at least their U.S. audience); or else they badly misjudged by not consulting with a reasonable spectrum of theists. If they were truly promoting science, they would not throw in unnecessary (and completely non-scientific) stumbling blocks in addition to the already formidable stumbling block that 'evolution' itself already poses to so many U.S. Christians. Words like "unguided" or phrases like "entirely random" (much less entire less-than-historical scenarios designed to portray the church as some sort of monolithic anti-science entity) could all have been easily avoided had they truly been interested in reaching out to a religious crowd already suspicious of modern science. That they import religious atheism into their science may seem subtle to some, but such red-flag words and messages leap out to the many whose ears listen for those very confirmations of their worst fears. If their dedication to these dogmas is to play out in all the rest of the series, then I'm not so sure it would be a bad thing for it all to remain fairly obscure to the public, which is unfortunate, being a missed opportunity.

If the professed agnosticism of Tyson or Sagan before him were truly dominant in their presentation, it could easily have been more even-handed. But to me it looks like they let a positively religious atheism motivate at least some of their presentation, giving support to the warfare model. And (even just for the sake of science here in the U.S.) that warfare model needs to be exposed as the incoherent and long-discredited nonsense that it is.

3/18/2014 at 3:29:18 PM GMT
Posts: 53
With effort, I was allowed to substitute more physics for biology in high school, so I feel qualified to speak more as a likely target viewer (an average Joe), so perhaps my points will be helpful as such. In recent years, admittedly, I have read a little on this subject and find some points made to be problematic for me. Correction is welcome, just spare me a grade. :)

1) Tyson mentioned that, following Darwin’s publication, that an “uproar has never subsided”. This overstates the case, though he didn’t make a big deal about it. Certainly there have been small groups in opposition, but this is not true for religion as a whole, especially Christianity. I see this sort of rhetoric used when self-promoters take the stage. The implied “us against them” stance stirs listener’s interest – a temptation for most media outlets, especially blogs – but often at the expense of fairness and accuracy.

2) It was stated, that “Darwin discovered the actual mechanism of evolution”. I thought Darwin’s model, which added natural selection and branching as new tenets, was initially unacceptable for the fact that he could not provide a plausible mechanism to reproduce the new traits perpetuating new varieties. It wasn’t until genetics entered the picture decades later that Darwin was recognized for hitting the nail on the head.

3) For the sake of brevity I suppose, Wallace was ignored, though he was first in the eyes of Darwin himself. Darwin and Wallace worked together and did a joint paper which was largely ignored. Both had discovered natural selection independently.

4) Is there something wrong with my eyes? I don’t see well underwater, though I have the impression this is where they will work best. Yet I do think they were wise to address the evolution of the eye because Paley’s example case is a great one to consider. It isn’t that hard to infer that natural selection applies even to such things as bacterial motors, and maybe we will see this presented as well, given a noticeable atheistic bent.

5) A common claim that troubles me is the statement that the “…theory of evolution, like gravity, is a scientific fact”. This conflation isn’t necessary and, worse, detrimental to the entire show since the scientific method should be their banner. This error comes, I think, from what I stated in no. 1. The differences between religion (and philosophy) and science are distinct, each with potential efficacy. Fact and theory are not the same. Many theories have come and gone, and that’s a fact. *wink* My hope is they will do better with these points in the shows to follow.

6) Again we hear that life and its origins is “the greatest story ever told”. The Big Bang theory form last week is , in my opinion, the greater marvel of the ages, since it implies an Engineer of omnipotence and supreme intellect.

7) There was very little argument made to support life on Titan. There should be many arguments. Carbon, for instance, is especially important to life’s probability and Titan is loaded with it. We will see much more on this in coming episodes, especially now that we have passed the 1000 mark in number of confirmed exoplanets, about a dozen in the habitable zone.

8) The demonstration by astronaut Don Pettit aboard the ISS of sugar and salts quickly combining is a great one when considering both planetary and life formations. As it applies to larger solar system objects, however, the problem remains (though not mentioned yet in the show) that larger objects (> 1 cm or so) break other objects apart. It is great when we can connect the dots, but there is a noticeable void here that needs stating.

I am enjoying, nevertheless, the show as a whole. The artistry and animation are nicely done, and Tyson is a wonderful presenter, if not my favorite public astrophysicist.  On the downside, the universal laws and finely tuned constants of science arguably suggest a Designer that I fear will be avoided entirely, but we’ll see.

Last edited Tuesday, March 18, 2014
3/18/2014 at 5:47:29 PM GMT
Posts: 23
G. Cooper, regarding your #4, I had the same question about his statement on the evolution of eyes: "...and then a disaster happened ... they crawled out of the water ..." or words to that effect. I too thought, "disaster? what disaster? I see just fine."

And your #5 was also something that caught my attention in the show. I know what their motivations were in referring to evolution as a fact rather than a theory. But it was an ill-informed choice if they were hoping to educate the public. To call evolution a mere "fact" is actually a demotion from the "theory" that more accurately describes the whole enterprise. And that is *not* a demotion that some creationists take it to be ... saying with approval that it is *only* a theory (which is also a misunderstanding of "theory" --hence paying evolution an unintended compliment). A theory is actually a large system or organized way of looking at how many disparate observed phenomena fit together. The wider the scope of the theory, the more powerful it is. Evolution is very much a theory. As a geometry teacher I volunteer "theorem" as a word that better fits with "facthood" since it is a single (proven) assertion. Theory is something else entirely -- well-founded by evidence to be sure, but real scientists don't bandy about the word "proven"; not if they are being formal.