Not so emberassing…

Posted October 30, 2010 by intellectuallyfulfilledatheist
Categories: Biology, Evolution, Logic, Religion, Science

That video’s hilarious.  I laughed my ass off.  I was able to answer every question without sounding like an idiot before they were off the screen.

First the creator of the video sets the stage by misrepresenting evolution.  He does so the popular way…he rolls cosmology into it…the big bang.  He also misrepresents the big bang.  According to big bang cosmology there was never nothing.  At the moment of the big bang everything expanded very rapidly for a very brief amount of time…but the key is that everything already existed to expand.  There was never nothing, there’s no reason to believe there was ever nothing, it’s unscientific to argue for a state of the universe that we never observe existing in the universe.  You tell me where I can look and see a complete absence of matter and/or energy and/or spacetime anyplace in the universe.  Nonexistence of anything doesn’t appear to be a natural state.

As for why cosmology shouldn’t be considered part of evolution…evolution is a process which requires 3 things.  1) self replicating systems, 2) the self replicating systems must have traits which can be inherited by the next generation of the system by some mechanism, and 3) this mechanism for inheritability of traits must be variable by some mechanism.  Then if the system satisfies the Markov property (as our biological systems do) evolution becomes an inevitable result.  I wrote an argument for evolution being inevitable in any system which meets these requirements here:

There is also the subtle implication of some kind of special importance of “complexity” in reality complexity is merely an index as to how simple something will be for the average person to immediately and completely comprehend.  The more complex a thing is considered to be the less likely the average person will immediately and completely comprehend it.  More specifically, though, this can be measured by considering the number of components in a system and the number of possible interactions between all of the components and possible states for each component to exist and interact in.  There more of each of these things there are the less likely the average person will be able to immediately and completely comprehend a given system.  Nothing about this definition of complexity precludes the possibility of extremely intricate self organization, however.

Also no one claims that abiogenesis happened only once, but on earth only one organism is the ancestor of all species suggesting that only one instance in which it happened stuck.  The conditions on earth now are likely unfavorable but even if there were pockets in which abiogensis could be happening on earth unchecked what are the odds that a simple proto-cell will be competitive against even the simplest organism which has been optimizing its fitness for billions of years?  Not good, would be the simple answer.

However as the real support for evolution is a proven stochastic mathematical model known as a Markov chain we don’t need to observe how evolution began to know that evolution happens.  Abiogenesis is more simply supported by the nonrandom nature of chemistry.

I will give 3 examples of a mutation increasing the useful, beneficial information of a genome.  The evolution of 3 novel enzymes for the metabolism of by products of nylon production, known as Nylonase.

The mutation of melanin in melanin producing fungi to allow them to use beta radiation as an energy source.;jsessionid=60453B62C83926110166087F4609F566.ambra01?uri=info:doi/10.1371/journal.pone.0000457&representation=PDF

The evolution of the ability of e.coli to metabolize citrate…the lack of this feature was previously considered a defining characteristic of the e.coli bacterium.

I can think of more, I’ll stick to just those.

I’ll name 2 transitional fossils.



I’ll also note that the question is loaded and belies a misunderstanding of evolution on the part of the creator of the video.  Markov chains such as evolution can only produce nested sets in a branching process.  The fundamental problem comes from confusing the classification system with an accurate representation of evolution, which is not the case.  The classification system in wide use was created by creationists before the theory of evolution existed.  It’s inherently incompatible with the theory but it is kept around because it’s useful enough and a better alternative has not been worked out yet.  Since evolutionary processes can only produce nested sets in reality you can never see one species turn into another.  Instead you should see traits from a transitional fossil being passed down and slightly modified by that species descendants.  In the case of Archeopteryx we see the flight features first found there in all of the bird species which are its descendants (flight feathers, wings, hollow bones, etc).  And in the case of Tiktaalik we see the 1 bone, 2 bones, lots of bones, digits limb pattern in all tetrapods.

As Markov chains are a proven mathematical fact so is evolution.

Evolution doesn’t deal with the appearances of atoms or quantum particles because neither are self replicating systems nor products of self replicating systems in which traits are inherited via a mechanism which is subject to variability.  As these are necessary for the process of evolution to occur any system which lacks these features or the products of any system which lacks these features cannot evolve or be a product of an evolutionary process.  Evolution as a more generic process does not require living things, however.  Living things are merely the only systems we know of which satisfy the requirements for an evolutionary process.

Evolution also does not say that everything came from nothing.  Instead evolution describes a set of processes which act on self replicating systems with traits which are inheritable by some mechanism which is variable if that system satisfies the Markov property as biological systems do.  The origin of the universe is not such a system so evolution can’t say anything about the origin of the universe.  Consequently big bang cosmology also does not say that everything came from nothing.

The watchmaker argument as proposed by the creator of this video fails for this same reason.  The reason why it’s ridiculous to assert that a watch must have come about by evolution is entirely due to the fact that rocks and watches are not self replicating systems, they have no traits which are inheritable by a mechanism which is variable and they do not satisfy the Markov property.  Thus they cannot evolve.  Complexity plays no important role except as simply a fact of life.  Living things are observed to satisfy all of the requirements for evolution, complex or otherwise the complexity just means it will be a challenge to uncover all of the specific details of the implementation of the evolutionary processes within our planet’s biological systems.

Also even the most complex life form is only finitely more complex than a watch, though again, the complexity is essentially unimportant.  I only bring it up as another point of error albeit a minor one.


Jason Mattera and reading comprehension

Posted July 24, 2010 by intellectuallyfulfilledatheist
Categories: Logic, Politics

Tags: , , , , , ,

The question is “I was wondering, which portions of the health care bill lower costs, is it the provision giving 7 billion to fund jungle gyms or the provision mandating that employers provide time off for breastfeeding?”

Before we get into the actual substance of the question I’d like to point out the fallacy here.  This is a complex question fallacy, Franken is essentially being asked to choose between alternatives where a satisfactory answer would require a lot more freedom and considerable time.  It should also not be lost on people that Mattera specifically picked his options so that they would appear to increase costs not lower them, also increase them in, what he would consider to be, wasteful ways.

Ironically the actual answer to his question is that both could lower costs in the long run, though they would increase costs in the short term.  Well at least the “7 billion to fund jungle gyms” would increase costs.  The mandate on employers to provide time off for breastfeeding doesn’t really increase costs for the government at all, while lowering costs in the long term because it is a well established fact that breastfed babies are more likely to be healthier throughout their lives.

So now to the substance.  Al Franken responds by asking Jason Mattera to show him in the bill where they give $7 billion to fund jungle gyms.  I don’t know what version of the bill Jason Mattera was using but he apparently finds this on page 1184 of HR 3590.  I went to the Government Printing Office’s website and downloaded the latest version of HR 3590, the PDF has an interesting feature, it begins on page 119, but it’s nice enough to tell me that, at least the latest version of HR 3590 (the one that is currently law) is only 906 pages long, it also has the full length of the document numbered from 1 to 906 in parenthesis.

It’s a good thing that Jason Mattera gets a good shot of the page he’s looking at because I was able to search the pdf for the phrase “creating healthier school environments” and I found what he was looking at on page 565 (447 of 906).  I don’t know how many people noticed what was immediately obvious to me, and apparently, Al Franken.

Nothing on this page mentions the number 7 billion.  If anyone knows where he got that number from I would love to see it, but he didn’t get it from HR 3590.  I didn’t see the $7 billion on that page so first I tried to look at the page before it.  Subtitle C section 4201 – Community Transformation Grants.  Nothing on this page says anything about $7 billion for jungle gyms either.  In fact nothing in the entire section states a specific funding amount for the Community Transformation Grants.  I also couldn’t find anything in any other section of the bill that stated a specific funding amount for the Community Transformation Grants.  This has me thinking that Jason Mattera made the number up to make his position sound more impressive.

Does it, though?  Let’s assume that the bill does indeed allocate $7 billion for these Community Transformation Grants, is that a bad investment?  Also it’s amusing to me that Jason Mattera doesn’t see providing physical activity infrastructure as something the federal government should do.  Amusing as it is something the federal government does.  The idea behind providing infrastructure for active living and healthier lifestyles, among other things to this end, is to promote long term health to decrease demand for costly health related services.

Essentially the $7 billion investment in healthy living related infrastructure, nutrition education, etc could potentially pay for itself and then some in the long term if successful in getting people to try to be healthier and being more aware of how their activities and habits effect their health and how that, in turn, effects their lives.  This is another example of a potential long term saving with a short term cost.  It speaks to prevention.  It’s both important, and relevant to the subject of the Patient Protection and Affordable Care Act, and consistent with the bill’s goals of prevention.

Al Franken was absolutely correct, though, the question was inaccurate, and that’s at best.

EDIT: For anyone interested in the estimated costs associated with obesity in the U.S. check out this link:

Is an individual mandate to purchase health insurance really such a bad thing?

Posted March 21, 2010 by intellectuallyfulfilledatheist
Categories: Politics

Tags: , , , ,

How many people are opposed to prohibiting insurance companies from denying coverage based on preexisting conditions?

Or how about more controls to make sure that insurance companies don’t find ways to drop your coverage if you do become ill and thus a liability instead of an asset for them?

It seems to me that not too many people are particularly against these provisions, where present, of the various health care reform bills, but what do those same people think would happen to health insurance companies, and as a result their ability to afford health care, if these provisions were implemented without a mandate on individuals to purchase health insurance?

Let’s think about this logically.  What incentive now is there for healthy people to purchase health insurance plans?  How many healthy people, in a world where preexisting conditions are guaranteed to be covered and health insurance companies have a much harder time dropping someone’s coverage for minor details but there is no mandate on purchasing health insurance, will opt to spend money on health insurance plans that they personally don’t need?  the obvious answer is probably not many.  If that healthy individual gets sick they’ll just purchase health insurance and their treatment will be covered.  The problem with this is that health insurance companies work in the first place right now because of the fact that they can deny people coverage if they have a preexisting condition which ensures that there are plenty of healthy people paying premiums to offset the cost of paying health care providers for the people who are sick with one of their policies, as well as the fact that they can get away with finding little reasons to drop coverage for people who get sick and become a liability for them.  But in a world where healthy people no longer have an incentive to pay for coverage while they’re healthy and there’s no mandate on them to do so health insurance companies will be faced with a disproportionate amount of liability.  More sick people will enroll and fewer healthy people.  Gosh I wonder what happens next.  Oh yes, insurance companies go bankrupt.  Now almost no one can afford health care.

It would be nice to live in a world where everyone recognized that to keep our health care system working they need to purchase health insurance even if they don’t need it right now.  But we don’t live in that world.  We don’t even live in a world where even everyone who does know that will do it.  Unfortunately we don’t live in a world where people can be counted on to improve a system and either recognize or carry out their responsibility to make the improvements work.

EDIT: I forgot to mention that the federal government is given by the constitution the right to levy taxes, and the portion of the reform bills that are referred to as the mandate on individuals to purchase health insurance and employers to offer health insurance really amounts to a new tax, akin to the inheritance taxes or capital gains taxes, except this will be a tax for which people who purchase health insurance plans, or businesses who offer health insurance plans to their employees, will be exempt.

Godel’s Incompleteness Theorem

Posted February 9, 2010 by intellectuallyfulfilledatheist
Categories: Logic

Tags: ,

We can prove that 2 + 2 = 4, and we can also readily prove that 2 + 2 /= 5. If our arithmetical system is consistent then we cannot also prove that 2 + 2 = 5, and we certainly know of no way in which to prove that 2 + 2 = 5, and if anyone ever does produce such a proof it would immediately render arithmetic useless since being able to prove a proposition and its contradiction means we would be able to prove absolutely anything at all, and, as a consequence, absolutely nothing.

However we cannot prove that it cannot be proven that 2 + 2 = 5, because in order to prove that it cannot be proven that 2 + 2 = 5 we would have to add axioms which would allow us to prove that 2 + 2 = 5 adding inconsistency to our arithmetical system. So the attempt to add completeness to our axiomatic arithmetical system also adds inconsistency. But the current state of the system, in which we can’t prove that it is actually impossible to prove that 2 + 2 = 5 leaves our axiomatic arithmetical system incomplete.

Godel’s conclusion was that any first order axiomatic logical system cannot be both consistent and complete. I believe this conclusion has been extended to higher order logical systems as well. I don’t think the paper explained or proved explicitly that proving that we can’t prove 2 + 2 = 5 means we can also prove that 2 + 2 = 5 but I know that the paper mentioned that this premise has indeed been proven. I haven’t tried to work out the proof of it myself, though.

Another response to thegodguy

Posted February 7, 2010 by intellectuallyfulfilledatheist
Categories: Cognition, Science

Tags: , , , , , , , , ,

This is my response to the second entry that I commented on in which my comment has not yet been authorized.  What I am responding to directly is here:’s-ideas/#comment-1535

Anyone interested may read the rest of the exchange by scrolling up from there.  Just for fun some time soon I’m thinking about, but never get around to posting some ideas concerning a theory of mind that a friend of mine and I are sort of kicking back and forth, it’s much more coherent than thegodguy’s seems to be, and doesn’t assume the supernatural where there is only clear evidence of the natural.

The Response

In which case you are suggesting the obvious, since no one claimed that neuroscience was not searching for deeper neural substrates. In fact I already said that the purpose of my original comment was not to explain cognition, only to explain why the way our brains map abstract concepts by linking them to physical objective concepts derived from sensory organs would explain why people tend to lean forward when thinking about the future and backwards when thinking about the past.

By the way Bryan the reason why the link didn’t work is because he left a slash out. I posted the correct link to the article in my first comment.  [I’ll post it again here: (for anyone curious what’s in the brackets here was not in my original comment)]

Using microtubules, though, to support the view that neuroscience is searching for deeper neural substrates does not also support the view that we should be looking also for a supernatural or nonphysical explanation. For one thing there’s no evidence that a nonphysical or supernatural cause qualifies as a “deeper” explanation, since we cannot derive potential supernatural or nonphysical explanations directly from observation we can make any supernatural or nonphysical explanation anything it needs to be to work. In this sense it’s similar to the proposed higgs mechanism with one important difference, where the higgs mechanism is falsifiable any proposed supernatural or nonphysical explanation to any given problem is not falsifiable. This has the important consequence that while the explanation may be false, no one will ever be able to prove that it is. The obvious result being that people can spend a lot of time pursuing an explanation that may ultimately have no basis in reality, and they’d never know it.

And for another thing you’re using deeper in two different word senses. False equivocation. The microtubules are deeper than examining just neurons because microtubules are components of neurons. In a very physical sense of the word microtubules are a deeper substrate. Assuming that the functions of seeing, imagining, and reasoning, are actually distinct and hierarchical forms of “seeing” suggesting deeper sensory structures that raise “seeing” to “higher powers” is assuming that there is something nonphysically deeper. It’s also neurologically inaccurate. For one thing the same neurons which are activated when we see an object are also activated when we imagine that object. This suggests that seeing and imagining have the same sensory structures. Reasoning is a fundamentally different process than seeing and it depends on multiple structures in the brain, not the visual cortex, though. And revelation is also not a distinct hierarchical form of “seeing”. People get revelations from other people, for instance, often through language, which activates a distinct part of the brain aside from the auditory cortex. Interestingly enough language is processed in a different part of the brain when it is spoken verses when it is written. Likewise when we read something it’s processed in a different part of the brain again from where we process language when we’re writing, and when we hear language we process it in a different part of the brain again from where we’re speaking. Doesn’t seem very efficient, but it explains why many aphasic people can understand language but not speak coherently, depending on how extensive the brain damage is. It also explains why a unique case from the psychological literature wasn’t able to read after trauma to a specific area of his brain, but he was able to write a journal. It also explains why dyslexic people aren’t also necessarily aphasic, and vice versa, obviously depending on the extent of the damage (at least in the case of acquired dyslexia). And abstraction is also not a cognitive process related in any way to “seeing”. This is all, of course, assuming you are not using some unique definition of “seeing”.

Also proposing that neurons have their own nervous system with more interior sensory capabilities is another example of imposing fundamental assumptions on observations. In this case the observation is nothing more than a proposal that quantum level fluctuations in microtubules within neurons allows the transference of information between neurons at rates which exceed what should be possible in a purely chemically mediated nervous system. This does not even suggest the idea that the microtubules act as sort of a nervous system within neurons nor does it suggest anything resembling sense organs within a neuron. Of course we could expand the definition of sensory capabilities to include the chemical reactions within cells which are catalyzed by the introduction of certain chemicals or other things. For instance in the eye the opsin proteins bind to retinal. When photons of certain wavelengths (containing energy within specific levels) strike these opsins the retinal changes shape and gets released by the opsin protein which then activates a G-coupled receptor which starts another cascade of chemical reactions which leads to the opening of calcium ion channels into the cells creating an electrical potential which discharges onto the optical nerves and then starts the cascade that resets everything. In this case we currently don’t consider the opsin proteins themselves to be sensory, though in this case they do work directly in a sensory organ. Instead the eye is a sensory organ because of the entire process, not because of the action of any component. But if we try to apply a definition to sensory that makes it so that similar actions in neurons can be considered sensory actions in neurons, then the opsins themselves could be considered equivalent to a sense organ in eye cells. Since a stimuli external to the cell causes cascades within the cells. And now even if we did this would not add anything to our understanding of how the eye works. It wouldn’t imply any actual deeper substrate to the operation in the eye any more than applying this definition to sensory would imply any deeper substrate to the operation of neurons. Specifically because it would just result in referring to already understood chemical reactions differently, but would not add to our understanding of those reactions.

A response to thegodguy

Posted February 7, 2010 by intellectuallyfulfilledatheist
Categories: Physics, Science

Tags: , , , , , , , , ,

There was something of a discussion going on between me and thegodguy, here is my latest response to the last comment he posted in response to what I posted before on this thread:

Since I posted this comment about 3 days ago as of this writing and he has yet to authorize it during his moderation process.  No doubt because it doesn’t say anything new, which is unsurprising because I’m not hypothesizing or theorizing, only explaining existent theories and philosophy of science.  And since the flaws in his own hypothesis about reconciling science with religion have their foundation in his misunderstanding of existent scientific theories and philosophy of science I don’t see why me not presenting anything new should be a basis for censoring me.  Especially in light of the fact that the correct way to explain flaws whose basis is in fundamental misunderstandings of something is to explain what was misunderstood, and why the understanding was flawed.  Either way, though, he apparently has censored me, at least implicitly, by not authorizing the following response.  You can read the entire discussion by scrolling up.  This isn’t the only thread I commented on in which the comment has yet to be authorized, and there is also a third I didn’t bother commenting on, but I will post my response here after I post the response to the other two.  People might find it interesting, if my responses aren’t too long, to read my comments on his blog entries and then read his responses to my comments and see how little of what I say he actually directly addresses during the course of his responses as he, instead, directs me to his book Proving God which allegedly contains “better ideas” about the subjects in these comments.  I fail to see how, though, given that his demonstrated understanding of relevant scientific theories and philosophy of science in general is severely lacking.

The Response

Actually Quantum Mechanics and General Relativity are not contradictory at all.  There is every reason to believe that they are compatible with the biggest problems arising from the fact that General Relativity is background independent while Quantum Mechanics is background dependent (holding time to be invariable).  The Higgs mechanism is a proposed explanation for why there are massive particles.  It works well on paper and in mathematical simulations but it may, of course, be incorrect in reality.  What makes it scientific, though, is that it is a testable hypothesis.  As you’ve acknowledged by mentioning the experiments, being done at CERN’s Large Hadron Collider later this year and around the end of last year.  The data is still being analyzed, and the experiments aren’t specifically looking for a higgs boson, but if one is found that would verify the higgs mechanism.  And if one is not found that would falsify the proposed higgs mechanism.  Personally I would be inclined myself to think of the higgs boson as most likely nonexistent except that it’s not too different from the W and Z gauge bosons that transfer the weak force (and to which they are supposed to give mass) or to phonons, in another way.  There’s also the fact that virtual particles seem even more unreal than the higgs boson, and yet have been demonstrated to exist.  So in light of the fact that weirder things have been proposed and confirmed I’m not as quick to dismiss the higgs boson out of hand.

My confidence that a theory of quantum gravity will be found that does not invoke the supernatural has a couple of sources.  First of all Loop Quantum Gravity is already able to eliminate the singularity around the planck epoch.  New research is always being done and the Large Hadron Collider gets stronger and stronger.  There are also some fascinating suggestions that gravity is itself an emergent entropic phenomenon.  This was suggested years ago by the fact that general relativity can be derived from thermodynamics, and was recently suggested again by Verlinde who argues that  gravity is not a fundamental force, but an emergent phenomenon which arises from the statistical behavior of microscopic degrees of freedom encoded on a holographic screen.  Lee Smolin subsequently demonstrated that Loop Quantum Gravity is a holographic theory which is not only compatible with Verlinde’s argument but which, when assuming a classical spacetime outside of the bounds of the entropic system, can derive newton’s equation of universal gravitation.  Further suggesting that Loop Quantum Gravity is a serious contender as a quantum theory of gravity.

By the way geometry is itself an abstraction, there’s no such physical thing as a circle or a sphere or a square.  Early geometers looked at things which were circular, spherical, or square and distilled from these objects those properties which they shared in common to develop the abstract concept of circularity, spherical, and squareness.  I dismiss only the assertion that your book actually offers new concepts which are actually insightful about quantum gravity, not any evidence which you so far, at least here, have not produced.  But more to the point you have yet to demonstrate here a particularly good understanding of what physicists are actually talking about or even what I’m saying.  Like when I mentioned the planck epoch in reference to why a quantum theory of gravity is needed, or what would be lost without one.  Likewise when you claim that general relativity and quantum mechanics are contradictory you demonstrate a lack of understanding of what you’re talking about.  In order for two things to contradict each other one of them has to be false if the other is true.  Which is false?  So are you saying that if General Relativity is correct Quantum Mechanics is false?  Or is it the other way around?  If either way is the case then why are scientists trying to reconcile general relativity with quantum mechanics at all?  It’s much more accurate to characterize the two theories as being complimentary than as being contradictory.

Including something is generally only done when something is demonstrated to exist.  I would love to see actual evidence of the supernatural.  Scientists actually already know what a quantum theory of gravity should and should not look like, what they don’t know are the specific details of the mathematical formulation.  In case I’m not being clear, by this I mean scientists already know specifically what questions a theory of loop quantum gravity must answer, we also have ideas about how to answer these questions.  These ideas lead to the various competing lines of inquiry which are attempting to tackle them.  String Theory, M Theory, Loop Quantum Gravity, just to name a few.  Personally I think the answer will be found in a combination of various techniques which will most likely only be possible when more time has been dedicated to trying to find a quantum theory of gravity.  Remember we’ve only been looking for a quantum theory of gravity for less than about 95 years.  Given that General Relativity is only about 95 years old I would say several years less than 95 years, even.  Afterall we couldn’t have been looking for a theory to reconcile general relativity with quantum mechanics before there was a theory of general relativity to reconcile with quantum mechanics.  We should also keep in mind that Quantum Mechanics was itself an infant science when general relativity was discovered, and it most likely took some time for people to explore both sciences relative to each other and discover that they were incompatible with one another.  And it should be noted that another important part of the problem is that not even all of the consequences of general relativity have been explored yet, and thus a better understanding of general relativity itself could likely suggest more solutions to the problem of reconciling it with quantum mechanics.  Conversely quantum mechanics has not been completely explored and more solutions will likely be suggested from that direction as well.  This is partially evident in the fact that already is the case, where deeper understandings of general relativity and quantum mechanics already are suggesting solutions to the problem of reconciling the two sciences to each other.

I’m sorry I’m boring you with my lectures and refresher courses in physics, I’m finding your condescension highly amusing, especially coupled with the fact that I only feel the need to explain what your comments seem to suggest you don’t understand.  Of course I’m not telling you anything new, but I suspect I’m telling you things which are actually new to you, which is probably partially why you haven’t really addressed much of what I’ve actually said in response to what you’ve said directly preferring instead to bring up new subjects in support of your position or nonsense or pointless phrases like “Quantum gravity possesses different and distinct qualities within the multi-level scaffolding of spacetime structure.”

I also get the “I’m a busy man” brushoff a lot.

I also think you flatter yourself if you think any serious scientist will read your book and feel worried or threatened by your proposals.  Or if you think your book will “shake up” or “challenge” their “entrenched institutions”

FDR’s “Voluntary” Social Security

Posted January 14, 2010 by intellectuallyfulfilledatheist
Categories: Politics

Tags: , , ,

Chain emails are a lot of fun.

via FDR’s “Voluntary” Social Security.