Sunday, January 30, 2011

I Came Across This...

Enclosed in this blog post is a poem that, for some reason, reminds me of the scientific community that is dominated by Darwinian thinking. Enjoy!

Their Way, by Bob Blues

I came with all my books, lived in dorms, followed directions. 
I worked, I studied hard, met lots of folks who had connections. 
I crammed, they gave me grades, and may I say not in a fair way. 
But more, much more than this, I did it their way. 
I learned all sorts of things although I know I'll never use them. The courses that I took were all required, I didn't choose them. You'll find that to survive it's best to act the doctrinaire way. And so I buckled down and did it their way.
Yes, there were times I wondered why I had to crawl when I could fly. I had my doubts, but after all, I clipped my wings, and learned to crawl. I had to bend, and in the end I did it their way.
And so, my fine young friends, now that I'm a full professor Where once I was oppressed, now I've become the cruel oppressor. With me you'll learn to cope, you'll learn to climb life's golden stairway.
What can I do? What can I do? Open your books. Read chapter two. And if it seems a bit routine, Don't come to me, go see the dean. As long as they give me my pay I'll do it their way.

Sunday, January 2, 2011

A Close Look At SETI And Intelligent Design

Seth Shostak of the SETI Institute has written an article on SETI and Intelligent Design, detailing the difference between SETI and Intelligent Design. He notes that intelligent design proponents have offered SETI’s methodology of detecting design as evidence that intelligent design is scientific. He then proceeds to respond to that claim.
     There are several problems with his article, some of which I will address here, in quote-and-reply fashion.

As just about everyone is aware, these folks use similar logic to infer a "designer" behind such biological constructions as DNA or the human eye. The apparent complexity of the product is offered as proof of deliberate blueprinting by an unknown creator--conscious action, presumably from outside the universe itself.

Complexity (or, more specifically, linear complexity) may be defined as randomness [Li and Vitanyi; Yockey 1992].
To quote Abel (2009),
“A random string is the most complex because its sequence cannot be enumerated using any algorithmically compressive string shorter than itself. Notice that this precise definition of linear complexity has nothing to do with meaning or function.”

So, Seth Shostak is wrong when he claims that “the apparent complexity of the product is offered as proof of deliberate blueprinting by an unknown creator.” Complexity in itself is not offered as evidence of intelligent design in a given biological system. A random string of nucleotides is complex but it can be easily explained as the result of random mutations; in such a case, intelligence is not a more adequate explanation for the origin of that random string of nucleotides.

The way this happens is as follows. When ID advocates posit that DNA--which is a complicated, molecular blueprint--is solid evidence for a designer, most scientists are unconvinced. They counter that the structure of this biological building block is the result of self-organization via evolution, and not a proof of deliberate engineering. DNA, the researchers will protest, is no more a consciously constructed system than Jupiter's Great Red Spot. Organized complexity, in other words, is not enough to infer design.

The problem with this paragraph, of course, is that intelligent design proponents do not infer design on the basis of organized complexity. Complexity in itself really isn’t part of the equation in the detection of intelligent design. Nor is organization. A cube that is exactly 10 in. x 10 in. x 10 in. is not complex, and it is not organized either, but it is indicative of intelligent design (a la Dr. Sean Pitman). In brief, intelligent design proponents do not infer design on the basis of complexity or organization.

In fact, the signals actually sought by today's SETI searches are not complex, as the ID advocates assume.

We don’t assume that the signals SETI researchers are looking for are complex.

A SETI radio signal of the type we could actually find would be a persistent, narrow-band whistle…. And yet we still advertise that, were we to find such a signal, we could reasonably conclude that there was intelligence behind it. It sounds as if this strengthens the argument made by the ID proponents. Our sought-after signal is hardly complex, and yet we're still going to say that we've found extraterrestrials. If we can get away with that, why can't they? Well, it's because the credibility of the evidence is not predicated on its complexity.

In that last sentence lies the fatal flaw in Shostak’s line of argumentation. In the case of intelligent design, the credibility of the evidence is not predicated on its complexity. The word “straw-man” immediately comes to mind.

If SETI were to announce that we're not alone because it had detected a signal, it would be on the basis of artificiality. An endless, sinusoidal signal - a dead simple tone - is not complex; it's artificial. Such a tone just doesn't seem to be generated by natural astrophysical processes.

We’re on to something now. Intelligent design proponents use the exact same methodology:
If intelligent design proponents were to announce that a certain biological system was intelligently designed, it would be on the basis of artificiality (whatever “artificiality” is supposed to mean). A biochemical system that cannot be explained by Darwinian processes is not necessarily complex (and let’s not forget how “complexity” is defined). Such a biological system just doesn't seem to be generated by Darwinian processes.

In addition, and unlike other radio emissions produced by the cosmos, such a signal is devoid of the appendages and inefficiencies nature always seems to add - for example, DNA's junk and redundancy.

Note the phrase “nature always seems to add.” The intelligent designer(s), for example, could have designed the flagellum, and afterwards “nature” added other components which made it less efficient.

So that's one point: the signals SETI seeks are really not like other examples drawn from the bestiary of complex astrophysical phenomena. That speaks to their artificiality.

So that's one point: the biological systems with which intelligent design proponents infer design are really not like other examples drawn from the bestiary of complex Darwinian phenomena. That speaks to their artificiality.

In summary, SETI detects intelligence behind a radio signal on this basis,
(1)   The signal is not  known to be generated by natural astrophysical processes.
(2)   The signal is produced by human intelligence.
(3)   Also, context (i.e., where in the universe the signal is found). However, this is irrelevant to the field of intelligent design, since it would be difficult to imagine what would be an appropriate “context” to determine that the flagellum was intelligently designed.

Intelligent design proponents detect intelligent design in biological systems on this basis,
(1) The biological system is not known to be generated by mindless processes.
(2) The signal is known to be generated by human intelligence.

Why would a radio signal consisting of a string of the first 100 prime numbers be indicative of an intelligence, as suggested by Seth Shostak? It is because,
  1. There is no known mindless process that can explain the origin of such a radio signal,
  2. There is a known intelligent mechanism that can explain the origin of that radio signal.
And this is exactly the same methodology intelligent design uses to detect design in biological systems.


 Li, M.; Vitanyi, P. An Introduction to Kolmogorov Complexity and Its Applications, 2nd Ed.

  Yockey, H.P. Information Theory and Molecular Biology. Cambridge University Press:
Cambridge, 1992; p. 408.

Abel, David L. The Capabilities of Chaos and Complexity. International Journal of Molecular Sciences, 10(1): 247-291(2009).

Monday, December 27, 2010

The Comedy of Errors: A Response To "Darwin Killed God" Blog (Part 2)

TheHumanApe’s blog is hardly deserving of attention, but nevertheless the job of shredding his ridiculous literature will be done.
     He devotes a number of his blog posts to providing the evidence for evolution. For example, he quotes Jerry Coyne (author of “Why Evolution is True”) on why ERVs, embryology, et al., all demonstrate the validity of common descent. He describes how fossils and protein sequences provide confirmation of common descent. However, he makes the fatal error of equating evidence of common descent for evidence of a non-directed model of common descent. He cannot accept the prospect that evolution was guided. While I am not in anyway a theistic evolutionist, there is evidence in biology that certain parts of life were involved in a guided evolution. For example, a sequence analysis of the protein alpha-importin suggests that alpha-importin in unicellular organisms would guide the evolution of beta-canenin, and with the origin of beta-canenin, multicellular life forms would arise (see Mike Gene’s blog “The Design Matrix”). If TheHumanApe stubbornly clings to the belief that even a guided evolution is  “magic,” then I’d love to hear his response to this.

       TheHumanApe gives some treatment to chromosome 2, which he calls “undeniable evidence for evolution.” He is apparently ignorant of the possibility that Homo sapiens originally had 48 chromosomes, and then a fusion reduced that number to 46. The only thing chromosome 2 proves is that homo sapiens used to have 48 chromosomes.

He comes up with even more “undeniable evidence” for evolution – namely, the evidence from DNA sequences and molecular phylogenies. He is, of course, unaware of the fact molecular nested hierarchies can be explained by tissue constraints on protein sequences. A neutral substitution in one organism is not necessarily neutral in another, due to differences in the number of cell types. As such, the evidence from DNA sequences can hardly be considered “undeniable evidence.”

I found a particular portion of his blog amusing.
 “Of course the idiot calls evolution ‘Darwinism’…. Again Christians, please read this carefully: Biologists are called ‘biologists’. It would help if you practiced saying the word "biologists" a few dozen times so you get it right next time.”

Right. It’s always difficult to get this point across to laymen like TheHumanApe: we use the term “Darwinian” to distinguish “Darwinian” evolution from Lamarckian evolution, saltationism, orthogenesis, et al. There are Darwinian biologists, there are Lamarckian biologists, etc. Biologists use the term ‘Darwinian’ to distinguish between the different evolutionary models. Of course, laymen like TheHumanApe still can’t get that straight.

Note that nowhere, absolutely nowhere, in his blog does he provide evidence against the following statement: certain features of the biological world are more adequately explained by an intelligence. He assumes that by providing a mountain of evidence for common descent, then this must mean that the flagellar motility system was not intelligently designed. One could provide all the proof in the world that humanity descended through a Darwinian process, but this would not prove that the same is true for the flagellar motility system.

One thing he said I found to be the most entertaining:
 “I left the following comment for…an uneducated moron, a typical superstitious idiot.”

I.e., I am an uneducated moron and a typical, superstitious idiot. I find that to be, in short, hilarious.

Well, I think I’ll stop it there since I don’t want to waste anymore time on something that he won’t respond to. Cheers!

The Comedy of Errors: A Response To "Darwin Killed God" Blog (Part 1)

Last night, I took a look at the comments of my blog post “Bad Design Disproves Intelligent Design? Really?” As I was reading the comments there, the aroma of nuts wafted towards my eyes – roasted nuts. Except that this guy thinks I’m nutty.
      A quick glance at his blog shook my confidence in human sanity (warning: this guy’s blog contains dozens and dozens of expletives). Of course, it’s obvious that he lacks even the most rudimentary knowledge and training in any of the biological sciences; and, for that matter, I am finding it difficult to believe that he even understands the basic methodology of science.
   In this Monday evening blog post, I will do my best not to come down too hard on this deluded atheist. Normally I wouldn’t spend my time responding to an individual of his intellectual caliber, but for lack of something else to blog about, I will make a response to particular blog posts of this guy.
    The first thing we notice when we go to his blog is his statement that,
 “Evolution does not need defending because it's a basic scientific fact.”

He then proceeds to write scores upon scores of blog posts defending evolution as a scientific fact. The shear volume of his textual nonsense is a remarkable testimony to the amount of time he has on his hands – time that should perhaps be used to contribute to the advancement of science, instead of rantings and ravings that simply do nothing to add to science’s advancement. The bulk of his rhetoric consists of the argument “Darwin right. Intelligent Design magic. Christians bad. Darwin right.”

Now, before we eviscerate his blog, we will respond to the comment he left on my blog.
Let’s begin.

 “Here's a translation of your gibberish that makes it more honest:

MAGIC as a scientific proposition, holds that certain features of the biological world are more adequately explained by a MAGIC MAN rather than a mindless process.”

Firstly, intelligent design does not invoke any magic. Intelligent design is a method of design detection, similar to SETI. Does SETI invoke magic? Or let me ask him the question in terms he might find more understandable:
(1)   Does the method of detecting intelligence in SETI science invoke magic?
(2)   Does the method of detecting intelligence in ID science invoke magic?
(3)   Why or why not?

Also note that ID does not define the designer, so the phrase “magic man” is silly.

 “By the way, Why Evolution is True by Jerry Coyne talks about "bad design" that makes perfect sense if evolution is true (it's true, evolution is a basic scientific fact).”

Please explain how the imperfect design of the flagellar motility system makes the origin of the flagellum more adequately explained in the light of evolution. This should be good.

 “One more thing. Magic is NOT a scientific proposition.”

I agree. Magic is not science. Intelligent design is science.

 “Scientists don't invoke magic…”

Intelligent design does not invoke magic either.

Now, we will respond to his blog with another post.

Sunday, December 26, 2010

Bad Design Disproves Intelligent Design? Really?

Supposedly, bad design is a refutation of intelligent design. How is bad design and intelligent design compatible? This is one of the most common arguments raised against intelligent design, albeit one of the more egregious ones. The argument goes like this: an intelligent designer would not have designed biological system X in this way, therefore Darwinian evolution dunnit.
I think one of the first things Darwinians need to learn when attacking intelligent design is exactly what it posits. Intelligent design, as a scientific proposition, holds that certain features of the biological world are more adequately explained by an intelligence rather than a mindless process.
     So, we hold that only certain features in biology are more adequately explained by an intelligence. This alone is sufficient to overturn this argument against intelligent design. But what about flaws in the design of systems that are purported to be intelligently designed, such as the flagellum? First off, bad design is seen in objects that humans design. A broken down, badly-running watch does not indicate that it is not intelligently designed.Maybe the designer(s) of biological system X was having a bad day, and "it" made an error in designing that biological machine.
   Now we come to the philosophical argument from bad design: namely, that bad design proves that the designer was not God. Proponents of this argument ask, "If God is perfect, then how could a perfect God made a bad design?"

I answer,
P1: God is perfect, and humans are not perfect. God is omnipotent, and you are not.
P2: An imperfect, non-omnipotent being is incapable of discerning poor designs of a perfect, omnipotent Being.
P3: Therefore, we cannot assert that the design of a perfect Being is imperfect, for we are not omnipotent. 

I am expecting a response like "that's just special pleading" or "you are using the God-works-in-mysterious-ways argument." Obviously, these responses are only appeals to emotion, as they do not attack any of the premises in the above argument.

Thursday, December 16, 2010

Evolution Computer Simulation Under Fire

A new peer-reviewed paper has been published by BIO-Complexity, an intelligent design journal. Entitled A Vivisection of the ev Computer Organism: Identifying Sources of Active Information, this paper demonstrates that most of the success of the EV computer simulation in finding a target, is not due to the evolutionary algorithm, but rather "the success of ev is largely due to active information introduced by the Hamming oracle and from the perceptron structure."

"It is not due to the evolutionary algorithm used to perform the search. Indeed, other algorithms are shown to mine active information more efficiently from the knowledge sources provided by ev."

So, intelligent design has not contributed anything to the biological sciences, has it? I beg to differ. Undoubtedly, this paper has contributed something to science.
If you haven't noticed, there's been a lot going around with computer simulations and evolution. Consider this computer simulation that absolutely proves the flagellum could have easily evolved - one of my personal favorites:

"Dr. Jackson Martin, Director and Professor of the Flagellum Project at the Hoboken Nature Institute, today announced completion of software that successfully demonstrates the evolution of the bacterial flagellum. Critics of evolution have claimed that the flagellum is too complex to evolve using the gradual changes required by natural selection.
'The flagellum is very complicated,' said Martin. 'Like a motor, it has a rotor, a stator, and complex control mechanisms.'
Martin and his students have demonstrated, however, that the complex flagellum can be easily created using the forces of natural selection.
'We have not only shown that the flagellum can be evolved, it’s hard not to evolve the flagellum.”
In simulation software called EvolFlag, Martin and his students carefully apply gradual modifications to an initial set of boundary conditions.

Martin’s most impressive demonstration was evolution of the bacterial flagellum from common table salt.
'Salt, of course, contains no biochemicals,' offered Martin. 'The ability to evolve a fully functional flagellum from simple table salt is a tribute to the miracle of evolution' . . ."

I'm impressed.

Tuesday, December 7, 2010

The Reports of My Death Have Been Greatly Exaggerated

Even though I haven't been blogging for a while, the reason is not, I repeat, is not, because I have expired. The real reason is that I've been incredibly busy with academics. But never fear! Once this week is over I plan to start blogging regularly again. I hope this relieves those of you who suspected that the Darwinians had finally caught up with me and I was merely a smoldering heap. However, I also know that many of you are not relieved, since many of you would look forward to the prospect of my expiration.
Stay tuned.