Monday, March 30, 2009

TT Blogs and Comments

Bilbo posted Phineas Gage at Telic Thoughts. The blog entry contains some notable comments. This one for example. From John A. Designer's comment:

Over at UD Allen MacNeill wrote something that I think has some relevance here. He argues that, “the program for a digital computer is analogous to the “mind” that “runs” in the circuits of our digital processor “brain”. They are two different things: the electrons flowing through the various logic circuits in the processor are not the same thing as the processors themselves, and vice versa.”

I think Professor MacNeill would agree that such analogies, like all analogies, can be problematic. However, I do agree with him that there is something very loosely analogous between what we call mind and consciousness and computer software. For example, just as the computers hardware does not create it’s own software the brain architecture does not create mind and consciousness. Even though a computer hardware is designed to run software it is functionally useless without software (operating software, program files etc.) Software is something that is added to the hardware and I believe that the evidence supports the idea that mind and consciousness are ontologically independent things, and therefore in that sense they are added to the brain. That is a kind of dualism that philosophers and theologians refer to as hylomorphism.

MacNeill continues, “The analogy goes deeper, of course. A digital computer can “exist” without a program running in it, but if it does, it is essentially analogous to either a simple analog input device or a comatose or dead brain (depending on whether there is current flowing through any part of the circuitry or not). However, a program cannot exist unless it is “running” or “stored” in some physical form. Either it is running in the circuits of a digital computer, or it is stored in some analog/hard form. So, brains can exist without minds, but minds cannot exist without brains, in the same way that digital computers can exist without programs, but programs can’t exist without computers in which they can run.”

I disagree that programs don’t exist without a computer. I have a couple of computer programs right now sitting in my desk drawer that I haven’t yet installed on my computer. I don’t think it is accurate to describe them as not existing. It would be more accurate to describe the computer software as being symbiotic or functionally interdependent– one cannot function without the other.

I also think there are other brain function that are more analogous to computer programs: memory, symbolic and verbal communication. For example, consider the cases of people suffering from aphasia which is the result of stroke, brain tumor or head injury etc.

“People with Broca’s aphasia have damage to the frontal lobe of the brain. They frequently speak in short phrases that make sense but are produced with great effort. They often omit small words such as ”is,” ”and,” and ”the.” For example, a person with Broca’s aphasia may say, ”Walk dog,” meaning, ”I will take the dog for a walk,” or ”book book two table,” for ”There are two books on the table.” People with Broca’s aphasia typically understand the speech of others fairly well. Because of this, they are often aware of their difficulties and can become easily frustrated. People with Broca’s aphasia often have right-sided weakness or paralysis of the arm and leg because the frontal lobe is also important for motor movements.”

A materialist might argue that this makes his case. A non materialist would argue that there is still a self aware consciousness that is not reducible to brain physiology.

In other words, even if there are some brain functions that are analogous to computer programs, there are still higher functions, mind and consciousness, that have no real computer analog, which why strong AI remains virtually an intractable problem.

I added this comment:

The computer circuit patterns are intelligible only to a mind with knowledge of binary code. In other words the patterns themselves are not analogies but rather symbols sequenced according to code and correlated to specific concepts by an observing human mind. To claim the digital circuitry is analogous to the concepts coded for is to commit a fundamental error. These sentences are symbols traced to an underlying binary code. Neither the code nor the letters correlate to the concepts expressed by them without an interpreting mind conscious of the symbolic coding convention. The underlying issue of consciousness is sidestepped rather than explained.

Allen MacNeill supplied comments on which ours were focused in his usual thoughtful and civil style. The whole exchange can be viewed at the link.

I also posted this comment on an open thread indicating that Japan has dabbled in Obamanomics in that it increased its government debt as a percentage of its gross national product without obtaining growth as a result. The opposite took place- economic stagnation. The percentages went from 45 to 170 percent according to economist Barry Elias.


Thursday, March 26, 2009

Life and Death

A Question of Life or Death is a Zenit article. It notes church history relevant to abortion as written about in a book authored by Dennis Di Mauro titled A Love for Life: Christianity's Consistent Protection of the Unborn.

In the book's introduction Di Mauro, secretary of the National Pro-Life Religious Council and president of Northern Virginia Lutherans for Life, asserts that Christianity has been, is now, and will be in the future, a pro-life religion.

The first chapters of the book examine the Biblical passages that reveal a pro-life message. Di Mauro then turns to the testimony of the early Fathers of the Church. From the very start of the Church, in writings such as the late first-century Didache, abortion was regarded as immoral.

Apologists, such as the second-century Athenagorus, or the author of the second or third-century Epistle to Diogenetus, also clearly regarded the life in the womb as human, Di Mauro explains.

The Epistle states: "They [Christians] marry as do all others; they beget children, but they do not destroy their offspring."

At the end of the second century Tertullian, in defending Christianity against accusations of infant sacrifice, replied saying that for Christians homicide has been forbidden and that it is not permitted to destroy what has been conceived in the womb. Tertullian also believed that a child received its soul at the moment of conception, Di Mauro notes.

By the fourth century, the book explains, the councils of the Church began to proscribe punishments for those who procured abortions. In fact, transgressors were only re-admitted to the Church on their deathbeds.

In 305 the Synod of Elvira, in Spain, condemned abortion and proscribed excommunication for those who procured abortions.

HT: Clare


Wednesday, March 25, 2009

Feeling Good About Naturalism Doesn't Make it Real

Tom Gilson has a good blog entry posted at his blog Thinking Christian. It is titled “Creationism Feels Right, but That Doesn’t Make it So: Scientific American.” Analysis of the piece shows why the views expressed in the Scientific American article could aptly be described by the phrase: Naturalism Feels Right but that Doesn't Make it So. Tom did a good job of dismantling the SA article's logical foundations.


Monday, March 23, 2009

Flawed Understanding

When Science Is a Siren Song is an article appearing at The Washington Post. Quoting:

The problem with this fascinating study? It appears to be wrong. An analysis led by Stan Young of the National Institute for Statistical Sciences found that the original conclusion was based on poor statistics and is probably the result of chance.

So far, Young's rebuttal, published in January, has received little notice. That it is ignored by many of the media outlets that lavished attention on the original report isn't surprising; in fact, the most remarkable thing is how ordinary that lack of attention may be. A lot of science, it turns out, can't withstand serious scrutiny. Thoughtful analysis by John Ioannidis suggests that more than half of published scientific research findings can't be replicated by other researchers.

Part of the problem is that we've been conditioned to trust university research. It is based, after all, on the presumably lofty motives of its practitioners. What's not to like about science carried out by academics who have nobly dedicated their lives to understanding the unknown, furthering knowledge and serving humanity?

There are too many studies about which false conclusions are drawn. Sometimes this is attributable to research data. More often it is a function of misunderstanding on the part of writers or the general public. More from the liked article:

Does all this mean the system is broken? Surprisingly, no. Ultimately, science tends to be self-correcting, and flawed ideas are eventually recognized and disregarded. There really does seem to be a marketplace of ideas, and many good ideas eventually gain traction and persist, while many attractive but incorrect hypotheses eventually fall under the weight of compelling evidence. The system is far from perfect -- especially with regard to the exploitation of the most junior (and most vulnerable) researchers, who support much of this ecosystem -- but like capitalism, it may represent the best available option.

Self-correction is reliable in the long term. It is the short run which occassions misunderstandings. The problem with the short run is that many readers, who are not professionals, are likely to retain inaccurate information indefinitely.

HT: Clare


Friday, March 20, 2009

Demented Logic

Man-Caused Disasterists is the title of the linked to article from Viewpoint. RLC treats us to new politically correct lexicon courtesy of Obama's choice for Secretary of Homeland Security Janet Napolitano. The exchange as sourced from Ace of Spades HQ:

SPIEGEL: Madame Secretary, in your first testimony to the US Congress as Homeland Security Secretary you never mentioned the word "terrorism." Does Islamist terrorism suddenly no longer pose a threat to your country?

NAPOLITANO: Of course it does. I presume there is always a threat from terrorism. In my speech, although I did not use the word "terrorism," I referred to "man-caused" disasters. That is perhaps only a nuance, but it demonstrates that we want to move away from the politics of fear toward a policy of being prepared for all risks that can occur.

Note the explanation for replacing the word terrorism with the more vague "man-caused disasters." It allegedly demonstrates two things:

1. The want to move away from the politics of fear.

Could someone within the administration inform Obama and his economic advisors of the need to move away from the politcs of fear. The politics of fear has been a potent weapon used to scare Americans and lawmakers into believing that alloting trillions of dollars to corporate bailouts and government spending is required to save the economy. The U.S. economy sports the world's largest GNP and has been around longer than the 200 plus years during which the U.S.A. has existed but we needed Obama and some ill-advised policy decisions by George Bush to save the economy. The arrogant chest-thumping by these free spending fools is hard to bear. Let's have a look at the second explanation:

2. Replacing the word terrorism with double speak is associated with a desire to move toward a "policy of being prepared for all risks that can occur."

There's a non-sequitur. Being prepared for all risks entails many things delineated by words like planning, implementation, alertness and more. None of the preceeding has anything to do with Orwellian phrases except in the mind of Janet Napolitano.


Tuesday, March 17, 2009

Feline Affection

The blog Criacionismo, written in Portuguese, has a fantastic blog entry about a friendship between a lioness named Meg and a zoologist named Kevin Richardson. The awesome physical power of Meg is directed toward swimming with Kevin and showering him with licks and embraces in scenic South Africa. There is a photo and some film you can view at Vislumbres de outro mundo.


Saturday, March 14, 2009

Proofreading and Protein Fidelity

Cells get two chances, not just one, to fix their mistakes is a Biology News item about a cellular proofreading function which helps ensure a high degree of fidelity in protein synthesis. Mistakes in the synthesis process are rare and it is believed that about one error for every 10,000 linked amino acids occurs.

A key enzyme involved in proofreading is known as Phenylalanyl-tRNA synthetase (PheRS); an enzyme having an important role to play in maintaining cellular quality control. Its specific function entails correct amino acid selection allowing for proper sequencing of amino acid polymers within a protein. The relevant amino acid is phenylalanine.

Michael Ibba is the senior author of the discussed study whose research results were published in the journal Molecular Cell. Ibba is an associate professor of microbiology at Ohio State University. The research revealed that prior to protein formation a check on the amino acid polymers is made. The enzyme PheRS is able to correct a mistake resulting from its own activity. PheRS has two catalytic domains.

Disrupting the function of enzymes involved in proofreading can be a valued function of antibiotics. E. coli was used in the experiments.


Thursday, March 05, 2009

Making Sense of Antisense

David Tyler posted an entry at the ARN ID blog titled Post details: Hidden biological information via antisense transcription. DNA is double stranded and the terms sense and antisense are used to distinguish the strands with respect to the transcription process. Tyler links to the press release Mammalian Transcriptome Mapped, and It Makes Antisense. The press release contains this informative description:

RNA, which is a single strand of nucleotides, is made by enzymes as an exact base-to-base copy of DNA. Since DNA is double-stranded, only one of these strands, the so-called sense strand, encodes for proteins. In normal DNA transcription, the two strands are split apart, and only the sense strand is copied. The other DNA strand, the "antisense" strand, can also be transcribed into RNA. Antisense transcription is the "reverse" expression of genomic DNA. If the same molecule of DNA is transcribed into antisense RNA, then the transcript has the reverse sequence as the original DNA sequence.

Antisense RNA transcripts can exert function because they can bind to the RNA transcripts for which they are complementary messengers and modulate their expression into proteins. In fact, synthetic antisense molecules have been widely used to inhibit conventional genes, including applications as anti-viral and anti-cancer drugs, which are currently on the market or in clinical trials.

The complementary nature of nucleotde bases makes regulatory functions a natural outgrowth of base pairing.

Hat Tip to Clare