What Is A Code?

Lots of heat surrounding this question.

My take is that a code must be a system for conveying meaning.

In my view, an essential feature of a code is that it must be abstract and and able to convey novel messages.

DNA fails at he level of abstraction. Whatever “meaning” it conveys cannot be translated into any medium other than chemistry. And not just any abstract chemistry, but the chemistry of this universe.

Without implementing in chemistry, it is impossible to read a DNA message. One cannot predict what a novel DNA string will do.

DNA is a template, not a code.

Go to it.

Is Time the Enemy of Error

They laughed at me and made jokes but I proved beyond the shadow of a doubt and with… geometric logic… that a duplicate key to the wardroom icebox DID exist, and I’d have produced that key if they hadn’t of pulled the Caine out of action. I, I, I know now they were only trying to protect some fellow office

For some of us old farts Captain Queeg is a symbol of reasonableness over reason.

For me, he is the patron saint of cranks, and a crank is someone who employs geometric logic in the service of silly axioms and premises.

Queeg is, for me, the archetype of someone who thinks great arguments are settled by reason.

My own thought is that if theology and philosophy could be decided by reason, the great debates would have been settled long ago.

My thought is that theologies and philosophies go in and out of fashion over time. Some rise in favor because they are useful and productive, but most just drift.

Over time, ideas gain or lose market share, but seldom die out altogether or become universal.

I’m sure there’s a name for this.

Miracles are a Glaring Problem for Evolution, and Here’s Why

The movement against miracles was, not surprisingly, influential in the natural sciences. Simply put, if we’re not to appeal to miracles, then the world must have arisen naturalistically. This had a profound effect on the critical thinking, or lack thereof, of the time. Speculative hypotheses, with little basis in fact, enjoyed serious consideration and triumphant acceptance.

The bar was placed exceedingly low for such theories as pure conjecture became acceptable and celebrated science. Monumental scientific problems with the notion of spontaneous origins went ignored and evolutionary theories (from cosmological to biological) soon became “fact.”

Today strictly naturalistic, evolutionary, theories are a given. They simply are accepted as true, or as true as anything in science can be. And it also is a given that miracles are false. But what evolutionists prefer to overlook is that there is a causal relationship here. The latter made way for, and mandated, the former.


I don’t want to mischaracterize Intelligent Design, but…

Estimating the reproducibility of psychological science


We conducted replications of 100 experimental and correlational studies published in three psychology journals using high-powered designs and original materials when available.

Ninety-seven percent of original studies had significant results (P < .05). Thirty-six percent of replications had significant results;

No single indicator sufficiently describes replication success, and the five indicators examined here are not the only ways to evaluate reproducibility. Nonetheless, collectively these results offer a clear conclusion: A large portion of replications produced weaker evidence for the original findings despite using materials provided by the original authors, review in advance for methodological fidelity, and high statistical power to detect the original effect sizes. Moreover, correlational evidence is consistent with the conclusion that variation in the strength of initial evidence (such as original P value) was more predictive of replication success than variation in the characteristics of the teams conducting the research (such as experience and expertise).

Faith vs Fact (Coyne’s book reviewed by Steven Pinker)


Seems to fit in with recent threads.

His latest book, Faith Versus Fact, is
intended not to pile on the arguments
for atheism but to advance the debate
into its next round. It is a brief against the
faitheists — scientists and religionists
alike — who advocate a make-nice
accommodation between science and
religion. As with Michael Corleone’s offer
to Nevada Senator Pat Geary in The
Godfather Part II, Coyne’s offer to religion
on the part of science is this: Nothing.
This sounds more imperialistic and
scientistic than it really is, because Coyne
defi nes ‘science’ broadly, to encompass
any system of belief grounded by reason
and evidence, rather than faith. On
this defi nition, many of the humanities,
such as history and philosophy, count
as ‘science’, not just the traditional
physical and social sciences.

Coyne quotes several historical and
recent writers, particularly Carl Sagan
and the philosophers Yonatan Fishman
and Maarten Boudry, while adding some
examples of his own, to show how the
existence of the God of scripture is a
testable empirical hypothesis. The Bible’s
historical accounts could have been
corroborated by archaeology, genetics
and philology. It could have contained
uncannily prescient truths such as “thou
shalt not travel faster than light” or “two
strands entwined is the secret of life.” A
bright light might appear in the heavens
one day and a man clad in white robe and
sandals, supported by winged angels,
could descend from the sky, give sight
to the blind, and resurrect the dead. We
might discover that intercessory prayer
can restore hearing or re-grow amputated
limbs, or that anyone who speaks the
Prophet Mohammed’s name in vain is
immediately struck down by lightning,
while those who pray to Allah five times a
day are free from disease and misfortune.


Easy DNA Editing Will Remake the World. Buckle Up.

A little bit of this and a little bit of that. A new and cheap way to implement genetic engineering, and a way to bypass the usual rules of population genetics.

The stakes, however, have changed. Everyone at the Napa meeting had access to a gene-editing technique called Crispr-Cas9. The first term is an acronym for “clustered regularly interspaced short palindromic repeats,” a description of the genetic basis of the method; Cas9 is the name of a protein that makes it work. Technical details aside, Crispr-Cas9 makes it easy, cheap, and fast to move genes around—any genes, in any living thing, from bacteria to people. “These are monumental moments in the history of biomedical research,” Baltimore says. “They don’t happen every day.”

ANY GENE TYPICALLY has just a 50–50 chance of getting passed on. Either the offspring gets a copy from Mom or a copy from Dad. But in 1957 biologists found exceptions to that rule, genes that literally manipulated cell division and forced themselves into a larger number of offspring than chance alone would have allowed.

A decade ago, an evolutionary geneticist named Austin Burt proposed a sneaky way to use these “selfish genes.” He suggested tethering one to a separate gene—one that you wanted to propagate through an entire population. If it worked, you’d be able to drive the gene into every individual in a given area. Your gene of interest graduates from public transit to a limousine in a motorcade, speeding through a population in flagrant disregard of heredity’s traffic laws. Burt suggested using this “gene drive” to alter mosquitoes that spread malaria, which kills around a million people every year. It’s a good idea. In fact, other researchers are already using other methods to modify mosquitoes to resist the Plasmodium parasite that causes malaria and to be less fertile, reducing their numbers in the wild. But engineered mosquitoes are expensive. If researchers don’t keep topping up the mutants, the normals soon recapture control of the ecosystem.

Push those modifications through with a gene drive and the normal mosquitoes wouldn’t stand a chance. The problem is, inserting the gene drive into the mosquitoes was impossible. Until Crispr-Cas9 came along.

Emmanuelle Charpentier did early work on Crispr.Today, behind a set of four locked and sealed doors in a lab at the Harvard School of Public Health, a special set of mosquito larvae of the African species Anopheles gambiae wriggle near the surface of shallow tubs of water. These aren’t normal Anopheles, though. The lab is working on using Crispr to insert malaria-resistant gene drives into their genomes. It hasn’t worked yet, but if it does … well, consider this from the mosquitoes’ point of view. This project isn’t about reengineering one of them. It’s about reengineering them all.

Do Animals Have A Sense Of Self?

Professor Hills and Professor Stephen Butterfill, from Warwick’s Department of Philosophy, created different descriptive models to explain the process behind the rat’s deliberation at the ‘choice points’.
One model, the Naive Model, assumed that animals inhibit action during simulation. However, this model created false memories because the animal would be unable to tell the differences between real and imagined actions.

“The study answers a very old question: do animals have a sense of self? Our first aim was to understand the recent neural evidence that animals can project themselves into the future. What we wound up understanding is that, in order to do so, they must have a primal sense of self.”

“As such, humans must not be the only animal capable of self-awareness. Indeed, the answer we are led to is that anything, even robots, that can adaptively imagine themselves doing what they have not yet done, must be able to separate the knower from the known.”

Read more at: http://phys.org/news/2015-06-self-awareness-unique-mankind.html#jCp

Wagner’s Multidimensional Library of Babel (Piotr at UD)

I’ve wanted to start this discussion for several weeks, but wasn’t sure how to present Wagner’s argument. Fortunately Piotr has saved me the trouble with a post at UD.

Piotr February 24, 2015 at 1:35 pm

Do you mind if I begin with a simple illustrative example? Let’s consider all five-letter alphabetic strings (AAAAA, QWERT, HGROF, etc.). By convention, a string will be “functional” if it’s a meaningful English word (BREAD, WATER, GLASS, etc.). Functionality is therefore not a formal property of the string but something dictated by the environment. There are 26^5 = 11881376 (almost 12 million) possible five-letter strings. The number of five-letter words in English (excluding proper nouns and extremely rare, dialectal or archaic words) is about 6000, so the probability that any randomly generated string is functional is about 0.0005.

Any five-letter string S can produce 5×25 = 125 “mutants” differing from S by exactly one letter. If you represent the sequence space as a five-dimensional hypercube (26x26x26x26x26), a mutation can be defined as a translation along any of the five axes.

It would appear that the odds of finding a functional mutant for a given string should be about 125×0.0005 = 1/16 on the average. In fact, however, it depends where you start. If S is functional, the existence of at least one functional mutant is almost guaranteed (close to 90%). For most English words there are more than one functional mutants. For example, from SNARE wer get {SCARE, SHARE, SPARE, STARE, SNORE, SNAKE, SNARK…}. Though some functional sequences are isolated or form small clusters in the sequence space, most of them are members of one huge, quite densely interconnected network. You can get from one to another in just a few steps (often in more than one way), which is of course what Lewis Carroll’s “word ladder” puzzle is about:


You can ponder the example for a moment; I’ll return to it later.


The whole thread is worth a look.

I might add that there is a rather crude GA at http://itatsi.com that does something not entirely unlike a word ladder.

Manifesto for a Post-Materialist Science


9. Studies of the so-called “psi phenomena” indicate that we can sometimes receive meaningful
information without the use of ordinary senses, and in ways that transcend the habitual space
and time constraints. Furthermore, psi research demonstrates that we can mentally influence—
at a distance—physical devices and living organisms (including other human beings). Psi research
also shows that distant minds may behave in ways that are nonlocally correlated, i.e. the
correlations between distant minds are hypothesized to be unmediated (they are not linked to
any known energetic signal), unmitigated (they do not degrade with increasing distance), and
immediate (they appear to be simultaneous). These events are so common that they cannot be
viewed as anomolous nor as exceptions to natural laws, but as indications of the need for a
broader explanatory framework that cannot be predicated exclusively on materialism.

10. Conscious mental activity can be experienced in clinical death during a cardiac arrest (this is
what has been called a “near-death experience” [NDE]). Some near-death experiencers (NDErs)
have reported veridical out-of-body perceptions (i.e. perceptions that can be proven to coincide
with reality) that occurred during cardiac arrest.

UD discussion link:


Two Billion Years Without Evolution?

Over at UD, we have a thread entitled:

Why does defending Darwin increasingly remind one of defending communist economics?

It features some quotes from J. William Schopf, regarding some ancient fossils that appear morphologically identical to modern microorganisms.

“It seems astounding that life has not evolved for more than 2 billion years — nearly half the history of Earth,” said J. William Schopf, a UCLA professor of earth, planetary and space sciences in the UCLA College who was the study’s lead author. “Given that evolution is a fact, this lack of evolution needs to be explained.”


“The rule of biology is not to evolve unless the physical or biological environment changes, which is consistent with Darwin,” said Schopf, who also is director of UCLA’s Center for the Study of Evolution and the Origin of Life. The environment in which these microorganisms live has remained essentially unchanged for 3 billion years, he said.

Jerry Coyne has blogged the same topic:

At UD, Mapou has posted:

The only problem with this is that random mutations, the engine of change in Darwinian evolution, do not care whether the environment changes or not. Mutations keep occurring no matter what. You just got to love Darwinists.

Which, ironically, is the same thing Jerry Coyne says.

Barry Arrington and Company: Does A=A?

This is a little test of reasoning ability. I would prefer that for the first few days, only ID advocates post answers. These questions, and the underlying reasoning, are widely discussed on the internet, so you may have encountered them. If you have, I would appreciate knowing that fact. Also, for those who have seen them before, I would like to know how you did the first time you encountered them.

If anyone spots a typo or logical error, I’d appreciate hearing about is so it can be corrected.

The answers I’m looking for are in three parts:

First — yes or no — can the puzzles be solved by reason, assuming ordinary knowledge of the vocabulary. There are no tricks or unusual meanings involved.

Second, provide the answer.

Third, the provide the reasoning or proof.

Uncommon Descent frequently invokes logic and reason. this is a challenge to anyone who posts at UD. Feel free to post your answers on this thread or at UD.

Here are the questions:

1. [The original editor has been sacked. Re-Edited to straighten out the mess: The price of a cheeseburger is $2.20, the price of a plain hamburger plus the price of the added cheese.] A plain hamburger costs two dollars more than the added cheese. How much does a plain hamburger cost?

2. In Elbonia, one person in ten thousand has Ebola. A new test is so good that anyone who is infected will test positive. But three percent of uninfected people will also test positive. John, a citizen of Elbonia tests positive. What is the probability that John has Ebola?

3. I have a deck of picture cards. They have automobiles on one side and living things on the other side. I have looked through them, and I think they follow the following rule: if a card has a GM automobile on one side, it will have an animal on the other side. After shuffling, I deal out four cards.

Cat, Ford, Petunia, Chevy

What cards must I turn over to test my hypothesis?

4. William is tweeting Betty, but Betty is tweeting John. William is in love, but John is not. Is a person in love tweeting a person who is not in love?

5. Elbonia has invented a treatment for Psoriasis. During a recent blind test, of the patients who were given the treatment 197 improved and 95 did not.

Of the patients who were given a placebo, 45 improved and 20 did not.

Is the treatment effective?

Memories pass between generations

We’ll be hearing about this from UD. Might as well play with it here.


In the smell-aversion study, is it thought that either some of the odour ends up in the bloodstream which affected sperm production or that a signal from the brain was sent to the sperm to alter DNA.

Honest False Testimony

I’m kind of busy, and negligent in posting here, but I simply couldn’t resist starting this discussion. We touched on it a while back, and it pushes a lot of my buttons. I think it lies behind most disagreements. (All disagreements on this site, because we assume honesty.)

Based on her work, and that of others, Tavris shows three ways that different people can present conflicting narratives of the same event—not because any of them are lying, but because they are presenting what she calls “honest false testimony.” That is, their views of what really happened aren’t made up, but are tinged by several factors that makes them believe they are telling the truth.


Should Everything Be Cured?

The debate regarding homosexuality reminds me of a larger issue. What do we mean by normality, and do we want everyone to be normal?

For example, some forms of deafness are inherited, and some deaf parents do not want their children “cured”. I do not know how homosexual parents feel about this. (There are gay parents. Some adopt children, and some marry and have children by conventional means.)

Not everyone who deviates from majority traits considers their variation to be a handicap. I come from a family where left-handedness is common. It causes some problems, the most notable of which is with using scissors. I wonder if parents would go for some simple and inexpensive intervention that would guarantee right-handedness. I also have color-blindness in the family, including a nephew who is totally color-blind. There are some benefits to these traits.

I thought it would be fun to make a list of such differences and toss around opinions about whether they are actually detrimental and whether people would readily adopt medical technology that normalized children.

It’s obviously controversial, but I hope we can play nice.

Pinker: The Sense of Style



Steven Pinker is about to release a new book on writing. I’m holding my breath.

When you write you should pretend that you, the writer, see something in the world that’s interesting, that you are directing the attention of your reader to that thing in the world, and that you are doing so by means of conversation.

That may sound obvious. But it’s amazing how many of the bad habits of academese and legalese and so on come from flouting that model. Bad writers don’t point to something in the world but are self-conscious about not seeming naïve about the pitfalls of their own enterprise. Their goal is not to show something to the reader but to prove that they are not a bad lawyer or a bad scientist or a bad academic. And so bad writing is cluttered with apologies and hedges and somewhats and reviews of the past activity of people in the same line of work as the writer, as opposed to concentrating on something in the world that the writer is trying to get someone else to see with their own eyes.

If I were running a forum, I would ask posters to follow Pinker’s rules for writing.

I Don’t care If You Are Wrong

Just some random, unorganized thoughts regarding the recent hostilities.

1. I don’t care if you are wrong.
2. Your disagreeing with me does not diminish my life.
3. I have no need to beat you into submission.
4. If I disagree with you, I would like to know why you believe what you believe.
5. I would like for you to understand my position, and I appreciate any effort you make to understand me.
6. To these ends I will ask questions designed to probe our differences.
7. If you don’t or can’t respond to my satisfaction, I will try to accept the impasse and move on.
8. These are more what you’d call “guidelines” than actual rules.

Why Would Anyone Care?


A few months ago we had a discussion of whether non-human animals can be the subject of morality.

Over on UD, Mung opined that animals are meat robots, incapable of suffering.

EDIT: Wrong UD poster. Mapou, not Mung. Apologies.

Apparently the Bible neglects to mention the possibility that animals can be the subject of morality, or that torturing animals can be a sin. But some IDists have declared that torturing babies is self-evidently wrong.

So is microwaving kittens self-evidently wrong? Or self-evidently okay, because it isn’t forbidden by scripture? What Would William Do? Or Mung? Apparently we have secular laws against this. Why?

I’d like to ask this at UD, but I can’t.

“The Advance of Knowledge Over Faith”

This post is inspired by a phrase appearing in the latest Discovery Institute essay, in which they worry about the direction being taken by the new “Cosmos” TV series.

Evolution News and Views

The DI quotes Cosmos producer, Seth MacFarlane, as promoting “…the advancement of knowledge over faith.”

This quote seems to come from an interview in Esquire Magazine.


There really isn’t much to the interview, but the phrase does kind of jump out and beg to be discussed.

The capriciousness of intelligent agency

Scordova at UD asks a question that I find interesting.


By way of contrast, intelligent agencies, particularly those intelligent agencies which we presume have free will, cannot be counted upon to behave in predictable manners in certain domains. Even presuming some intelligent agencies (say machine “intelligence”) are deterministic, they can be an unpredictable black box to outside observers. This makes it difficult to make direct experimental confirmation of certain ID inferences.

It has long been my contention that the defining behavior of science is the search for regularity.

Some regularities can be refined into mathematical equations, which we generally call laws of nature.

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