On continuing to challenge "settled science"

"Question the Answer" -- in Every Field but Evolution
Sarah Chaffee March 31, 2016 12:39 PM

Walking on the University of Washington campus here in Seattle last week, I saw a banner proclaiming, "QUESTION THE ANSWER." It's fitting that this flag is on the campus of a research university, where scientists and students from all disciplines seek knowledge. It's healthy to confront the fluidity and uncertainty of scientific truth. In reality, though, when it come to the mechanisms of evolution, current thinking discourages "questioning the answer" -- in the lab, and in the biology classroom.

An article in Quartz ("Many scientific 'truths' are, in fact, false") reminds readers of how many recent scientific findings have turned out not to be reproducible. But author Olivia Goldhill looks on the bright side, observing that it is all part of the scientific process.

For example, a 2005 paper found that of 34 well-regarded medical research results that were retested, "41% had been contradicted or found to be significantly exaggerated." A project that sought to reproduce 100 psychological experiments had only a 40% success rate. The publication notes that "[b]y some estimates, at least 51% -- and as much as 89% -- of published papers are based on studies and experiments showing results that cannot be reproduced."

Goldhill attributes this phenomenon, which could be regarded as scandalous, to two factors: first, the push to publish, with journals preferring contributions that show significant results; and second, scientists mining large volumes of data for "significant" correlations.

Yet she sees a silver lining: "The idea that papers are publishing false results might sound alarming, but the recent crisis doesn't mean that the entire scientific method is totally wrong. In fact, science's focus on its own errors is a sign that researchers are on exactly the right path."

Or as Ivan Oransky at Retraction Watch told Quartz, "If you never find mistakes, or failures to reproduce in your field, you're probably not asking the right questions."

And they're correct, of course. But who will tell the evolutionists? Scientists and science teachers alike are expected to uphold allegiance to neo-Darwinism.

As scientists arguing for a new Extended Evolutionary Synthesis (EES) told Nature:

The number of biologists calling for change in how evolution is conceptualized is growing rapidly. Strong support comes from allied disciplines, particularly developmental biology, but also genomics, epigenetics, ecology and social science. We contend that evolutionary biology needs revision if it is to benefit fully from these other disciplines. The data supporting our position gets stronger every day.

Yet the mere mention of the EES often evokes an emotional, even hostile, reaction among evolutionary biologists. Too often, vital discussions descend into acrimony, with accusations of muddle or misrepresentation. Perhaps haunted by the spectre of intelligent design, evolutionary biologists wish to show a united front to those hostile to science. Some might fear that they will receive less funding and recognition if outsiders -- such as physiologists or developmental biologists -- flood into their field.

So groupthink and self-censorship are, or should be, a concern. Meanwhile, one-sided teaching of evolution misinforms students about the nature of science. It may lead them to see neo-Darwinism as a "fact" rather than an area of ongoing scientific debate. It certainly lends support to the mistaken idea that scientific ideas, once established, are no longer open to questioning.

Pedagogy in general benefits from critical thinking, not excluding on the subject of science. As Nature notes, "[S]tudents gain a much deeper understanding of science when they actively grapple with questions than when they passively listen to answers."

"Science isn't about truth and falsity, it's about reducing uncertainty," Brian Nosek, the psychology professor who tried to repeat 100 experiments, told Quartz. "Really this whole project is science on science: Researchers doing what science is supposed to do, which is be skeptical of our own process, procedure, methods, and look for ways to improve."


Neo-Darwinism is ripe for just such an approach.

Commonsense about entropy.

The Common Sense Law of Physics
Granville Sewell March 27, 2016 1:16 PM

While the first formulations of the second law of thermodynamics were all about heat, about thermal entropy, many general physics texts generalize the second law beyond thermodynamics, with statements such as "In an isolated system, the direction of spontaneous change is from order to disorder" (Classical and Modern Physics, Kenneth Ford, 1973), and give examples of irreversible "entropy" increases that have nothing to do with thermal entropy, such as tornados turning towns into rubble, explosions destroying buildings, or fires turning books into ashes.

In these examples, "entropy" is generally used simply as a synonym for "disorder." In a 1970 Smithsonian article, for example, Isaac Asimov (Smithsonian, Volume 1, August 1970, p. 4) writes:

We have to work hard to straighten a room, but left to itself, it becomes a mess again very quickly and very easily.... How difficult to maintain houses, and machinery, and our own bodies in perfect working order; how easy to let them deteriorate. In fact, all we have to do is nothing, and everything deteriorates, collapses, breaks down, wears out -- all by itself -- and that is what the second law is all about.

The development of civilizations on a barren planet would seem to be a spectacular violation of these more general statements of the second law. How could a few fundamental, unintelligent, forces of physics alone rearrange the fundamental particles of physics into human brains, computers, jet airplanes, and Apple iPhones?

Asimov recognizes the problem in his Smithsonian article. He writes:

You can argue, of course, that the phenomenon of life may be an exception [to the second law]. Life on earth has steadily grown more complex, more versatile, more elaborate, more orderly, over the billions of years of the planet's existence. From no life at all, living molecules were developed, then living cells, then living conglomerates of cells, worms, vertebrates, mammals, finally Man. And in Man is a three-pound brain which, as far as we know, is the most complex and orderly arrangement of matter in the universe. How could the human brain develop out of the primeval slime? How could that vast increase in order (and therefore that vast decrease in entropy) have taken place?

But Asimov concludes that there is no conflict with the second law here, because:

Remove the sun, and the human brain would not have developed.... And in the billions of years that it took for the human brain to develop, the increase in entropy that took place in the sun was far greater; far, far greater than the decrease that is represented by the evolution required to develop the human brain.

This "compensation" argument, used by every physics text which discusses evolution and the second law to dismiss the claim that what has happened on Earth may violate the more general statements of the second law, was the target of my article "Entropy, Evolution, and Open Systems," published in the proceedings of the 2011 Cornell meeting Biological Information: New Perspectives (BINP).

In that article, I showed that the very equations of entropy change upon which this compensation argument is based actually support, on closer examination, the common sense conclusion that "if an increase in order is extremely improbable when a system is isolated, it is still extremely improbable when the system is open, unless something is entering which makes it not extremely improbable." The fact that order can increase in an open system does not mean that computers can appear on a barren planet as long as the planet receives solar energy. Something must be entering our open system that makes the appearance of computers not extremely improbable, for example: computers.

My BINP article includes a section entitled "The Common Sense Law of Physics," which uses a little humor to show how silly Asimov's compensation argument really is:

I was discussing the second law argument with a friend recently, and mentioned that the second law has been called the "common sense law of physics." The next morning he wrote: "Yesterday I spoke with my wife about these questions. She immediately grasped that chaos results in the long term if she would stop caring for her home."

I replied: "Tell your wife she has made a perfectly valid application of the second law of thermodynamics. In fact, let's take her application a bit further. Suppose you and your wife go for a vacation, leaving a dog, a cat, and a parakeet loose in the house (I put the animals there to cause the entropy to increase more rapidly, otherwise you might have to take a much longer vacation to see the same effect). When you come back, you will not be surprised to see chaos in the house. But tell her some scientists say, 'But if you leave the door open while on vacation, your house becomes an open system, and the second law does not apply to open systems...you may find everything in better condition than when you left.' I'll bet she will say, 'If a maid enters through the door and cleans the house, maybe, but if all that enters is sunlight, wind, and other animals, probably not.'"

Imagine trying to tell my friend's wife that, provided her house is an open system, the fact that chaos is increasing in the rest of the universe -- or on the sun, provided sunlight enters through the door -- means that chaos could decrease in her house while she is gone. Even if the door is left open, it is still extremely improbable that order in the house will improve, unless something enters that makes this not extremely improbable -- for example, new furniture or an intelligent human.

Suppose we take a video of a tornado sweeping through a town, and run the video backward. Would we argue that although a tornado turning rubble into houses and cars represents a decrease in entropy, tornados derive their energy from the sun, and the increase in entropy outside the Earth more than compensates the decrease seen in the video, so there is no conflict with the second law? Or would we argue that what we were seeing was too difficult to quantify, so we can't be sure there is a problem? Some things are obvious even if they are difficult to quantify.

In Signature in the Cell, Stephen Meyer appeals to common sense, in applying the second law to information: "Most of us know from our ordinary experience that information typically degrades over time unless intelligent agents generate (or regenerate) it. The sands of time have erased some inscriptions on Egyptian monuments. The leak in the attic roof smudged the ink in the stack of old newspapers, making some illegible.... Common experience confirms this general trend -- and so do prebiotic simulation experiments and origin-of-life research."

I have found that Darwinists, after reading this article, or my more recent 2013 Bio-Complexity article (both of which are reproduced in my Discovery Institute Press book In the Beginning and Other Essays on Intelligent Design) quickly see how silly the compensation argument is, and immediately retreat to the original, early, statements of the second law, saying that the second law of thermodynamics should never have been generalized beyond thermodynamics, and evolution does not violate the second law as applied to thermal entropy. Nevertheless, I'm sure general physics texts are still being written that apply it much more generally, and still dismiss the spectacular increase in order seen on our planet by saying, entropy can decrease in an open system.


Many others who read the article will ask, How could an idea as dumb as the compensation argument have been believed by so many intelligent scientists, for so long? That's a question that many people are finally starting to ask about Darwinism itself.

Another failed Darwinian prediction XIV.

Gene phylogenies are congruent:

Just as evolution predicts that gene trees and species trees should be congruent, it also predicts that different gene trees should be congruent. In 1982 David Penny and co-workers tested this prediction. They wrote that “The theory of evolution predicts that similar phylogenetic trees should be obtained from different sets of character data.” Their character data came from five different proteins and they concluded “there is strong support from these five sequences for the theory of evolution.” (Penny, Foulds and Hendy) But in later years, as more genetic data became available, it was clear that different genes led to very different evolutionary trees. As one study explained, the sequences of genes, “often disagree and can seldom be proven to agree.” (Doolittle and Bapteste) It is now well understood that “Gene and genome trees conflict at many levels” (Haggerty, et. al.) and that “Incongruence between gene trees is the main challenge faced by phylogeneticists in the genomic era.” (Galtier and Daubin) For evolutionists this failed prediction will require more complicated models of evolutionary history. As Penny now writes, he is “not rejecting the tree per se but enriching the tree concept into a network.” (Penny)

References

Doolittle, W., E. Bapteste. 2007. “Pattern pluralism and the Tree of Life hypothesis.” Proceedings of the National Academy of Sciences 104:2043-2049.

Galtier, N., V. Daubin. 2008. “Dealing with incongruence in phylogenomic analyses.” Philosophical Transactions of the Royal Society B 363:4023-4029.

Haggerty, L., et. al. 2009. “Gene and genome trees conflict at many levels.” Philosophical Transactions of the Royal Society B 364:2209-2219.

Penny, D. 2011. “Darwin’s Theory of Descent with Modification, versus the Biblical Tree of Life.” PLoS Biol 9:e1001096.

Penny, D., L. Foulds, M. Hendy. 1982. “Testing the theory of evolution by comparing phylogenetic trees constructed from five different protein sequences.” Nature 297:197-200.

A clash of titans XI

The Watchtower Society's commentary on Paul's epistle to the Galatians.

GALATIANS, LETTER TO THE
The inspired letter written in Greek, by Paul an apostle, “to the congregations of Galatia.”—Ga 1:1, 2.

Writership. The opening sentence names Paul as the writer of this book. (Ga 1:1) Also, his name is used again in the text, and he refers to himself in the first person. (5:2) A portion of the letter, in the way of an autobiography, speaks of Paul’s conversion and some of his other experiences. The references to his affliction in the flesh (4:13, 15) are in harmony with expressions seemingly relating to this affliction in other Bible books. (2Co 12:7; Ac 23:1-5) Paul’s other letters were usually written by a secretary, but this one, he says, was written with his “own hand.” (Ga 6:11) In his other writings, almost without exception, he sends the greetings of himself and those with him, but in this letter he does not. Had the writer of the letter to the Galatians been an impostor, he would very likely have named a secretary and would have sent some greetings, as Paul usually did. Thus the writer’s form of address and his honest direct style vouch for the letter’s authenticity. It would not reasonably be fabricated this way.

The letter is not usually contested as being a letter of Paul’s except by those who attempt to discredit Paul’s writership of all the letters commonly attributed to him. Among evidences from outside the Bible supporting Paul’s writership, there is a quotation that Irenaeus (c. 180 C.E.) makes from Galatians and ascribes to Paul.

To Whom Addressed. The question of which congregations were included in the address “the congregations of Galatia” (Ga 1:2) has long been a controversy. In support of the contention that these were unnamed congregations in the northern part of the province of Galatia, it is argued that the people living in this area were ethnically Galatians, whereas those of the S were not. However, Paul in his writings usually gives official Roman names to the provinces, and the province of Galatia in his time included the southern Lycaonian cities of Iconium, Lystra, and Derbe as well as the Pisidian city of Antioch. In all these cities Paul had organized Christian congregations on his first evangelizing tour when he was accompanied by Barnabas. That the congregations in the cities of Iconium, Lystra, Derbe, and Pisidian Antioch were addressed agrees with the way the letter mentions Barnabas, as one apparently known by those to whom Paul was writing. (2:1, 9, 13) There is no indication elsewhere in the Scriptures that Barnabas was known to Christians in the northern part of Galatia or that Paul even made any trips through that territory.

Paul’s exclamation, “O senseless Galatians,” is no evidence that he had in mind only a certain ethnic people who sprang exclusively from Gallic stock in the northern part of Galatia. (Ga 3:1) Rather, Paul was rebuking certain ones in the congregations there for allowing themselves to be influenced by an element of Judaizers among them, Jews who were attempting to establish their own righteousness through the Mosaic arrangement in place of the ‘righteousness due to faith’ provided by the new covenant. (2:15–3:14; 4:9, 10) Racially, “the congregations of Galatia” (1:2) to whom Paul wrote were a mixture of Jews and non-Jews, the latter being both circumcised proselytes and non-circumcised Gentiles, and no doubt some were of Celtic descent. (Ac 13:14, 43; 16:1; Ga 5:2) All together, they were addressed as Galatian Christians because the area in which they lived was called Galatia. The whole tenor of the letter is that Paul was writing to those with whom he was well acquainted in the southern part of this Roman province, not to total strangers in the northern sector, which he apparently never visited.

Time of Writing. The period covered by the book is of an undetermined length, but the time of writing has been set between approximately 50 and 52 C.E. It is implied in Galatians 4:13, that Paul made at least two visits to the Galatians before he wrote the letter. Chapters 13 and 14 of the Acts of Apostles describe a visit of Paul and Barnabas to the southern Galatian cities that took place about 47 to 48 C.E. Then, after the conference regarding circumcision in Jerusalem, about 49 C.E., Paul, with Silas, went back to Derbe and Lystra in Galatia and to other cities where Paul and Barnabas had “published the word of Jehovah” (Ac 15:36–16:1) on the first tour. It was evidently after this, while Paul was at another point on his second missionary tour, or else back at his home base, Syrian Antioch, that he received word that prompted him to write to “the congregations of Galatia.”

If it was during his year-and-a-half stay in Corinth (Ac 18:1, 11) that Paul wrote this letter, then the time of writing was likely between the autumn of 50 and the spring of 52 C.E., the same general period during which he wrote his canonical letters to the Thessalonians.

If the writing was done during his brief stop in Ephesus or after he got back to Antioch in Syria and “passed some time there” (Ac 18:22, 23), it would have been about 52 C.E. Ephesus is an unlikely place for writing, though, both because of his short stay there and because if Paul had been so close when he heard of the deflection in Galatia, it is to be expected that he would have personally visited the brothers or explained in his letter why it was not possible for him to do so at the time.

What his letter says about the Galatians “being so quickly removed from the One who called [them]” (Ga 1:6) may indicate that the writing of the letter was done soon after Paul had paid a visit to the Galatians. But even if the writing had not taken place until 52 C.E. in Syrian Antioch, it would still have been relatively soon for such a deflection to occur.

Canonicity. Early evidence of the book’s canonicity is found in the Muratorian Fragment and in the writings of Irenaeus, Clement of Alexandria, Tertullian, and Origen. These men referred to it by name along with most or all of the other 26 books of the Christian Greek Scriptures. It is mentioned by name in the shortened canon of Marcion and even alluded to by Celsus, who was an enemy of Christianity. All the outstanding lists of the books in the canon of the inspired Scriptures, up to at least the time of the Third Council of Carthage, in 397 C.E., included the book of Galatians. We have it preserved today, along with eight of Paul’s other inspired letters, in the Chester Beatty Papyrus No. 2 (P⁠46), a manuscript assigned to about 200 C.E. This gives proof that the early Christians accepted the book of Galatians as one of Paul’s letters. Other ancient manuscripts, such as the Sinaitic, Alexandrine, Vatican No. 1209, Codex Ephraemi rescriptus, and Codex Claromontanus, as well as the Syriac Peshitta, likewise include the book of Galatians. Also, it harmonizes completely with Paul’s other writings and with the rest of the Scriptures from which it frequently quotes.

Circumstances Relating to the Letter. The letter reflects many traits of the people of Galatia in Paul’s time. Gallic Celts from the N had overrun the region in the third century B.C.E., and therefore Celtic influence was strong in the land. The Celts, or Gauls, were considered a fierce, barbarous people, it having been said that they offered their prisoners of war as human sacrifices. They have also been described in Roman literature as a very emotional, superstitious people, given to much ritual, and this religious trait would likely influence them away from a form of worship so lacking in ritual as Christianity.

Even so, the congregations in Galatia may have included many who formerly had been like this as pagans, as well as many converts from Judaism who had not entirely rid themselves of scrupulously keeping the ceremonies and other obligations of the Mosaic Law. The fickle, inconstant nature attributed to the Galatians of Celtic descent could explain how at one time some in the Galatian congregations were zealous for God’s truth and a short time later became an easy prey for opponents of the truth who were sticklers for observance of the Law and who insisted that circumcision and other requirements of the Law were necessary for salvation.

The Judaizers, as such enemies of the truth might be called, apparently kept the circumcision issue alive even after the apostles and other elders in Jerusalem had dealt with the matter. Perhaps, too, some of the Galatian Christians were succumbing to the low moral standards of the populace, as may be inferred from the message of the letter from chapter 5, verse 13, to the end. At any rate, when word of their deflection reached the apostle, he was moved to write this letter of straightforward counsel and strong encouragement. It is evident that his immediate purpose in writing was to confirm his apostleship, counteract the false teachings of the Judaizers, and strengthen the brothers in the Galatian congregations.

The Judaizers were crafty and insincere. (Ac 15:1; Ga 2:4) Claiming to represent the congregation in Jerusalem, these false teachers opposed Paul and discredited his position as an apostle. They wanted the Christians to get circumcised, not seeking the Galatians’ best interests, but so that the Judaizers could bring about an appearance of things that would conciliate the Jews and keep them from opposing so violently. The Judaizers did not want to suffer persecution for Christ.—Ga 6:12, 13.

To accomplish their objective, they claimed that Paul’s commission came to him secondhand, that it was only from some men prominent in the Christian congregation—not from Christ Jesus himself. (Ga 1:11, 12, 15-20) They wanted the Galatians to follow them (4:17), and in order to nullify Paul’s influence, they had to paint him first as no apostle. Apparently they claimed that when Paul felt it expedient, he preached circumcision. (1:10; 5:11) They were trying to make a sort of fusion religion of Christianity and Judaism, not denying Christ outright but arguing that circumcision would profit the Galatians, that it would advance them in Christianity, and that, furthermore, by this they would be sons of Abraham, to whom the covenant of circumcision was originally given.—3:7.

Paul thoroughly refuted the contentions of these false Christians and built up the Galatian brothers so that they could stand firm in Christ. It is encouraging to note that the Galatian congregations did remain true to Christ and stood as pillars of the truth. The apostle Paul visited them on his third missionary tour (Ac 18:23), and the apostle Peter addressed his first letter to the Galatians, among others.—1Pe 1:1.

[Box on page 881]

HIGHLIGHTS OF GALATIANS

A letter emphasizing appreciation for the freedom that true Christians have through Jesus Christ

Written a year or perhaps several years after the Galatians had been informed about the decision of the governing body that circumcision is not required of Christians

Paul defends his apostleship

Paul’s apostleship was not of human origin but was by appointment from Jesus Christ and the Father; he did not consult with the apostles in Jerusalem before beginning to declare the good news; not until three years later did he briefly visit Cephas and James (1:1, 13-24)

The good news he proclaimed was received, not from men, but by revelation from Jesus Christ (1:10-12)

By reason of a revelation, Paul, with Barnabas and Titus, went to Jerusalem regarding the circumcision issue; he learned nothing new from James, Peter, and John, but they recognized that he had been empowered for an apostleship to the nations (2:1-10)

At Antioch, when Peter wrongly separated himself from non-Jewish believers in fear of certain visiting brothers from Jerusalem, Paul reproved him (2:11-14)

A person is declared righteous only through faith in Christ, not works of law

If a person could be declared righteous by works of law, Christ’s death would have been unnecessary (2:15-21)

Galatians received God’s spirit because of their responding in faith to the good news, not because of works of law (3:1-5)

True sons of Abraham are those who have faith like his (3:6-9, 26-29)

Because of being unable to keep the Law perfectly, those seeking to prove themselves righteous by works of the Law are under a curse (3:10-14)

The Law did not invalidate the promise associated with the Abrahamic covenant, but it served to make transgressions manifest and acted as a tutor leading to Christ (3:15-25)

Stand fast in Christian freedom

Jesus Christ, by his death, released those under law, making it possible for them to become sons of God (4:1-7)

Returning to an arrangement of observing days, months, seasons, and years would mean going back into slavery and coming into a position like that of Ishmael, the son of the servant girl Hagar; with his mother he was dismissed from Abraham’s household (4:8-31)

Having been liberated from sin and no longer being bound by the Law, they were to resist anyone who would induce them to accept a yoke of slavery (1:6-9; 5:1-12; 6:12-16)

Do not abuse your freedom but yield to the influence of God’s spirit, manifesting its fruitage in your life and shunning the works of the flesh (5:13-26)


Readjust in a spirit of mildness anyone taking a false step; but all are individually obligated to carry their own load of responsibility (6:1-5)

Yet more on pre-evolutionary design II

An Engineered "Minimal" Microbe Is Irreducibly Complex, Thus Evidence of Intelligent Design.

Ann Gauger March 24, 2016 4:00 PM

Science Magazine published a paper last week, "Design and synthesis of a minimal bacterial genome," describing the creation of a bacterium with a stripped-down genome. The paper represents twenty years of work by many scientists, including celebrated biochemist J. Craig Venter. They managed to reduce the genome by almost half, from over 900 genes to 473, a little bit at a time. The paper has made a splash across the Internet (see, for example, articles from Associated Press and Bloomberg).

Why on earth would the researchers do such a thing? The hope is that this minimal bacterium will provide a useful vehicle for future synthetic biology, enabling the production of useful medicines to treat disease.

But there is another reason they spent twenty years on this project. It's an attempt to answer a basic question. What's the minimum amount of genetic information needed to get a functioning cell? Estimates have ranged from 250 to 300 genes, depending on what kind of cell and where it is living. For the bacterium M. mycoides, the starting point of their work, the answer seems to be about 470 genes. Scientists want to know the answer because the simplified cell may allow them to tease apart how the genes interact, and what all of them do. It's easier to tackle 400 genes than over 900, or in the case of the common bacterium E. coli, over 4,000.

This work has already yielded some interesting results. They still don't know what 30 percent of the reduced genome does, just that the genes are essential. Second, genes that appear to be nonessential by themselves can become essential when another gene is deleted. Clearly there are complex interactions going on among the 473 genes.

All of this leads to an obvious question. This little bacterium has to be able to copy its DNA, transcribe and translate it into protein, plus be able to coordinate all the steps involved in cell division. It has to be able to make all the things it can't get from its environment. That's a lot of information to be stored and used appropriately. Hence 473 genes.

But where did the cell come from in the first place? It's a chicken-and-egg problem. Given the number of things the cell has to do to be a functioning organism, where does one begin? DNA or RNA alone is not enough, because protein is needed to copy the DNA and to carry out basic cellular processes. But protein is not enough by itself either. DNA is needed to stably inherit the genetic information about how to make proteins.

Some people propose that RNA could do the trick, because under just the right circumstances, and with an experimenter's help, RNA can copy itself, partially. The idea is that if just the right sequence of RNA were to come along, it could serve as both an RNA enzyme (or ribozyme) and as the template for reproducing itself.

That leaves aside bigger problems. Ribozymes can only carry out a few simple chemical reactions, while even a minimal cell needs many kind of reactions. Second, how did the switch to DNA and proteins happen? No one has a clue. Last, let's not forget the problem of interdependence, or irreducible complexity as biochemist Michael Behe calls it in his book Darwin's Black Box. The minimal cell, he writes, is a system "composed of several [many in this case] well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning."

Irreducible systems are evidence of intelligent design, because only a mind has the capacity to design and implement such an information-rich, interdependent network as a minimal cell.

Think about the design of a basic car. You need an engine, a transmission, a drive shaft, a steering wheel, axles and wheels, plus a chassis to hold it all together. Then there's gas, and a way to start the whole thing going. (I have undoubtedly left out something, but you get my point.) Having one or two of these things won't make a functioning car. All the parts are necessary before it can drive, and it takes a designer to envision what is needed, how to fit it together, and then to build it.

Whether you're talking about a car or a minimal cell, it won't happen without a designer.

Darwinism vs. the real world XXIV

   Heat and Temperature -- What's the Difference? 

Howard Glicksman March 23, 2016 12:41 PM 

Editor's note: Physicians have a special place among the thinkers who have elaborated the argument for intelligent design. Perhaps that's because, more than evolutionary biologists, they are familiar with the challenges of maintaining a functioning complex system, the human body. With that in mind, Evolution News is delighted to offer this series, "The Designed Body." For the complete series, see here . Dr. Glicksman practices palliative medicine for a hospice organization.

We live in a world made up of matter. Matter consists of atoms and molecules that follow the laws of nature. Organic life is made up of atoms and molecules that are organized into cells. Our body has trillions of them. Heat and temperature are physical phenomena and, although related to each other, they are not the same thing.

Heat is the transfer of energy from one object to another. When a machine uses energy, it naturally gives off heat. This applies to the body as well. When our cells use oxygen to release energy from glucose, they give off heat. The laws of nature not only cause the release of heat when energy is used, they also cause the transfer of heat from a warmer object to a cooler object when they come in contact with each other. When you touch a hot stove, the transfer of heat from it to your fingers will burn them. Grab an ice cube and the transfer of heat from your hand to it will cause it to melt.

In contrast, temperature is a measure of an object's internal energy, reflected in its amount of random molecular motion. This energy is often derived from heat but can come from other sources, like electrical and nuclear energy. The higher an object's temperature, the more random motion there is among its molecules. Conversely the lower an object's temperature, the less random motion there is among its molecules.

For some molecules, like H2O, the amount of random motion can affect its physical state. If the temperature of H2O is below 32oF (0oC), it is a solid -- ice. And when its temperature is between 32oF-212oF (0oC-100oC), H2O is liquid water. Finally, when the temperature of H2O is greater than 212oF (100oC) it is a gas called water vapor or steam. The effects of heat on an object's temperature, physical state, and functional capacity apply not only to working machines but to the cells of the body as well.

Everybody knows that going outside in the sun during the summer will make you feel hot. And going outside without a coat in the winter will make you feel cold. And most people know that the temperature inside the body (core temperature) is normally higher than on the skin (surface temperature). All you have to do is blow on your hands and feel the heat to figure that out. As humans, we are warm-blooded, while most reptiles, amphibians, fish, and insects, are cold-blooded. But most people do not understand why and how the body follows the rules and keeps its core temperature within a certain range to stay alive. That's what the next few articles in this series will explain.

Just as a machine can malfunction if it is too hot or too cold, so too, the cells that make up the organs of the body can malfunction if the core temperature is too high or too low. The core temperature of the body is a reflection of the amount of random molecular motion within its cells. Most of the enzymes the body uses for its metabolic processes work best within an ideal temperature range. For the human body the normal range for the core temperature is 97o-99oF (36o-37oC).

If the core temperature rises too high or drops too low, it may affect not only the function of the enzymes but also the integrity of the proteins and the plasma membrane. A core temperature greater than 107oF (42oC) usually causes structural and enzymatic protein breakdown, causing impairment of cellular respiration and destabilization of the plasma membrane. This ultimately results in brain malfunction, loss of temperature control, muscle breakdown, and multi-system organ failure. A core temperature below 91oF (33oC) usually causes a significant reduction in enzyme activity and metabolic function, resulting in a marked decrease in energy production. This too leads to brain malfunction, loss of temperature control, impaired muscle function, and multi-system organ failure.

Clearly, it is important for the body to control its core temperature. To understand how thermoregulation is accomplished, you must first understand how the laws of nature affect the body with respect to heat and temperature.

The core temperature of the body is affected mainly by two processes: how much heat the body produces from the energy its cells use to function and how much heat the body gains from, or loses to, its surroundings.

The chemical reactions in the body can either release or use up energy. The sum total of all these chemical reactions is called the metabolism. Chemical reactions that release energy while breaking down complicated molecules, like glucose (C6H12O6), into simpler ones, like carbon dioxide (CO2) and water (H2O), are called catabolic reactions. Chemical reactions that use energy to build more complex molecules, like proteins, from simpler ones, like amino acids, are called anabolic reactions. Both catabolic and anabolic reactions take place side by side in the cell.

The cell is only able to harness about one quarter of the energy that is released from the breakdown of complex molecules like carbohydrates, fats, and proteins. It places this energy in special energy-storage molecules (e.g., ATP). The remaining three-quarters of the energy is released into the body as heat. The energy-storage molecules, like ATP, then transfer their energy within the cell so it can be used for anabolic processes and functional activities. These include things like the synthesis of proteins for cell structure and enzymes that promote vital chemical reactions, ion pumps (like the sodium-potassium pump) for cellular integrity and function, muscle contraction, gland and nerve cell function, and gastrointestinal absorption. All of these processes ultimately result in the release of heat. So most of the energy the body uses eventually results in the release of heat.

When the body hasn't eaten for a while and is at total rest, the amount of energy it requires to maintain its cellular integrity and total organ function is called its basal metabolic rate (BMR). Think of the BMR as being like the amount of energy a car uses while idling in traffic. It needs a minimum amount of energy just to keep the engine running before the driver steps on the accelerator. So too, the BMR is a measure of the amount of energy the body uses just to maintain its cellular and organ function while it waits to be put into action. And just like a car, the faster the body moves and the more work it does, the more energy it needs, the more heat it releases, and the higher its internal energy and temperature. So the laws of nature regarding the release of heat when energy is used to do work affects the body's core temperature, not only when it is at complete rest (BMR) but with any level of activity.

Since the body is surrounded by air (or sometimes water) it is always losing heat to, or gaining heat from, its environment. Since most people prefer to stay in surroundings where their core temperature (97o-99oF, 36o-37oC) is higher than the ambient temperature, the body is usually constantly losing heat to its surroundings. In the same way that heat radiates from the sun, much of the heat produced by the body's metabolism is lost through the skin into the surroundings. This accounts for about one-half of the body's heat loss.

Conduction involves the transfer of heat from one object to another by direct contact. If the body comes in contact with something cooler or warmer than itself, as when swimming in a cold river or sitting in a hot sauna, then heat is transferred to or from the body by conduction. Heat loss by conduction usually takes place between the skin and the air surrounding the body and is often aided by convection. Convection is the phenomenon where heated air at the surface of the skin moves away from the body and is replaced by cooler air, which is more effective in taking away heat. This is why a cool breeze against the skin causes more heat loss. Conduction, aided by convection, generally accounts for about one-quarter of the body's heat loss.

Finally, evaporation takes place when water on a surface absorbs heat from it and is released into the air as water vapor. Heat loss by evaporation takes place from the lungs, the mouth, and, most importantly, from perspiration on the surface of the skin. Evaporation accounts for about one-quarter of the total heat lost from the body.

In summary, the laws of nature demand that heat be released when energy is used to do work. The body invariably produces heat from its metabolism, which allows it to live and function normally within its environment. The laws of nature also demand that a warmer object transfer heat energy to a cooler one when they come in contact with each other. Since the body is surrounded by air that is usually cooler than its core temperature, this means that it is usually losing heat to its environment. The body's core temperature is therefore determined by its total production of heat through its metabolism and how much heat it loses to, or gains from, its surroundings.

The molecules that make up the cells and perform the functions of the body work best within a given temperature range. To control its core temperature and stay healthy, the body must take into account these two laws of nature that naturally cause internal heat production and the transfer of heat to, or from, the environment. Next time, we'll look at how the body does it and whether, given this understanding of how life works, the explanations of evolutionary biology are satisfying.

On irreconcilable differences between Darwin and God.

Character and Theology Aside, What About Denis Lamoureux's Science?

David Klinghoffer March 21, 2016 12:43 PM

As Denyse O'Leary points out, it's a good thing Stephen Meyer was thereon stage in Toronto, migraine attack or not. Otherwise, between atheist Lawrence Krauss and theistic evolutionist Denis Lamoureux, there would have been little to debate. Perhaps surprisingly, Lamoureux focused his attack on Meyer, even while proclaiming him his "brother in Christ" and flinging buttery approval at Krauss. Simple humanity, it seems, would have dictated turning your fire away from the stricken man and directing it at your shared opponent.

But I leave it to his fellow Christians to reflect on Dr. Lamoureux's character, and how little daylight there is between his "theistic" position and Krauss's atheism. What, though, about his science?

In defending Darwinism, Lamoureux's signal contribution drew on his expertise in teeth. Evolving them was a snap -- "Teeth emerged. Very easy to do." Paleontologist Günter Bechly, a pretty impressive scientist, begs to differ, on that as well as other points raised by Lamoureux. He blogs about the "Lamoureux delusion." First on the question of dental evolution:

Lamoureux elaborated on the origin of teeth from placoid scales on the jaws of Paleozoic acanthodian "sharks". However, his own diagram showed that these placoid scales already included all crucial morphological features of teeth (upper enamel layer, lower dentine layer, pulp cavity, bony base). That dermal denticle scales on jaws gradually grew larger to form teeth is not a convincing example of macroevolution, but rather just quantitative change through microevolution that is not even denied by Young Earth Creationists. At best, his example is evidence for common descent with modification, which is fully compatible with Intelligent Design and thus cannot be used against it. Finally, the example has no bearing at all on the crucial question, if an unguided Neodarwinian process can explain the pattern of morphological change over time, and therefore it is impotent as an argument against Intelligent Design anyway.

On Lamoureux and the "oldest bilaterian":

To refute Stephen Meyer's claims in his book "Darwin's Doubt", Lamoureux presented the discovery of alleged 585 million year old traces of early bilaterian animals from the Ediacaran period. This evidence is based on a Science publication byPecoits et al. (2012). However, Lamoureux forgot to mention that the dating and identification of these traces is highly disputed (see here and here). Actually, the most recent publication on this issue by Mángano & Buatois (2014) clearly states that "With respect to the Ediacaran, we agree with more conservative estimations that the oldest bilaterian trace fossils are dated to approximately 560 Ma ... The oldest subdivision (Avalon; 575-560 Ma) does not contain undisputed bilaterian trace fossils, and therefore has not been considered ... An earlier appearance of bilaterian trails (585 Ma) has been recently suggested. However, the age of the trace-fossil-bearing strata is highly contended, probably being Late Palaeozoic".

It is especially noteworthy that large unicellular organisms (protists) can produce traces on the sea floor that are remarkably similar to those of bilaterian animals, as Matz et al. (2008) showed in a study titled "Giant deep-sea protist produces bilaterian-like traces".

On nylonase:

Lamoureux mentioned the discovery of Nylon-eating bacteria as empirical proof that evolution can create new complex specified information and new proteins (nylonase enzyme) within only 40 years of time. This is actually an "old hat" in the creation vs evolution debate (see Wikipedia), and it sounds impressive only when one ignores two facts:

1. Dembski (2001) established in his book "No Free Lunch" a value 500 Bits as complexity threshold for Complex Specified Information (CSI), which could not originate by natural processes given the probabilistic resources of our universe. It has not been established that the new information in nylonase matches this threshold and thus represents CSI at all (see here).
2. Newer research by Negoro et al. (2007) has shown that the nylonase enzyme did not evolve by gene duplication and frameshift mutation as originally assumed, but arose from a pre-existing carboxyesterase enzyme, which already had some capacity to degrade nylon oligomers. In other words: Nylonase is NOT new information (also see here)!

On the "God of the gaps" objection, Bechly agrees that "explaining lightning and thunder with Thor's activity" would be "a God of the Gaps argument." But ID is different, obviously:

As Intelligent Design theorist Stephen C. Meyer explained in the same debate and in his books "Signature in the Cell" and "Darwin's Doubt", Intelligent Design makes an inference to the best explanation, not based on an argument from ignorance (what we do NOT know), but based on what we DO know about causes now in operation that could bring about the effect in question.

These are fighting words:

Indeed it is Theistic Evolution which is a redundant and dispensable concept (see this Forbes article), because it is either Neodarwinism in a cheap tuxedo (which it usually is), or it is a cowardly euphemism for Intelligent Design. In either case it is not a genuine alternative to Neodarwinism or Intelligent Design.

"Neo-Darwinism in a cheap tuxedo" -- I like that. Or maybe in rented clerical attire.

The appearance of evenhandedness?

Larry Moran -- Voice of Reason

Ann Gauger March 21, 2016 1:58 PM

We weren't the only ones to notice Krauss's "shenanigans" duringSaturday's debate with Meyer and Lamoureux. Over at his blogSandwalk, biochemist Larry Moran of the University of Toronto (where the event took place) posted a straightforward commentary, without innuendo or name-calling (aside from his usual label of "intelligent design creationists").

The main point that he picked up from Stephen Meyer's presentation was the argument that ID predicted the functionality of most of the genome, rather than its being mostly junk. ID proponent Richard Sternberg made this claim in the 1990s, and it is being confirmed by ongoing research and the ENCODE project. Moran argues that ENCODE doesn't demonstrate what ID proponents claim, and that the genome still is full of junk. But that's an argument that time and more research will answer.

The really interesting thing is what happened in the comments section after the post. He acknowledged that some ID proponents do science in good faith (in contrast to Krauss's repeated assertions during the debate):

I believe that there are ID proponents who are attempting to perform science in good faith.

Let's not quibble over when ID proponents made a prediction and whether it counts as a true predication [sic]. Right now, they are staking the reputation of ID on the claim (= prediction) that most of our genome is functional.

We'll see what happens when they realize the truth.

Then further on, in response to an attack on ID by a poster he says,

Bill says,

But the point is moot. ID is not a scientific endeavor. Never has been. It's a political movement with a social agenda to inject religion into American public schools. Simple as that.

The debate took place in Canada where we allow the teaching of religion in public schools. None of us give a damn about the American Constitution. We're interest[ed] in knowing whether the science is valid or not.

If the Intelligent Design proponents have legitimate complaints about evolution and if they have good scientific arguments in favor of design then those ideas should be taught in Canadian schools in spite of what some judge in Pennsylvania said ten years ago.

Lawrence Krauss tried to show that ID was not science but he did a horrible job. Meyer countered by presenting a lot of science forcing Krauss to deal with the very science that he said ID doesn't do!

Bill, you are being dangerously naive if you think you can simply dismiss the ID movement because it's not science (according to your definition). The general public doesn't care. All they see is serious attacks on evolution that look a lot like science.

Yes, ID is a movement and so are the desires to do something about climate change or GMO's. There are lots of "movements" with social and political agenda[s]. Many of them deal with science in one way [or] another. It's the role of scientists to evaluate the scientific arguments in spite of the agenda. We have to show that the goal of the movement is either compatible or incompatible with the scientific facts.

Yes. That's the level at which the debate should be held.

It doesn't mean that Moran agrees with us. He's just being fair. He even granted Meyer some points in the debate, before expressing his own view:

During the debate, Stephen Meyer emphasized [the] random nature of evolution and its inability -- according to him -- to come up with new protein folds and new information in a reasonable amount of time.

Krauss misunderstood the argument, which was based on the frequency of mutations, and tried to dismiss it by pointing out that evolution is not random -- it's directed and guided by natural selection.

Meyer corrected him by pointing out that the issue was the probability of mutations and not the probability of fixation once the mutation occurred. (This was when he was struggling with a migraine so he didn't do as good a job as he could have.)

Krauss stumbled on for a bit emphasizing natural selection and the fact that evolution is not random.

That was embarrassing. I think Krauss gets most of his information about evolution from Richard Dawkins so he (Krauss) probably doesn't know about random genetic drift or historical contingency or any of the other features of the history of life that make it "random" (in the colloquial sense).

I suspect that Krauss still holds on to the Dawkins view that life has the appearance of design. Truth is, in the big picture, life really doesn't have the appearance of design. Certainly our genome doesn't look designed and my back was not designed for walking upright as it let's me know every morning when I get out of bed.

Designed or not, Professor Larry Moran has distinguished himself as someone even-handed in his assessment of this debate. Thanks for the voice of reason, Dr. Moran.