On not getting carried away by science hype.

Has Craig Venter Produced Artificial Life?
Jonathan Wells 


"Artificial life, the stuff of dreams and nightmares, has arrived." So proclaimed The Economist on May 20th, after a team of scientists headed by J. Craig Venter [2] announced that it had replaced the natural DNA in a bacterial cell with DNA they had artificially synthesized.

According to University of Pennsylvania philosopher and bioethicist Arthur Caplan, "Venter and his colleagues have shown that the material world can be manipulated to produce what we recognize as life. In doing so they bring to an end a debate about the nature of life that has lasted thousands of years. Their achievement undermines a fundamental belief about the nature of life that is likely to prove as momentous to our view of ourselves and our place in the Universe as the discoveries of Galileo, Copernicus, Darwin and Einstein."

Whoa! Wait a minute!

What Venter and his team did was to determine the sequence of the DNA in one of the world's simplest bacteria, use the sequence information to synthesize a copy of that DNA from subunits sold by a biological supply company, then put the synthetic copy of DNA into a living bacterial cell from which the natural DNA had been removed.

As Nicholas Wade pointed out in The New York Times, Eckard Wimmer and his colleagues did something similar in 2002 by synthesizing poliovirus RNA. Wimmer and his colleagues then used that synthetic RNA to make functioning polioviruses. But viruses are not living cells. No one has ever been able to make a living cell from its DNA--not even Craig Venter.

A virus is just RNA or DNA in a protein capsule. The viral RNA or DNA can't make more of itself, nor can it make the capsule. Viral RNA or DNA must first be put into a living cell (or, in the case of Wimmer's experiment, into an extract carefully prepared from living cells), because only the cell (or its extract) contains the complex molecular machinery needed to make more RNA or DNA and to manufacture the protein capsule.

By themselves, however, RNA and DNA are biologically inert. Only a living cell is alive, and in our experience, life always comes from life. That's why spontaneous generation doesn't happen. That's why origin-of-life researchers have not even come close to solving their problem. And that's why Venter and his team couldn't create life; they had to start with it. There is much more to living cells--even relatively simple cells--than is dreamt of in Arthur Caplan's philosophy.

In contrast to Caplan's exaggerated claims, CalTech biologist and Nobel laureate David Baltimore said that Venter has "overplayed the importance" of his results, which represent "a technical tour de force" rather than a scientific breakthrough. Venter "has not created life, only mimicked it," Baltimore said.

Boston University bioengineer James Collins called Venter's work: 
an important advance in our ability to re-engineer organisms, not make new life from scratch. Frankly, scientists don't know enough about biology to create life. Although the Human Genome Project has expanded the parts list for cells, there is no instruction manual for putting them together to produce a living cell. It is like trying to assemble an operational jumbo jet from its parts list--impossible. Although some of us in synthetic biology have delusions of grandeur, our goals are much more modest.

These realistic assessments probably wouldn't impress the anonymous author of The Economist article. "Pedants may quibble," the writer complains, that "the researchers had to use the shell of an existing bug to get that DNA to do its stuff."

Shell? But oh, what an amazing shell it is! And from that shell of life, what discoveries may come? Ay, there's the rub.

On I.D and agreeing to disagree.

Debating Common Ancestry
John G. West 

As those of us at Discovery Institute have emphasized for a long time, intelligent design is not incompatible with the idea that living things share a common ancestor. In other words, one can believe that nature displays evidence of intentional design, and still believe in common descent.

Indeed, I would argue that one of the forebears of the modern intelligent design movement is none other than Alfred Russel Wallace, who is credited with Darwin as co-discoverer of the theory of evolution by natural selection. Wallace believed that nature displayed powerful evidence of design by an overruling intelligence. Today, Discovery Institute has a number of affiliated scholars who similarly affirm the idea of common descent, including biologist Michael Behe and geneticist Michael Denton. Denton makes his views clear in his book Evolution: Still a Theory in Crisis, which Discovery Institute Press published earlier this year.

Of course, we have other affiliated scholars who are strongly critical of universal common descent, the claim that all living things are descended from one original primordial organism. I think that our diversity on this issue is a good thing.

You can see it on display in the recent, fascinating exchanges between ID proponents Cornelius Hunter (a biologist and Discovery Institute Fellow) and ID-supporter Vincent Torley, a gifted philosopher who writes at Uncommon Dissent. This type of robust exchange on the evidence for common descent is the sort of thing you would be hard pressed to find among supporters of modern Darwinism, either atheist or religious.

Although supporters of Darwinism typically try to claim the mantle of being fearless free-thinkers, many of them appear to have an exceptionally narrow tolerance for genuine diversity of thought, especially when it comes to allowing any debate on the scientific evidence relating to evolution. In my experience, this narrow tolerance for scientific debate relating to evolution is just as true among religious supporters of Darwin's theory as it is among secularists.


Indeed, I have come across many religious supporters of Darwin's theory who make common descent a litmus test on whether one is "anti-science" and who won't entertain any discussion of the scientific evidence. On this and other topics, I think it's the ID community that is showing the way.

The Watchtower Society's commentary on 1st and 2nd Kings

KINGS, BOOKS OF:

Books of the Holy Scriptures relating the history of Israel from the last days of King David until the release of King Jehoiachin from prison in Babylon.

Originally the two books of Kings comprised one roll called Kings (Heb., Mela·khimʹ), and in the Hebrew Bible today they are still counted as one book, the fourth in the section known as the Former Prophets. In the Greek Septuagint the Books of the Kings were called Third and Fourth Kingdoms, the Books of Samuel having been designated First and Second Kingdoms. In the Latin Vulgate these books were together known as the four books of Kings because Jerome preferred the name Regum (Kings), in harmony with the Hebrew title, to the literal translation of the Septuagint title Regnorum (Kingdoms). Division into two books in the Septuagint became expedient because the Greek translation with vowels required almost twice as much space as did Hebrew, in which no vowels were used until the second half of the first millennium of the Common Era. The division between Second Samuel and First Kings has not always been at the same place in the Greek versions. Lucian, for one, in his recension of the Septuagint, made the division so that First Kings commenced with what is 1 Kings 2:12 in our present-day Bibles.

Writing of the Books. Although the name of the writer of the books of Kings is not given in the two accounts, Scriptural indications and Jewish tradition point to Jeremiah. Many Hebrew words and expressions found in these two books appear elsewhere in the Bible only in Jeremiah’s prophecy. The books of Kings and the book of Jeremiah complement each other; events, as a rule, are briefly covered in one if they are fully described in the other. Absence of any mention of Jeremiah in the books of Kings, although he was a very prominent prophet, could be expected if Jeremiah was the writer, because his activities were detailed in the book bearing his name. The books of Kings tell of conditions in Jerusalem after the exile had begun, indicating that the writer had not been taken to Babylon, even as Jeremiah was not.—Jer 40:5, 6.

Some scholars see in the books of Kings what they consider to be evidence of the work of more than one writer or compiler. However, except for variation because of the sources used, it must be observed that the language, style, vocabulary, and grammar are uniform throughout.

First Kings covers a period of about 129 years, commencing with the final days of King David, about 1040 B.C.E., and running through to the death of Judean King Jehoshaphat in about 911 B.C.E. (1Ki 22:50) Second Kings begins with Ahaziah’s reign (c. 920 B.C.E.) and carries through to the end of the 37th year of Jehoiachin’s exile, 580 B.C.E., a period of about 340 years. (2Ki 1:1, 2; 25:27-30) Hence the combined accounts of the books of Kings cover about four and a half centuries of Hebrew history. As the events recorded therein include those up to 580 B.C.E., these books could not have been completed before this date, and because there is no mention of the termination of the Babylonian exile, they, as one roll, were undoubtedly finished before that time.

The place of writing for both books appears to have been, for the most part, Judah, because most of the source material would be available there. However, Second Kings was logically completed in Egypt, where Jeremiah was taken after the assassination of Gedaliah at Mizpah.—Jer 41:1-3; 43:5-8.

The books of Kings have always had a place in the Jewish canon and are accepted as canonical. There is good reason for this, because these books carry forward the development of the foremost Bible theme, the vindication of Jehovah’s sovereignty and the ultimate fulfillment of his purpose for the earth, by means of his Kingdom under Christ, the promised Seed. Moreover, three leading prophets, Elijah, Elisha, and Isaiah, are given prominence, and their prophecies are shown to have had unerring fulfillments. Events recorded in the books of Kings are referred to and elucidated elsewhere in the Scriptures. Jesus refers to what is written in these books three times—regarding Solomon (Mt 6:29), the queen of the south (Mt 12:42; compare 1Ki 10:1-9), and the widow of Zarephath and Naaman (Lu 4:25-27; compare 1Ki 17:8-10; 2Ki 5:8-14). Paul mentions the account concerning Elijah and the 7,000 men who did not bend the knee to Baal. (Ro 11:2-4; compare 1Ki 19:14, 18.) James speaks of Elijah’s prayers for drought and rain. (Jas 5:17, 18; compare 1Ki 17:1; 18:45.) These references to the actions of individuals described in the books of Kings vouch for the canonicity of these writings.

The books of Kings were largely compiled from written sources, and the writer shows clearly that he referred to these outside sources for some of his information. He refers to “the book of the affairs of Solomon” (1Ki 11:41), “the book of the affairs of the days of the kings of Judah” (1Ki 15:7, 23), and “the book of the affairs of the days of the kings of Israel” (1Ki 14:19; 16:14).

One of the oldest extant Hebrew manuscripts containing the books of Kings in full is dated 1008 C.E. The Vatican No. 1209 and the Alexandrine Manuscript contain the books of Kings (in Greek), but the Sinaitic Manuscript does not. Fragments of the books of Kings evidently dating from the B.C.E. period have been found in the Qumran caves.

The framework of these books shows that the writer or compiler gave pertinent facts about each king for the purpose of chronology and to reveal God’s estimate, favorable or unfavorable, of each king. The relationship of their reigns to the worship of Jehovah stands out as the most important factor. After considering the reign of Solomon, there is, with some exceptions, a general set pattern for describing each reign, as two parallel lines of history are interwoven. For the kings of Judah there is usually given first an introductory synchronism with the contemporaneous king of Israel, then the age of the king, the length of his reign, the place of rule, and the name and home of his mother, the latter being an item of interest and importance because at least some of the kings of Judah were polygamous. In concluding the account for each king, the source of the information, the burial of the king, and the name of his successor are given. Some of the same details are provided for each king of Israel, but the king’s age at the time of his accession and the name and home of his mother are not given. Information supplied in First and Second Kings has been very useful in the study of Bible chronology.—See CHRONOLOGY.

The books of Kings are more than just annals or a recital of events as in a chronicle. They report the facts of history with an explanation of their significance. Eliminated from the account, it seems, is anything that does not have direct bearing on the developing purpose of God and that does not illustrate the principles by which Jehovah deals with his people. The faults of Solomon and the other kings of Judah and Israel are not disguised but are related with the utmost candor.

Archaeological Evidence. The discovery of numerous artifacts has furnished certain confirmation that the books of Kings are historically and geographically accurate. Archaeology, as well as living proof today, confirms the existence of the cedar forests of Lebanon, from which Solomon obtained timbers for his building projects in Jerusalem. (1Ki 5:6; 7:2) Evidence of industrial activity has been found in the basin of the Jordan, where Succoth and Zarethan once stood.—1Ki 7:45, 46.

Shishak’s invasion of Judah in Rehoboam’s time (1Ki 14:25, 26) is confirmed by the Pharaoh’s own record on the walls of the temple of Karnak in Egypt. A black limestone obelisk of Assyrian King Shalmaneser III found at Nimrud in 1846 depicts perhaps an emissary of Jehu bowing before Shalmaneser, an incident that, though not mentioned in the books of Kings, adds testimony to the historicity of Israel’s King Jehu. The extensive building works of Ahab, including “the house of ivory that he built” (1Ki 22:39), are well attested by the ruins found at Samaria.

The Moabite Stone relates some of the events involved in King Mesha’s revolt against Israel, giving the Moabite monarch’s version of what took place. (2Ki 3:4, 5) This alphabetic inscription also contains the Tetragrammaton.

The name Pekah is found in an annalistic text credited to Tiglath-pileser III. (2Ki 15:27) The campaign of Tiglath-pileser III against Israel is mentioned in his royal annals and in an Assyrian building inscription. (2Ki 15:29) The name Hoshea has also been deciphered from inscriptions of Tiglath-pileser’s campaign.—2Ki 15:30; Ancient Near Eastern Texts, edited by J. Pritchard, 1974, pp. 282-284.

While some of Assyrian King Sennacherib’s engagements are mentioned in his annals, the angelic destruction of his army of 185,000 when it threatened Jerusalem is not mentioned (2Ki 19:35), and we would not expect to find in his boastful records an account of this overwhelming setback. Notable archaeological confirmation of the last statement in the books of Kings has been found in cuneiform tablets excavated at Babylon. These indicate that Jaʼukinu (Jehoiachin) was imprisoned in Babylon and mention that he was provided with rations from the royal treasury.—2Ki 25:30; Ancient Near Eastern Texts, p. 308.

Fulfillments of Prophecy. The books of Kings contain various prophecies and point to striking fulfillments. For example, 1 Kings 2:27 shows the fulfillment of Jehovah’s word against the house of Eli. (1Sa 2:31-36; 3:11-14) Prophecies regarding Ahab and his house were fulfilled. (Compare 1Ki 21:19-21 with 1Ki 22:38 and 2Ki 10:17.) What was foretold concerning Jezebel and her remains came true. (Compare 1Ki 21:23 with 2Ki 9:30-36.) And the facts of history confirm the veracity of the prophesied destruction of Jerusalem.—2Ki 21:13.

Among the many points highlighted in the books of Kings is the importance of adherence to Jehovah’s requirements and the dire consequences of ignoring his just laws. The two books of Kings forcefully verify the predicted consequences of both obedience and disobedience to Jehovah God.

[Box on page 171]

HIGHLIGHTS OF FIRST KINGS

A concise summary of the history of both the kingdom of Judah and the kingdom of Israel from the last days of David until the death of Jehoshaphat

Originally the first book of Kings was part of one scroll with Second Kings

Solomon is known for outstanding wisdom at the start of his rule, but he ends up in apostasy

Nathan, by decisive action, blocks Adonijah’s attempt to be king in Israel; Solomon is enthroned (1:5–2:12)

Asked by Jehovah what he desires, Solomon requests wisdom; he is additionally granted riches and glory (3:5-15)

Divinely given wisdom is evident in Solomon’s handling of the case of two prostitutes, each claiming to be the mother of the same baby boy (3:16-28)

King Solomon and Israel under his rule prosper; the king’s unparalleled wisdom is world famous (4:1-34; 10:14-29)

Solomon builds Jehovah’s temple and later a palace complex; then all the older men of Israel gather for the inauguration (5:1–8:66)

Jehovah sanctifies the temple, assures Solomon of permanence of the royal line, but warns against unfaithfulness (9:1-9)

The queen of Sheba comes to see Solomon’s wisdom and prosperity for herself (10:1-13)

In old age, Solomon is influenced by his many foreign wives and goes after foreign gods (11:1-8)

The nation is split in two; calf worship is instituted to prevent those in the northern kingdom from going up to Jerusalem

Because of Solomon’s apostasy, Jehovah foretells division of the nation (11:11-13)

After Solomon’s death, his son Rehoboam threatens to impose a heavier yoke on the people; ten tribes revolt and make Jeroboam king (12:1-20)

Jeroboam establishes worship of golden calves in the northern kingdom to prevent his subjects from going to Jerusalem for worship and possibly wanting to reunite the kingdom (12:26-33)

The southern kingdom, Judah, has both good kings and bad ones

Rehoboam and Abijam after him allow detestable false worship (14:21-24; 15:1-3)

Abijam’s son Asa and his son Jehoshaphat actively promote true worship (15:9-15; 22:41-43)

The northern kingdom, Israel, is marred by power struggles, assassinations, and idolatry

Jeroboam’s son Nadab becomes king; Baasha assassinates him and seizes the throne (15:25-30)

Baasha’s son Elah succeeds to the throne and is assassinated by Zimri; Zimri commits suicide when facing defeat by Omri (16:6-20)

Omri’s victory leads to civil war; Omri finally triumphs, becomes king, and later builds Samaria; his sins are even worse than those of earlier kings (16:21-28)

Ahab becomes king and marries the daughter of Ethbaal, king of the Sidonians; he introduces Baal worship into Israel (16:29-33)

Wars between Judah and Israel end with an alliance

Wars take place between Jeroboam and both Rehoboam and Abijam; Baasha fights against Asa (15:6, 7, 16-22)

Jehoshaphat makes an alliance with Ahab (22:1-4, 44)

Jehoshaphat and Ahab battle together against Ramoth-gilead; Ahab is killed (22:29-40)

Prophetic activity in Israel and Judah

Ahijah foretells ripping of ten tribes away from David’s house; later he proclaims Jehovah’s judgment against Jeroboam (11:29-39; 14:7-16)

Shemaiah conveys Jehovah’s word that Rehoboam and his subjects should not fight against the rebellious ten tribes (12:22-24)

A man of God announces Jehovah’s judgment against the altar for calf worship at Bethel (13:1-3)

Jehu the son of Hanani pronounces Jehovah’s judgment against Baasha (16:1-4)

Elijah foretells a prolonged drought in Israel; during the drought, he miraculously extends the food supply of a widow and resurrects her son (17:1-24)

Elijah proposes a test on Mount Carmel to determine who is the true God; when Jehovah is proved true, the Baal prophets are killed; Elijah flees for his life from Ahab’s wife Jezebel, but Jehovah sends Elijah to anoint Hazael, Jehu, and Elisha (18:17–19:21)

Micaiah foretells Ahab’s defeat in battle (22:13-28)

[Box on page 172]

HIGHLIGHTS OF SECOND KINGS

Continuation of the history of Judah and of Israel begun in First Kings; it reaches to the destruction of Samaria and then of Jerusalem, due to unfaithfulness

The writing of it was likely completed in Egypt about 27 years after Jerusalem’s destruction by Babylon

After Elijah, Elisha serves as Jehovah’s prophet

Elijah predicts Ahaziah’s death; he also calls down fire upon two disrespectful military chiefs and their companies of 50 sent to get the prophet (1:2-17)

Elijah is taken away in a windstorm; Elisha receives his official garment (2:1-13)

Elisha divides the Jordan and heals water in Jericho; his inspired advice saves the allied armies of Israel, Judah, and Edom from perishing for lack of water and results in defeat of Moabites; he increases a widow’s oil supply, resurrects a Shunammite woman’s son, renders poisonous stew harmless, multiplies a gift of bread and grain, heals Naaman of leprosy, announces that Naaman’s leprosy would come upon greedy Gehazi and his offspring, and causes a borrowed axhead to float (2:14–6:7)

Elisha warns the king of Israel in advance of surprise attacks by the Syrians; a Syrian force comes to seize him but is stricken with temporary mental blindness; the Syrians besiege Samaria, and Elisha is blamed for the resulting famine; he foretells the end of the famine (6:8–7:2)

The commission given to Elijah is completed when Elisha tells Hazael that he will become king of Syria and sends a messenger to anoint Jehu as king over Israel (8:7-13; 9:1-13)

Jehu acts against Ahab’s house, eradicating Baal worship from Israel (9:14–10:28)

Elisha, on his deathbed, is visited by Jehu’s grandson King Jehoash; he foretells three victories over Syria (13:14-19)

Israel’s disrespect for Jehovah leads to exile in Assyria

The calf worship started by Jeroboam continues during the reigns of Jehu and his offspring—Jehoahaz, Jehoash, Jeroboam II, and Zechariah (10:29, 31; 13:6, 10, 11; 14:23, 24; 15:8, 9)

During Israel’s final days, King Zechariah is assassinated by Shallum, Shallum by Menahem, Menahem’s son Pekahiah by Pekah, and Pekah by Hoshea (15:8-30)

During Pekah’s reign, Tiglath-pileser III, king of Assyria, exiles many Israelites; in the ninth year of Hoshea, Samaria is destroyed and Israel is taken into exile because of disrespecting Jehovah; Israel’s territory is populated by other peoples (15:29; 17:1-41)

Religious reforms in Judah bring no lasting change; Babylon destroys Jerusalem and takes God’s people into exile

Jehoram of Judah marries Athaliah, daughter of Ahab and Jezebel; Jehoram apostatizes, as does his son Ahaziah after him (8:16-27)

When Ahaziah dies, Athaliah tries to kill off the seed of David so that she herself can rule; Jehoash, son of Ahaziah, is rescued by his aunt and eventually made king; Athaliah is killed (11:1-16)

As long as High Priest Jehoiada lives and advises him, Jehoash restores true worship, but ‘sacrificing on the high places’ persists during his reign and that of his successors—Amaziah, Azariah (Uzziah), and Jotham (12:1-16; 14:1-4; 15:1-4, 32-35)

Jotham’s son Ahaz practices idolatry; Ahaz’ son Hezekiah makes good reforms, but these are undone by the subsequent bad reigns of Manasseh and Amon (16:1-4; 18:1-6; 21:1-22)

Amon’s son Josiah undertakes firm measures to rid the land of idolatry; he is killed in a battle with Pharaoh Nechoh (22:1–23:30)


Judah’s last four kings are unfaithful: Josiah’s son Jehoahaz dies in captivity in Egypt; Jehoahaz’ brother Jehoiakim reigns after him; Jehoiakim’s son and successor Jehoiachin is carried into Babylonian exile; Jehoiakim’s brother Zedekiah reigns until Jerusalem is conquered by the Babylonians and most survivors of the conquest are taken into exile (23:31–25:21)

The real world continues to school scientists.

Why Does Biology Still Have the Ability to Surprise Us?
Ann Gauger 

About forty years ago, a biochemistry professor told my class that now that the genetic code had been worked out and the lac operon discovered, the only thing left for us students was to work out the details. Boy, was he wrong!

If there's one thing I've learned over the last forty years, it is that every ten years or so the biological apple cart is upset, and a long-established "fact," an assumption based on incomplete knowledge, is proven to be wrong.

I am sure you can find textbooks that still include some of these old "facts." Below is a partial list of those assumptions that have had to be revised, and some that are still under discussion.

1. Old fact: DNA is stable and genes don't hop around.

New discovery: Mobile genetic elements can hop from place to place in the DNA, duplicating themselves and changing gene expression. Sometimes they carry surrounding genes with them.

2. New "old" fact: Mobile genetic elements are selfish DNA that replicate themselves without benefit to the organism, thus cluttering the genome with garbage.

New discovery: Mobile genetic elements appear to be involved in the regulation of many important genes, and their distribution in the genome is nonrandom.

3. Old fact: A gene is an uninterrupted stretch of DNA that encodes a single protein. Genes are arranged like beads on a string.

New discovery: Genes in eukaryotes are interrupted, sometimes multiple times, by non-coding sequences called introns. The introns get spliced out of the messenger RNA before the message is translated. Because of splicing, one gene can produce many different but related proteins.

New discovery: Genes can overlap one another on the same stretch of DNA, on the same strand or on opposite strands. Thus one piece of DNA can produce multiple different proteins.

Take home message: 1 stretch of DNA ? 1 gene ? 1 protein

4. Old fact: There are only 3 forms of RNA: messenger RNA, transfer RNA, and ribosomal RNA.

New discovery: New classes of short and long RNA transcripts serve to regulate gene expression.

5. Old fact: Pseudogenes are useless broken remnants of former genes.

New discovery: Not all pseudogenes are useless. Pseudogenes can be transcribed, and their products can be used to regulate the expression of their full-length sister genes. Related to #4.

6. Old fact: The genome is full of junk, the remnants of wasteful evolutionary processes and selfish DNA (see #1, #2 and #5 above).

New discovery: "Junk" DNA isn't junk after all. It has many important regulatory functions in the cell.

Revolutionary discoveries like these often happen when someone tries something new, stumbles across some contrary evidence, and begins to question the validity of an established "fact." The results have been astonishing -- and have even won the Nobel Prize. Because of these discoveries we have gained a new and better, though still imperfect understanding of biology.

Why should we still have the "facts" wrong? After all, we've been studying biology for sixty years after the discovery of DNA's structure, and 50 years after the code was worked out.

Perhaps a better question would be, "Why does biology have the ability to surprise us?" It's because life is much more sophisticated than anything we can imagine. We look at biology from our very limited perspective, and at almost every turn we are puzzled or amazed. You can even read it in the understated, carefully couched language of published articles, where words like "surprising" or "unexpected" appear often.

Remember that biochemistry professor who claimed that all the important work in biology was done? He also said we'd never find gears or wheels in biology. Poor guy!

You'd think that scientists would be more cautious about our pronouncements if we can be so wrong. But we are only human, like everyone else, and our accepted "facts" are often deeply entrenched in our thinking. In truth, though, only one rock solid "fact" exists -- that some time in the not too distant future a strongly held "fact" will be proven mistaken.


Like Darwinian evolution, perhaps?

Unhyped.

Richard Lenski and Citrate Hype -- Now Deflated
Michael Behe 

Dishonesty comes in degrees, from the white lie told to spare another's feelings to criminal fraud for one's own financial gain. Somewhere in the middle lies hype in science. Certainly a bit of innocent, accentuate-the-positive spinning of research results can help a scientist catch people's attention. Unfortunately, that can escalate into hucksterism that seriously exaggerates the importance of the work.

Most scientists aren't even tempted to try it, because most areas of research aren't sexy enough to pull it off. It is a problem, however, for those who work on topics that catch the news media's attention: cures for cancer; cloning; grand theories of the universe; and, of course, evolution.

Which brings us to Michigan State's Richard Lenski. As longtime readers of Evolution News and Views well know, to study evolution, for more than 25 years Lenski's lab has continuously grown a dozen lines of the bacterium E. coli in small culture flasks, letting them replicate for six or seven generations per day and then transferring a portion to fresh flasks for another round of growth. The carefully monitored cells have now gone through more than 60,000 generations, which is equivalent to over a million years for a large animal such as humans. (It's dubbed the Long Term Evolution Experiment -- LTEE.) As I've written before, the work itself is terrific. However, the implications of the work are often blown seriously out of proportion by a cheerleading science news media eager for stories to trumpet.

In 2008 Lenski's group reported that after more than 15 years and 30,000 generations of growth one of the E. coli cell lines suddenly developed the ability to consume citrate, which for technical reasons had been present in the liquid culture medium. Later work by the Michigan State team showed the ability was due to the duplication and rearrangement of a gene for a protein that normally imports citrate into the cell, but only when no oxygen is present. The mutation allowed the protein to work when oxygen was present, as it was throughout the LTEE.

It was an interesting, if modest, result -- a gene had been turned on under conditions where it was normally turned off. But the authors argued it might be pretty important. In their paper they wrote that the mutant's ability could be the result of "historical contingency" -- that is, a rare, serendipitous event that might alter the course of evolution. They also remarked that, since an inability to use citrate in the presence of oxygen had been a characteristic used to help define E. coli as a species, perhaps the mutation marked the beginning of the evolution of a brand new species.

One scientist who thought the results were seriously overblown was Scott Minnich, professor of microbiology at the University of Idaho and -- full disclosure -- a colleague of mine as a Fellow at Discovery Institute's Center for Science & Culture. Minnich knew that decades ago the microbiologist Barry Hall had isolated an E. coli mutant that could also use citrate after only a few weeks of growth (also cited in Lenski's paper), and that other studies had shown mutants could be isolated rapidly if they were selected directly -- that is, if they were grown where the only available food source was the selecting substrate such as citrate, rather than a mixture of the selecting substrate plus glucose, as in Lenski's experiment.

So Minnich's lab re-did the work under conditions he thought would be more effective. The bottom line is that they were able to repeatedly isolate the same mutants Lenski's lab did as easily as falling off a log -- within weeks, not decades. In an accompanying commentary highlighting the Idaho group's paper in the Journal of Bacteriology, the prominent UC Davis microbiologist John Roth and his colleague Sophie Maisnier-Patin agreed that Lenski's "idea of 'historical contingency' may require reinterpretation."

Richard Lenski was not pleased. Although in a response on his blog he acknowledged up front that the Idaho group's science was "fine and interesting," he insisted that yes the mutation was too historically contingent. Roth and Maisner-Patin's comments to the contrary supposedly represented "a false dichotomy." After all, historical contingency just "means that history matters," and whether Lenski's cells developed the mutation clearly depended on how they had been treated in his lab. Ipso facto, it was contingent.

But of course it's vacuous to say simply that "history matters." Any near-certain outcome can be prevented if necessary conditions for it to occur aren't present. A ball will always roll down a hill -- unless someone puts a barrier in front of it. The fact that the Minnich lab easily and repeatedly obtained the same results with multiple bacterial strains and growth conditions shows they are not some special example of historical contingency, if that phrase has any nontrivial meaning at all. Rather, under the right conditions it's a humdrum, repeatable result.

Lenski also tried to split hairs over the question of speciation. He faulted Minnich for writing skeptically of Lenski's citrate mutation, "This was interpreted as a speciation event." Lenski countered that in their initial paper his group had only been wondering out loud if the mutant would "eventually become" a distinct species. It's a process, not an event, you see. But Minnich's group had cited two publications in their paper that backed up their take on things. The first was a review paper where Lenski himself described the experiment and then remarked coyly, "That sounds a lot like the origin of species to me. What do you think?" (Wink, wink, nudge, nudge.)

The second was Elizabeth Pennisi's puff piece in Scienceon the LTEE in 2013 where she wrote (presumably after consulting with Lenski) "because one of E. coli's defining characteristics is the inability to use citrate for energy in the presence of oxygen, the citrate-consuming bacteria could be seen as a new species." If Lenski plays fast and loose with the public's perceptions of his work, he shouldn't complain when he's called on it.

In a disgraceful move, Lenski impugned Scott Minnich's character. Since he's a "fellow of the Discovery Institute" sympathetic with intelligent design, the skeptical discussion in Minnich's paper (which underwent thorough peer review by an excellent journal that chose to highlight it with commentary from eminent scientists) "suggests an ulterior nonscientific motive." (Apparently Lenski himself can speculate about all sorts of grand possibilities, ulterior-motive free.) You see, the Idaho scientists had the temerity to write, "A more accurate, albeit controversial, interpretation of the LTEE is that E. coli's capacity to evolve is more limited than currently assumed."

Well, perhaps someone personally involved in the work might see unending possibilities. But what should an objective observer call a situation where the exact same mutations occur time and time again? -- Limitless? Where a problem has no other solution except the one found? -- Flexible? Where deletion of either of the genes (citT or dctA) involved in the mutation prevents citrate utilization, as Minnich's group showed? -- Resourceful? Where none of the other thousands of genes in the cell can substitute? -- Inventive? Where even the easily obtainable mutation has apparently been of little use in nature? Earth-shaking?

With regard to citrate evolution, the Minnich lab's results have revealed E. coli to be a one-trick pony. And, as I've written previously, in other respects Lenski's own work has shown that E. coli evolves in his lab overwhelmingly by damaging loss-of-function and decrease-of-function mutations.


If that isn't "more limited than currently assumed," it's close enough. The take-home lesson is that, although the unvarnished work itself is great, the hype surrounding the LTEE has seriously misled the public and the scientific community. It's far past time that a pin was stuck in its balloon.

On Darwinian storytelling re: The emergence of the human race.

Does the Evidence Point to Mankind's Fully Natural Origin?
Denyse O'Leary 

n 2009, Mayor Bloomberg of New York held a special ceremony to laud the recently discovered fossil Ida (pictured above), said to be the "missing link" between humans and other primates. Bloomberg was

standing beside Ida's glass box, his arm around the shoulders of a school girl who was wearing a T-shirt with the TV tie-in logo: "The Link. This changes everything."

The Guardian's correspondent quipped, "The main thing Bloomberg was presumably hoping this would change was his prospects of winning an unprecedented third term as New York mayor." Bloomberg did win, but the Ida fossil was not so lucky; claims for it were shortly retrSignificantly, Bloomberg thought Ida improved his re-election chances before the fossil experts had spoken. And that she wouldn't have harmed his career if she failed their tests. Real and imagined "human evolution" is now so integral to our culture that demand outpaces authenticity. The disappointing history of Sahelanthropus, Orrorin, and Ardi, all hailed in 2001 as human ancestors, attests to the frustrating search for "missing links." Sediba, another supposed ancestor, fared no better in 2013. A science writer at Wired, not known for intelligent-design sympathies, derides the ceaseless buzz as "ancestor worship."

If he's right, we worship what we do not know. Pop culture's Ascent of Man gives no hint of the disorganization and confusion of current human evolution studies.

Late last year, it was announced that the oldest assumed human sequence then published (400 kya) baffles experts because it belongs to an unknown group, one more like Denisovans (an extinct type of human) than Neanderthals. The DNA results from the "Pit of Bones" site in Spain were described as baffling (Nature), perplexing (BBC), hard to make sense of (The Scientist ), don't quite know what to make of it (New Scientist), and creating new mysteries (New York Times) instead of neatly clarifying human evolution. October of that year had already brought the news that the human remains found at Dmanisi, Georgia, showed that many "separate species of human ancestors" never really existed and "may now have to be wiped from the textbooks." "Separate species" of human ancestors (that nonetheless interbreed)? There are many definitions of "species," so the term can be flung around freely, if accompanied by suitable credentials.

One researcher in a discipline that tries to keep track of the general direction of findings (theoretical anthropogeny) recently found no consensus as to when the human race arose, after he offered colleagues a spread ranging from ~60,000 to ~500,000 years ago. In this context, it hardly seems worth mentioning that no known hominin (assumed human) is clearly an ancestor of both Neanderthals and current humans.

For all practical purposes, today's humans are orphans, seeking our roots via scraps and artifacts, many of unknown authenticity or significance. If we are convinced that any discovery we make is better than uncertainty, we are in a suitable frame of mind to explore the questions.

When interpreting accounts, we need to keep in mind several narrative biases that can become distortions. When it comes to us lay readers, the story already incorporates these distortions. Usually, we won't know what has been put in or left out in order to fit the narrative bias -- unless a new find provokes a crisis in which the facts just will not fit the mold. We saw several examples of that above, from 2013.

The controlling bias is fully natural evolution: Humans evolved over a long period of time from a shrew-like creature into our current state. There is much less evidence for this proposition than the TV documentaries would have us assume. Granted, the evidence is a bit better than for the multiverse (which obliterates the very idea of evidence). It's also a bit better than for origin of life by purely natural means, which is impossible in the known universe.

At least some parts of human evolution might have happened according to purely natural laws or the vagaries of circumstances. Put another way, we could assume so for the sake of argument, without immediately finding ourselves in trouble with the rules for logic or the evaluation of evidence. We will, however, find ourselves dealing with one very large problem indeed: Human evolution includes the origin of the human mind. Theoretical physicist Roger Penrose has said:

If you look at the entire physical cosmos, our brains are a tiny, tiny part of it. But they're the most perfectly organized part. Compared to the complexity of a brain, a galaxy is just an inert lump.
"Why aren't we more like chimps?," New Scientist asked plaintively in 2012, encapsulating the current perspective in six words, and implicitly ruling out alternative approaches to enquiry. Well, one way we are different is that we acquired a history, a history of choices made, skills learned, and insights passed on. Let us see what our found collection of scraps and artifacts can tell us.acted.

On science and metaphysics

One Long Argument -- Responding to VJ Torley on Human-Ape Common Descent
Cornelius Hunter 

At Uncommon Descent, VJ Torley has analyzed my criticism of S. Joshua Swamidass's recent article, "Evidence and Evolution." From this analysis, one would think that I mercilessly berated a poor fellow who was merely attempting to "extend an olive branch to creationists." After all, nowhere did Swamidass belittle or ridicule his opponents, and nowhere was there so much as a trace of smug superiority. And the guy is a Christian, not some atheistic reductionist. In fact, Swamidass does not even draw any conclusions in his article.

This is how Torley begins his article and unfortunately it gives those who have not read the two articles the wrong impression. I gave a lengthy, fact-based, scientific criticism of Swamidass's claims that was not dismissive or sarcastic. I did not accuse of Swamidass of belittling or ridiculing anyone, nor did I accuse him of smugness, academic or otherwise. And I did not question his religious beliefs. All of this was injected by Torley.

As for drawing conclusions, yes, contrary to what Torley says, Swamidass draws conclusions. He states in no uncertain terms that the evolutionary story "is by far the best scientific explanation of our origins." In fact, the evidence is stunning:

What is the evidence for human common ancestry with apes? The strongest evidence is a series of stunningly accurate predictions about human genomes that have been confirmed in recent decades as the human and ape genomes have been sequenced.
Swamidass goes on to suggest that microevolution is sufficient to explain the evolution of humans from a small, ape-like creature.

Throughout, Swamidass uses a scientist-versus-theologian, Warfare Thesis perspective. Scientists simply refer to the data whereas theologians must adjust their sights, drop their denial, and grapple with the undeniable truths of evolution. To object is futile and attempts to explain humans as a product of design are "lawyerly":

A common lawyerly objection to this evidence is that these similarities are "equally" explained by common "design." As scientists, our response to this objection is data.
Perhaps the theologian "could look for errors in the scientific analyses," but even that would be futile:

Still, even if he [the theologian] found standing for quibbles here and there, the overall picture would remain the same and the evidence against common ancestry, at best, would be subtle and debatable.
Swamidass presents a story in order to "reduce the fear some feel when encountering evidence that might contradict their understanding of the Bible."

This is all Warfare Thesis, and Torley finds it to be "irenic in tone, easy to follow, deeply learned, and absolutely right."

On the other hand Torley throws occasional ad hominems my way and finds that my critique of Swamidass's piece was "polemical and curtly dismissive in tone." In fact, my criticism was about Swamidass's arguments. I pointed out that his scientific claims were erroneous and that ultimately his arguments relied on metaphysical claims.

This is not to say there cannot be improvements in my article. It is, after all, a blog post. I'm thankful for feedback and corrections to my errors. But Torley's casting of the two articles is simply a misrepresentation. It seems that his criticism of my post is, in fact, more applicable to his article.

What About the Science?

Torley next castigates me for ignoring the main scientific evidence Swamidass presents. And what is Torley referring to? A series of references Swamidass made. So instead of addressing the key scientific claims made by Swamidass (which I did), I am supposed to do an expansive analysis on several references Swamidass provided as backup.

In fact I was planning on getting to those references at some point, time permitting, as they are yet more examples of failed science. But Torley's requirements and criticisms are unrealistic.

Torley next quotes from one of Swamidass's references, imagines what my response would be, and argues with it. This is getting silly.

Torley finishes with a series of erroneous rebuttals, ad hominems, and straw-man arguments. To be sure, Torley makes some good tangential points, but they are unfortunately the minority.

Not surprisingly Torley shares Swamidass's theological convictions, which underwrite their claims. Their contrastive reasoning, if correct, proves their case. As Torley writes:

On a special creationist account of human origins, there is absolutely no reason to expect that humans would have what appear to be the remains of genes used for making egg yolks in their DNA -- just as there is no particular reason to expect that humans would be more genetically similar to chimps than rats are to mice -- or for that matter, than foxes are to wolves, or horses are to donkeys. [Emphasis in original.]
No reason. If Torley is correct here then, yes, we can safely conclude for evolution. Likewise:

Reasoning on Bayesian grounds, these striking and singular facts have a high probability on the hypothesis of common descent, but are surprising (and hence improbable) on a hypothesis of separate creation. One can only conclude that these facts lend scientific support to the hypothesis of common descent.
True enough. Such reasoning is perfectly valid, but it hinges on metaphysical premises. From a scientific perspective, evolution and common descent are unlikely to say the least, but from a metaphysical perspective, they are compelling.


Religion drives science, and it matters.

How the case for design is as plain as the nose on your face

Smelling Design
Evolution News & Views

How's this for an admission that design principles motivate scientific progress?

For an engineer, successful design of a new product needs to meet multiple objectives such as maximizing targeted mechanical performance and minimizing the cost. Some of these objectives are incompatible, thus tradeoffs are necessary. Similarly, living organisms are also constantly ... optimizing multiple objectives such as growth rate and resistance to environmental fluctuations. A central task for systems biology is to unravel the corresponding mechanisms, or the design principles ultimately determined..., especially how a system prioritizes the multiple objectives and makes necessary compromises.
That's a great quote except for the parts we left out. In the first ellipsis, the authors of a paper in PNAS insert these words: "[are also constantly] under selection pressure to maximize their fitness to the environment through [optimizing]..." The second ellipsis adds, "by evolution." But since engineers are neither under the pressure of natural selection nor working by blind chance, the extraneous words destroy the comparison, and thereby contribute nothing to the meaning.

The paper deals with an interesting problem in biology. Our noses contain millions of olfactory sensory neurons (OSNs). Each neuron expresses one and only one type of olfactory receptor (OR, a molecular machine that recognizes a particular odor molecule). There are hundreds, in some animals thousands, of different receptor types. How does each receptor get its fair share in the distribution? It's "one of the most intriguing problems in neurobiology," the authors say; "how can both monoallelic and diverse expression of OR be ensured at the same time?"

The answer "remains elusive after several decades of intensive investigations" -- until one thinks like an engineer. At a key point in the paper, despite other attestations about evolution, they make their breakthrough with these words: "Then from an engineering perspective, a better design to achieve single-allele activation is..." and so forth [emphasis added]. The body hits the optimization target successfully just like a good engineer. Actually, it does it better. Their simple model, flowchart and all, is less sophisticated than the nose itself.

The final paragraph nicely states the centrality of design principles in their research (and says nothing more about evolution):

In summary, we have constructed and analyzed a comprehensive model that revealed a mechanism for achieving diverse and monoallelic OR gene expression. A proper combination of mechanisms, but none of the individual one, can achieve the desired diverse and monoallelic OR expression. Given that multiobjective optimization is ubiquitous in biological systems, this synergetic and sequential application of different mechanisms is likely to be a general design principle on biological process regulation, and shed light on problems in other fields as well. This work aims at using a minimal model to reveal the essential elements that regulate the OR selection process. For example, [four examples given].... Future studies will reveal these possible fine-tuning elements and address its implications in other processes of gene regulations.
A statement from the University of Pittsburgh about this paper doesn't mention design or evolution, but summarizes the principle finding as "a basic physics principle called cooperativity, in which elements in a system influence the behavior of one another rather than function independently." The synergy between neurons the scientists witnessed gave them the chills. "We are amazed that nature has solved the seemingly daunting engineering process of olfactory receptor expression in such a simple way," one said.

Designed Winnowing

Another paper, this one in Current Biology, addresses the same problem from another angle. "A genetic approach in mice reveals a new facet of odorant receptor (OR) regulation," the summary begins. "Adventitious expression of multiple ORs activates post-selection refinement (PSR)." As the neurons sort themselves out in the olfactory epithelium during development, failures occur. Some neurons, contrary to the rules, express more than one receptor. Don't worry; a cleanup crew is on hand to take care of them:

Here we used a genetic approach in mice to reveal a new facet of OR regulation that corrects adventitious activation of multiple OR alleles, restoring monogenic OR expression and unique neuronal identity. Using the tetM71tg model system, in which the M71 OR is expressed in >95% of mature OSNs and potently suppresses the expression of the endogenous OR repertoire, we provide clear evidence of a post-selection refinement (PSR) process that winnows down the number of ORs. We further demonstrate that PSR efficiency is linked to OR expression level, suggesting an underlying competitive process and shedding light on OR gene switching and the fundamental mechanism of singular OR choice.
This paper had no use for Darwinian theory. The "selection" they speak of is not natural selection, but rather the initial choice of OR that each OSN expresses. How could a blind process know that expressing multiple ORs on the same neuron is a problem? How could it know what needs to be winnowed down? The paper calls this "Cleaning Up After Feedback." It sounds designed. "The process we describe here may represent a 'failsafe' mechanism," they say, when the normal process doesn't generate a single outcome like it's supposed to (e.g., one OR per neuron). Their summary explains why that might happen, and how the body is prepared to deal with it:

OR regulation generates >2,000 transcriptional outcomes, endowing an equal number of OSN identities. This extreme selectivity results from a slow initial phase, when individual OR alleles are infrequently activated, followed by a feedback stage halting the process and preserving singular choice. Mathematical modeling has determined parameters for activation and feedback that ensure a high probability of singular expression. These analyses also defined a failure rate, when activation proceeds too quickly, or feedback proceeds too slowly, resulting in neurons expressing multiple ORs. OSNs are unlikely to use feedback suppression to restore singular OR expression once more than one allele is activated. We have revealed a post-selection refinement (PSR) mechanism, which restores singular OR expression and unique neuronal identity.
This is a nice supplement to a previous article here on olfaction two months ago, where we learned how individual olfactory receptors (ORs) respond to not only the shape but vibrational energies of odor molecules, and then took a look down the line at the olfactory bulb to see how the switchboard maintains its complex wiring. Those were design features of the operational adult nose. Now, we see that the design principles of optimization, feedback, and refinement are at work in the initial setup stages of the neurons and their receptors. "From an engineering perspective," it's clearly design all the way down.

But Wait, There's More

Yes, another recent paper shows a nose for "design principles" without mentioning evolution. This paper from Harvard, published in PNAS, uses the phrase "design principle" three times. The authors wanted to understand how a relatively small number of receptors can produce so many scent sensations. Humans only have about 300 ORs but can discriminate at least 2,100 odorant molecules. Other animals, like dogs, have much higher sensitivity. How is this possible? It's by design. "Such remarkable molecular discrimination is thought to use a combinatorial code," we know from earlier studies. Once again, we find optimization (an intelligent design science) at work. The receptor arrays are optimized for natural odor statistics, these scientists discovered:

We study a simple model of the olfactory receptors from which we derive design principles for optimally communicating odor information in a given natural environment. We use these results to discuss biological olfactory systems, and we propose how they can be used to improve artificial sensor arrays.
There you have it. Not only do the authors finding design principles useful for understanding the nose, they look forward to how to copy those principles for artificial noses. The optimization, by the way, continues all the way to the brain:

The activity of a single glomerulus is thus the total signal of the associated receptor type, so the information about the odor is encoded in the activity pattern of the glomeruli. This activity pattern is interpreted by the brain to learn about the composition and the concentration of the inhaled odor. We here study how receptor arrays can maximize the transmitted information.
Using an "information theoretic approach" to quantify how well a receptor array matches the odor statistics in the environment, they even make predictions:

Using an information theoretic model, we show that a receptor array is optimal for this task if it achieves two possibly conflicting goals: (i) Each receptor should respond to half of all odors and (ii) the response of different receptors should be uncorrelated when averaged over odors presented with natural statistics. We use these design principles to predict statistics of the affinities between receptors and odorant molecules for a broad class of odor statistics. We also show that optimal receptor arrays can be tuned to either resolve concentrations well or distinguish mixtures reliably. Finally, we use our results to predict properties of experimentally measured receptor arrays.

Naturally, biological noses, whether in humans or fruit flies, with their "remarkable molecular discrimination" abilities, vastly outperform the sensitivities of "artificial nose" devices created so far. Codes -- optimization -- information: design principles are propelling research into the secrets inside your nostrils.

Epistemology vs. Darwin.

Evolution May Obscure Reality, Says a Cognitive Scientist and Evolutionist

Sarah Chaffee

Writing here last month, I explained why Darwinian theory directly undermines UC Berkeley psychologist Tania Lombrozo's argument that our reasoning may be getting better because science is getting better. In truth, naturalistic evolution erodes confidence in human reasoning -- the basis of science.

But it's not only evolution skeptics who realize this. For an article in The Atlantic, Amanda Gefter interviewed UC Irvine cognitive scientist Donald D. Hoffman ("The Case Against Reality"):

Gefter: People often use Darwinian evolution as an argument that our perceptions accurately reflect reality. They say, "Obviously we must be latching onto reality in some way because otherwise we would have been wiped out a long time ago. If I think I'm seeing a palm tree but it's really a tiger, I'm in trouble."

Hoffman: Right. The classic argument is that those of our ancestors who saw more accurately had a competitive advantage over those who saw less accurately and thus were more likely to pass on their genes that coded for those more accurate perceptions, so after thousands of generations we can be quite confident that we're the offspring of those who saw accurately, and so we see accurately. That sounds very plausible. But I think it is utterly false. It misunderstands the fundamental fact about evolution, which is that it's about fitness functions -- mathematical functions that describe how well a given strategy achieves the goals of survival and reproduction. The mathematical physicist Chetan Prakash proved a theorem that I devised that says: According to evolution by natural selection, an organism that sees reality as it is will never be more fit than an organism of equal complexity that sees none of reality but is just tuned to fitness. Never.

Gefter: You've done computer simulations to show this. Can you give an example?

Hoffman: Suppose in reality there's a resource, like water, and you can quantify how much of it there is in an objective order -- very little water, medium amount of water, a lot of water. Now suppose your fitness function is linear, so a little water gives you a little fitness, medium water gives you medium fitness, and lots of water gives you lots of fitness -- in that case, the organism that sees the truth about the water in the world can win, but only because the fitness function happens to align with the true structure in reality. Generically, in the real world, that will never be the case. Something much more natural is a bell curve -- say, too little water you die of thirst, but too much water you drown, and only somewhere in between is good for survival. Now the fitness function doesn't match the structure in the real world. And that's enough to send truth to extinction. For example, an organism tuned to fitness might see small and large quantities of some resource as, say, red, to indicate low fitness, whereas they might see intermediate quantities as green, to indicate high fitness. Its perceptions will be tuned to fitness, but not to truth. It won't see any distinction between small and large -- it only sees red -- even though such a distinction exists in reality.

Gefter: But how can seeing a false reality be beneficial to an organism's survival?

Hoffman: There's a metaphor that's only been available to us in the past 30 or 40 years, and that's the desktop interface. Suppose there's a blue rectangular icon on the lower right corner of your computer's desktop -- does that mean that the file itself is blue and rectangular and lives in the lower right corner of your computer? Of course not. But those are the only things that can be asserted about anything on the desktop -- it has color, position, and shape. Those are the only categories available to you, and yet none of them are true about the file itself or anything in the computer. They couldn't possibly be true. That's an interesting thing. You could not form a true description of the innards of the computer if your entire view of reality was confined to the desktop. And yet the desktop is useful. That blue rectangular icon guides my behavior, and it hides a complex reality that I don't need to know. That's the key idea. Evolution has shaped us with perceptions that allow us to survive. They guide adaptive behaviors. But part of that involves hiding from us the stuff we don't need to know. And that's pretty much all of reality, whatever reality might be. If you had to spend all that time figuring it out, the tiger would eat you.

We cannot depend on evolution to give us the ability to grasp truth. Darwinism doesn't necessarily reveal reality to us; it can hide it. Here is research Hoffman published in the Journal of Theoretical Biology making the same argument. The idea that evolution doesn't necessarily generate an ability to grasp truth doesn't just come from advocates of intelligent design. And it has many serious implications.

In her recent book, Finding Truth: 5 Principles for Unmasking Atheism, Secularism, and Other God Substitutes, Nancy Pearcey highlights logical inconsistencies in holding to evolution. She notes: 

An especially damaging form of contradiction is self-referential absurdity -- which means a theory sets up a definition of truth that it itself fails to meet....An example of self-referential absurdity is a theory called evolutionary epistemology, a naturalistic approach that applies evolution to the process of knowing. The theory proposes that the human mind is a product of natural selection. The implication is that the ideas in our minds were selected for their survival value, not for their truth-value. 

But what if we apply that theory to itself? Then it, too, was selected for survival, not truth -- which discredits its own claim to truth. Evolutionary epistemology commits suicide.

Philosopher Thomas Nagel takes this in a slightly different direction in The View from Nowhere, noting how evolution can't produce our modern science:

In themselves, the advanced intellectual capacities of human beings, unlike many of their anatomical, physiological, perceptual, and more basic cognitive features, are extremely poor candidates for evolutionary explanation, and would in fact be rendered highly suspect by such an explanation. I am not suggesting, as Kant once did..., that reason has negative survival value and could from that point of view be replaced by instinct. But the capacity to form cosmological and subatomic theories takes us so far from the circumstances in which our ability to think would have had to pass its evolutionary tests that there would be no reason whatever, stemming from the theory of evolution, to rely on it in extension to those subjects. In fact if, per impossibile, we came to believe that our capacity for objective theory were the product of natural selection, that would warrant serious skepticism about its results beyond a very limited and familiar range. 

Purely naturalistic neo-Darwinism is self-defeating in its illogic. The consequences of this truth are far-reaching. Those consequences should include, at the very least, treating evolution as an ordinary idea, not as sacred dogma, while being open to considering other possibilities.