The deprivileging of mankind's status continues apace.

From the "Nothing Special" Files -- Apes and Their Theory of Mind

David Klinghoffer

This is just in from the laboratories of Nothing Special that I wrote about here the other day. Reports Karen Kaplan in the Los Angeles Times, "[H]umans' thinking abilities aren't quite as special as we'd like to think" (emphasis added). She knows that because of a new study in Science, "Great apes anticipate that other individuals will act according to false beliefs."

Of all the creatures in the animal kingdom, only humans were given credit for being able to ascertain the unstated thoughts, beliefs and desires of others. (Of course, said credit was doled out by humans.) ...
Ask yourself: Why the sarcastic tone? She goes on:

A notable version of this skill is the ability to recognize when someone else believes something that's false....
A team led by evolutionary anthropologist Christopher Krupenye at Duke University and comparative psychologist Fumihiro Kano of Kyoto University chose 41 chimpanzees, bonobos and orangutans. The researchers showed the apes a series of videos starring a regular person and a man dressed up as King Kong. In a variety of scenarios, King Kong would try to hide a rock-like object from the person. If the person saw what was going on, he'd find the rock in the expected place. If not, he didn't.

To test whether the apes understood what was going on, the scientists showed them additional videos in which King Kong tried to hide in one of two haystacks. Sometimes the person saw where King Kong went, and sometimes he didn't. Using an infrared eye-tracker, the researchers could see where the apes were looking -- and thus, where they expected the human to go.

In a second experiment, the apes watched more videos of King Kong trying to hide a rock from the person. Again, the researchers used eye-trackers to see if the apes could anticipate what the person would do.

In both cases, the chimpanzees, bonobos and orangutans correctly anticipated the person's actions -- even when the person looked for King Kong or the rock in the wrong place.

The moral, of course, is that humans are Nothing Special:

Thanks to these results, the claim that only humans can ascertain the mental states of others "is starting to wobble," primatologist Frans de Waal of the Yerkes National Primate Research Center at Emory University wrote in a commentary that accompanies the study....
De Waal seconded that notion, saying the results highlight "the mental continuity between great apes and humans."

It's a useful reminder that humans shouldn't be so quick to put themselves on a pedestal, he added.

The paper in Science is only a little more restrained in drawing the same lesson:

We humans tend to believe that our cognitive skills are unique, not only in degree, but also in kind. The more closely we look at other species, however, the clearer it becomes that the difference is one of degree. Krupenye et al. show that three different species of apes are able to anticipate that others may have mistaken beliefs about a situation.... The apes appear to understand that individuals have different perceptions about the world, thus overturning the human-only paradigm of the theory of mind.
Yet the business about knocking us down from a pedestal is based on a false premise: that we are at all surprised by these results. I'm not. Given that canines with their high emotional intelligence clearly intuit "unstated thoughts, beliefs and desires of others," as anybody with experience with dogs knows, why would the same not be true of apes?

That we share a limited capacity like this with chimps and orangutans comes as no shock. Therefore nothing is "starting to wobble." The results of the research do little to span the chasm between chimp and man. Instead the Nothing Special crowd uses the "pedestal" as a setup, a momentary fiction useful only for being immediately knocked over.

As Wesley Smith reminds us, dumping dirt on human exceptionalism is a preoccupation of popular science journalism -- not to mention professional science. It goes to show how powerful the will is among many smart and otherwise thoughtful people to believe humans are nothing special, and to convince others of the same thing. Where does that power come from?

An email correspondent notes the irony:

I have never been able to understand why so many people want so badly to believe there is Nothing Special about us, but they do. Only thing I can figure is that some of them just feel saying this makes them look special in the eyes of others.
Yes, right. Status is the key, but the psychology is very strange. Obviously I understand polishing your sense of self by advertising your accomplishments, associations, and possessions. But what drives this weird dynamic where feeling special depends on obsessively disclaiming specialness? We all know people who take pride in their humility. This is different. It seems to be more about sticking it -- "Nothing Special" -- in the face of others. That is the whole point of the L.A. Times article.


I am stumped. If you have any insights, please drop me an email and let me know. (Hit the orange button at the top of the page.)

Darwinism and mathematics are natural enemies.

Biologic Institute's Groundbreaking Peer-Reviewed Science Has Now Demonstrated the Implausibility of Evolving New Proteins

Casey Luskin January 22, 2015 10:51 AM

 

Ann Gauger already provided an excellent series of articles discussing her recent paper co-authored in BIO-Complexity. She explains why it is important for demonstrating intelligent design (see here, here, here, here, and here). However, I wanted to give a slightly different framing of the new data. My purpose here and in a follow-up post will be to explain how this latest ID research (as well as prior work in the field) addresses fundamental questions in the debate over Darwinian evolution and ID -- and comes up with very positive results.When Michael Behe published Darwin's Black Box in 1996, he outlined the concept of irreducible complexity as a biochemical challenge to Darwinian evolution. According to his argument, some structures require all of their parts (or a certain core minimum number) in order to function. In this game of all or nothing, such "irreducibly complex" structures cannot be built in the step-by-step manner of Darwinian evolution because they provide no advantage, of the kind evolution requires, until all their parts are present.
At the time and since, evolutionists responded by arguing that irreducibly complex features can be built through co-option. Under this view, biological parts might exist elsewhere in an organism where they are used for a different function. Sometimes, when a gene is duplicated, the extra copy could then be borrowed, retooled, and "co-opted" to perform a new function in a new system. Sounds easy, right?
Not so fast. Darwin observed that his theory "breaks down" when large leaps of complexity are needed in order to provide some advantage. What if retooling proteins to perform new functions requires such leaps? What if multiple mutations are needed to convert a protein to perform some new function? Should we follow many evolutionists and simply wave our hands and assume the co-option model of protein evolution is sufficient, or should we behave like scientists and test the viability of that model? Researchers at Biologic Institute have decided to take the latter approach, and to test the co-option model of protein evolution.
In 2011, Ann Gauger and Douglas Axe published a paper in BIO-Complexity, "The Evolutionary Accessibility of New Enzymes Functions: A Case Study from the Biotin Pathway." They reported results of their laboratory experiments trying to convert one enzyme (Kbl₂) to perform the function of a very similar enzyme (BioF₂), thought to be very closely related to Kbl₂. Because these proteins are both members of the GABA-aminotransferase-like (GAT) family, and are believed to be very closely related, this is the sort of evolutionary conversion that evolutionists say ought to be easily accomplished under the standard co-option model. However, after trying multiple combinations of different mutations, they found otherwise:

We infer from the mutants examined that successful functional conversion would in this case require seven or more nucleotide substitutions.

This presents a serious problem for Darwinian evolution since a 2010 paper by Axe found that a feature that would require more than two maladaptive mutations, or more than six neutral mutations, before providing an advantage could not arise in the entire history of the earth. Gauger and Axe (2011) concluded:

[E]volutionary innovations requiring that many changes would be extraordinarily rare, becoming probable only on timescales much longer than the age of life on earth. Considering that Kbl₂ and BioF₂ are judged to be close homologs by the usual similarity measures, this result and others like it challenge the conventional practice of inferring from similarity alone that transitions to new functions occurred by Darwinian evolution.

Their 2011 study thus provided a "disproof of concept" of the co-option model. However, it only looked at two proteins. What if other proteins are more easily convertible? Last December, in a landmark peer-reviewed paper published in BIO-Complexity, Axe, Gauger, and biologist Mariclair Reeves presented new research on additional proteins in the same family. They showed that these proteins too are not amenable to an evolutionary conversion to perform the function of BioF₂.
Now in their new study, "Enzyme Families-Shared Evolutionary History or Shared Design? A Study of the GABA-Aminotransferase [GAT] Family," Reeves, Gauger, and Axe examine nine other enzymes from the same GAT family. Once again, the idea was to see if it is possible to convert them to perform the function of BioF₂. They tested proteins that are closer to BioF₂, or more distant from BioF₂, than the enzyme they tested in their prior study (Kbl₂). But all of the proteins studied are in the same family, and are thought to be closely related.
First, they sought to determine if the enzymes could be converted to perform the function of BioF₂ through a single mutation. They created mutation libraries with every single possible mutation in those nine enzymes. No BioF₂ function was ever detected. As they explain:

The present study has added to our previous examination of these problems in several respects. We have shown, based on sequence alignment of α-oxoamine synthases (a subset of the GAT family), that our previous use of rational design did indeed target regions of Kbl₂ that are likely to be functionally significant. Furthermore we have now shown that the lack of a simple evolutionary transition to BioF₂ function is not at all unique to our initial choice of Kbl₂ as the starting point. Single mutations cannot convert any of eight other members of the GAT family to that function, despite the fact that all of these enzymes are regarded as close evolutionary relatives.

Then they tried double-mutation libraries. They were able to try 70 percent of the double-mutations in two enzymes that are thought to be the most likely candidates for conversion to function like BioF₂: Kbl₂ and another enzyme, BIKB, which is said to have both BioF₂ and Kbl₂ functions. They write:

[W]e have demonstrated that converting either Kbl₂ or BIKB to perform the function BioF₂ with two DNA base substitutions is at least mildly unlikely, in that neither conversion was found after examining over two thirds of the possibilities. Of course, many possibilities remain unexamined. Although it is certainly possible for a working combination to be among those unchecked possibilities, we think it is more informative at this point to ask the fundamental question of whether the available evidence as a whole really supports the idea that evolutionary recruitment is the cause of functional diversity in enzyme families.

This suggests that at least two mutations would be necessary to convert a protein in this family to perform the function of BioF₂. But it's likely that additional mutations would be necessary for these evolutionary conversions. To be specific, the co-option model requires that a gene become duplicated, and then overexpressed before it can evolve some new function. Thus, at least two more mutations are needed -- one to duplicate the gene and another to overexpress it.
However, one of their citations makes a compelling case that the gene duplication step poses a major obstacle to gene recruitment via gene duplication and mutation. They cite a paper from PLOS Genetics, "The Extinction Dynamics of Bacterial Pseudogenes," which notes:

In bacteria, however, pseudogenes are deleted rapidly from genomes, suggesting that their presence is somehow deleterious. The distribution of pseudogenes among sequenced strains of Salmonella indicates that removal of many of these apparently functionless regions is attributable to their deleterious effects in cell fitness, suggesting that a sizeable fraction of pseudogenes are under selection.

It concludes, "Although pseudogenes have long been considered the paradigm of neutral evolution, the distribution of pseudogenes among Salmonella strains indicates that removal of many of these apparently functionless regions is attributable to positive selection."
Don't miss the profound importance of this. What it means is that there is very likely a fitness cost associated with carrying an extra, useless copy of a gene, and therefore it can be advantageous to delete duplicate version. This has major implications for the co-option model of protein evolution, because it shows that producing a new protein does not involve "neutral evolution," but rather requires steps that very likely will impose a deleterious effect upon the organism.
Similar results were obtained in a 2010 BIO-Complexity paper reporting ID research, "Reductive Evolution Can Prevent Populations from Taking Simple Adaptive Paths to High Fitness," by Gauger and biologist Ralph Seelke. This paper found that when merely two mutations along a stepwise pathway were required to restore function to a bacterial gene, even then the Darwinian mechanism failed. But the reason why Darwinism failed is important.
Although one mutation restored partial function, the function was very slight. In the experiments, the gene was deleted before the second mutation could occur and restore full function. It was more advantageous to delete a weakly functional gene than to continue to express it in the hope that it would "find" the mutations that fixed the gene. This means that carrying a weakly functional gene is disadvantageous, and that it's more advantageous to just get rid of a gene duplicate that isn't contributing very much to the success of the organism.
So a fundamental component of the co-option model -- duplicating a gene -- very likely involves a deleterious step. What does that say about the potential for evolving complex traits? ID research has already addressed that question.
In a 2010 research paper that Douglas Axe published in BIO-Complexity, "The Limits of Complex Adaptation: An Analysis Based on a Simple Model of Structured Bacterial Populations," he determined that when deleterious mutations are involved, a trait that requires more than two disadvantageous mutations could never form over the history of the earth. In other words, if you are trying to evolve a trait that requires more than two deleterious mutations, it's not going to evolve.
Let's return now to the 2014 paper by Reeves, Gauger, and Axe. They experimentally found that at least two mutations would be necessary to convert the most likely co-option candidates in this enzyme family to function like BioF₂. But other mutations would be necessary as well -- at least one to duplicate the enzyme and another to overexpress it. This suggests at least four mutations would be required for this conversion. Given that, as we just saw, some of these mutations (such as duplication) would initially impose a disadvantage, the math says it would take some 10¹⁵ years for the necessary mutations to arise to co-opt a protein to function like BioF₂ -- over 100,000 times longer than the age of the earth! They thus conclude:

Based on these results, we conclude that conversion to BioF₂ function would require at least two changes in the starting gene and probably more, since most double mutations do not work for two promising starting genes. The most favorable recruitment scenario would therefore require three genetic changes after the duplication event: two to achieve low-level BioF₂ activity and one to boost that activity by overexpression. But even this best case would require about 10¹⁵ years in a natural population, making it unrealistic. Considering this along with the whole body of evidence on enzyme conversions, we think structural similarities among enzymes with distinct functions are better interpreted as supporting shared design principles than shared evolutionary histories.

This new paper thus provides a robust disproof of the co-option model, overturning a cornerstone argument that evolutionists have long used when trying to answer ID arguments like irreducible complexity. By testing the co-option model, Biologic Institute is not just asking the right questions and doing innovative research that addresses key issues in the debate over Darwinian evolution and intelligent design. They're also finding data that confirms that ID's earliest arguments were right all along.

Reasons to doubt the trinity III

Yet More on life's anti Darwinian bias IV

Armed Forces in the Cell Keep DNA Healthy
Evolution News & Views September 8, 2015 3:01 AM

Science reporters struggle for metaphors to describe the complex operations they see going on in the cell. For example:

The Orchestra

News from the University of Geneva likens the human genome to a "complex orchestra." Their research led to "unexpected" and "surprising" findings showing "harmonized and synergistic behavior" in the regulation of genes. The metaphor of a conductor keeping all the various players in harmony came to mind:

A team of Swiss geneticists from the University of Geneva (UNIGE), the École Polytechnique Fédérale de Lausanne (EPFL), and the University of Lausanne (UNIL) discovered that genetic variation has the potential to affect the state of the genome at many, seemingly separated, positions and thus modulate gene activity, much like a conductor directing the performers of a musical ensemble to play in harmony. These unexpected results, published in Cell, reveal the versatility of genome regulation and offer insights into the way it is orchestrated. [Emphasis added.]
The Armed Forces

Another metaphor popular among reporters is "armed forces." This metaphor will prove instructive as we read about DNA protection and damage repair. Let's look at some of the stages in this process where we will find soldiers, emergency medical technicians, ambulances and military hospitals in action, each well trained and equipped for defense.

Surveillance and Inspection

Any disciplined military operation requires high standards. Soldiers at boot camp know that drill sergeants can be ruthless when inspecting rifles, shoe shines, and barrack beds. Similarly, machines in the genome inspect DNA for errors and won't tolerate less than perfection. A news item from North Carolina State University describes MutS, a machine that inspects unzipped DNA strands looking for errors. Any mismatch makes this drill sergeant stop and stare the recruit in the face, even if he is one in a million.

Fortunately, our bodies have a system for detecting and repairing these mismatches -- a pair of proteins known as MutS and MutL. MutS slides along the newly created side of the DNA strand after it's replicated, proofreading it. When it finds a mismatch, it locks into place at the site of the error and recruits MutL to come and join it. MutL puts a nick in the newly synthesized DNA strand to mark it as defective and signals a different protein to gobble up the portion of the DNA containing the error. Then the nucleotide matching starts over, filling the gap again. The entire process reduces replication errors around a thousand fold, serving as our body's best defense against genetic mutations and the problems that can arise from them, like cancer.
First Response

If casualties occur, they have to be detected. A protein named ATF3 is captain of a squad that acts as "first responder" to DNA damage, as this from Georgia Regents University explains. Let's say a DNA strand breaks because of sunlight, chemotherapy or a cosmic ray. If not corrected quickly, the cell could become cancerous or die. What happens first?

In the rapid, complex scenario that enables a cell to repair DNA damage or die, ATF3, or activating transcription factor 3, appears to be a true first responder, increasing its levels then finding and binding to another protein, Tip60, which will ultimately help attract a swarm of other proteins to the damage site.
Combat Operations

Viruses have invaded! The armed forces go into high alert. The Salk Institute for Biological Studies describes the flurry of activities that result, because every organism "must protect its DNA at all costs."

Before panicking, the cell's commanding officers need intelligence. If a DNA break puts the cell in stress, was it a natural break, let's say from a cosmic ray, or from a virus, like an insurgent tossing a grenade? A false move could lead to friendly-fire casualties.

The researchers explain how the cell figures out if the DNA damage was internal or external. First, the MRN complex gives the "all hands on deck" signal. It stops replication and other cell operations until the break is mended.

What's interesting is that even a single break transmits a global signal through the cell, halting cell division and growth," says O'Shea. "This response prevents replication so the cell doesn't pass on a break."
The viral response begins the same way, the article continues, but doesn't give the global alarm. Instead, the alarm is localized, and sentries in the area dispatch the invaders. There's a reason for this. "If every incoming virus spurred a similarly strong response, points out O'Shea, our cells would be frequently paused, hampering our growth." But when the cell becomes preoccupied with DNA damage repair, the viruses can infiltrate.

A video clip in the article applies the armed forces metaphor:

Govind Shah: "DNA repair proteins serve as security guards inside the nucleus. They catch virus DNA and escort them out of the cell. If a cell experiences a huge amount of DNA damage, then these security guards will be pulled away from the viral DNA and allow the viral DNA to replicate to high levels."
Clodagh O'Shea: "We discovered that if you have DNA damage in your own genome, and the alarm goes off, actually that recruits in all of the forces: all of the police, national guard--everyone's there. All the forces are dealing with your own DNA damage, and there's nothing left to actually even see or actually turn off the virus."

This gave them an idea. Shah says, "So why not use this to kill cancer cells" with viruses engineered to enter tumor cells? The programmed response they discovered will cause the cell to let the viruses in while it's preoccupied with fixing DNA breaks. "If the cell can't fix the DNA break, it will induce cell death-a self-destruct mechanism that helps to prevent mutated cells from replicating (and thus prevents tumor growth)."

Medics

We're all familiar with the images of battlefield helicopters delivering medics to give first aid to the wounded, or airlifting them to the nearest triage station or hospital. The cell nucleus has hospitals, an article at Biotechniques says, and "A molecular ambulance for DNA" knows how to get the casualties to the emergency room.

Double-strand breaks in DNA are a source of stress and sometimes death for cells. But the breaks can be fixed if they find their way to repair sites within the cell. In yeast, one of the main repair sites resides on the nuclear envelope where a set of proteins, including nuclear pore subcomplex Nup84, serves as a molecular hospital of sorts. The kinesin-14 motor protein complex, a "DNA ambulance," moves the breaks to repair sites, according to a new study in Nature Communications.
Researchers at the University of Toronto found it "very surprising" was that the ambulance driver is the well-known motor protein kinesin-14 (see our animation of kinesin at work).

Hospital Staff

News from the University of Texas MD Anderson Cancer Center introduces some of the specialists in the DNA repair hospital: fumarase. a metabolic enzyme; DNA-PK, a protein kinase; and histone methylation enzymes that regulate the repair process. These skilled doctors perform restorative surgery for "DNA double-strand breaks (DSBs)," which "are the worst possible form of genetic malfunction that can cause cancer and resistance to therapy."

Clean-up Crew

Cells invest a lot of energy in their ribosomes, the organelles that translate DNA. Ribosomes are assembled from protein and RNA domains. What happens with the leftovers? An item from the University of Heidelberg describes molecular machines that barcode the fragments for delivery to a barrel-shaped shredder called the exosome. Though not described in military terms, the agents are under strict orders and required to pass through checkpoints.

According to Prof. Hurt, the production of ribosomes is an extremely complex process that follows a strict blueprint with numerous quality-control checkpoints. The protein factories are made of numerous ribosomal proteins (r-proteins) and ribosomal ribonucleic acid (rRNA). More than 200 helper proteins, known as ribosome biogenesis factors, are needed in the eukaryotic cells to correctly assemble the r-proteins and the different rRNAs. Three of the total of four different rRNAs are manufactured from a large precursor RNA. They need to be "trimmed" at specific points during the manufacturing process, and the superfluous pieces are discarded. "Because these processes are irreversible, a special check is needed," explains Ed Hurt.
The number of "armed forces" personnel involved in DNA defense and cell quality control is astonishing. It's beyond a well-conducted orchestra. It's like a military operation, with strict protocols, hierarchical command structure and trained specialists. These systems are goal-oriented: they exist to protect the genome. They are on duty inspecting components even when nothing is wrong. And when things do go wrong, they know just what to do, as if well-trained in following orders.

We aren't surprised to notice that these articles say nothing about evolution. Why? Because we all know from our experience that phenomena characterized by hierarchical command and control systems with documented procedures and skilled agents are always intelligently designed.