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.

Genetic evidence for common ancestry?Or give us a miracle and we'll explain the rest.

Stunning Evidence for Common Ancestry? S. Joshua Swamidass on the Chimp-Human Divergence

Cornelius Hunter

I once had a rare and valuable baseball card I wanted to sell. I placed an ad and was shortly contacted by a collector. But to my dismay he wasn't interested. He had probably looked at hundreds of baseball cards and it only required one look for him to know that my treasured card held no value for him. He did not attempt any negotiating tricks, just a polite "thank you" and off he went. I would have felt better about the encounter if he had tried to haggle with me to lower the price. For I would have had the comfort of knowing my card held at least some value. Apparently it didn't.

I too am a collector of sorts. And like that baseball card collector I have looked at hundreds of specimens. No matter how unlikely the source or the venue, I will go there and have a look. And in short order, I will know exactly what I am looking at, and if there is any value there. But unlike the baseball card collector, I'm not after something you can hold in your hand. 

What I am interested in are the arguments and evidences for evolution. Ever since Darwin, evolutionists have insisted that their idea is undeniable -- beyond all reasonable doubt. I find that complete certainty to be fascinating. So I search out, analyze, and categorize every justification and explanation for that conclusion that I can find.

My goal is to discover the strongest, most powerful, such arguments and evidences, and to understand how thoughtful people can have such certainty. This brings us to S. Joshua Swamidass, a professor in the Genomic Medicine Division at Washington University and author of a recent post at his website, "Evidence and Evolution." Given his credentials, he deserves to be listened to. Swamidass explains that the evidence for evolution is powerful and compelling. This evidence, which he describes as stunning, is definitely a specimen I want to have a look at.

In his post, Swamidass's focus is on human evolution. Evolutionists believe that we humans evolved from a small ape-like creature and that our closest relative on the evolutionary tree is the chimpanzee. The chimpanzee must be our closest relative, they reason, because the chimp's genome is closest to ours, and according to evolution, genetic mutations are the fuel behind evolutionary change.

The problem with this reasoning is that according to many other measures, the chimpanzee is not very similar to humans. There are enormous differences between the two species. Furthermore, in its morphology and behavior, the orangutan is closer to humans than the chimpanzee. Simply put, from an evolutionary perspective the genetic data are not congruent with the other data. Swamidass's evidence will need to overcome this obvious problem.

But that's not all.

The basic idea of humans arising via a long series of genetic mutations is, itself, not indicated by the science and is unlikely to say the least. Remember, the mutations have to be random. According to evolution, you can't have mutations occurring for some purpose, such as creating a design. And natural selection doesn't help -- it cannot induce or coax the right mutations to occur. This makes the evolution of even a single protein, let alone humans, statistically impossible. So this is another enormous problem Swamidass's evidence will need to overcome.

But that's not all.

The incredible designs in the human body are not the only thing those random mutations have to create -- they will also have to create human consciousness. Evolutionists may try to explain consciousness as an "emergent" property that just luckily arose when our brain somehow evolved. Or they may try to explain that consciousness is really no more than an illusion. But these are just more demonstrations of anti-realism in evolutionary thought. By that I mean, evolutionary theory constructs mechanisms and explanations that do not correspond to the real world. So this is another problem Swamidass will need to overcome.

But that's not all.

In recent decades the genomes of humans and chimps have been determined, and in an evolutionary paradigm they make no sense. One of the main problems is that the genes of the two species are almost identical. They are only about 1-to-2 percent different and, if you're an evolutionist, this means you have to believe that the evolution of humans from a small, primitive, ape-like creature was caused by only a tiny modification of the genome.

This goes against everything we have learned about genetics. You can insert far greater genetic changes with far less change arising as a consequence. It makes little sense that tiny genetic changes could cause such enormous design changes to occur. This is yet another problem for Swamidass to overcome.

But that's not all.

Not only is evolution limited to tiny genetic modifications to create the human, but the majority of those modifications would have had to be of little or no consequence. Here is how a 2005 paper on the chimpanzee-human genome comparisons put it:

In particular, we find that the patterns of evolution in human and chimpanzee protein-coding genes are highly correlated and dominated by the fixation of neutral and slightly deleterious alleles.

The paper is written from an evolutionary perspective, assuming that humans and chimpanzees share a common ancestor. Given that a priori assumption, they were forced to conclude that most of the mutations affecting protein-coding genes led to "neutral and slightly deleterious alleles." So not only are evolution's random mutation resources meager, in terms of both quality and quantity as explained above, but even worse, those mutations mostly led to "neutral and slightly deleterious alleles." This is no way to evolve the most complex designs in the world and it is yet another problem for Swamidass to overcome.

But that's not all.

When evolutionists search for genes in the human genome that do show signs of selection, rather than neutral drift (again, under the assumption of evolution), they find only a limited repertoire of functionality. For example, one study found genes involved in the sense of smell, in digestion, in hairiness, and in hearing. In other words, evolution is suggesting that we differ from the chimp mainly in those functions. It is a silly conclusion and another problem for Swamidass to explain.

But that's not all.

That 2005 paper also found a host of chimp-human comparisons that are nonsensical in evolutionary terms. In other words, if you are forced to interpret the genetic comparisons in terms of evolution, you end up with contradictions. For example, if you look at large segments of DNA, corresponding in the human and the chimp, you find unexplainable variations in the chimp-human differences:

Nucleotide divergence rates are not constant across the genome... The average divergence in 1-Mb segments fluctuates with a standard deviation of 0.25%, which is much greater than the 0.02% expected assuming a uniform divergence rate.

To explain these nonsensical findings evolutionists have to resort to a "then a miracle happened" hypothesis. The usual explanatory devices do not work, so they are left only with the claim that local variations in the mutation rate did it -- which amounts to special pleading:

[W]e suggest that the large-scale variation in the human-chimpanzee divergence rate primarily reflects regional variation in mutation rate.

Under evolution there is no scientific reason, beyond hand-waving speculation, for such variations. This is the equivalent of epicycles in geocentrism and so we have yet another problem for Swamidass to address.

But that's not all.

The supposed divergence rate between chimps and humans not only has an unexplainable variation in large, 1-Mb segments of DNA, it also has an unexplainable variation towards the ends of most chromosomes. This is another problem that seems to make no sense under evolution, which Swamidass must explain.

But that's not all.

This supposed divergence rate between chimps and humans also has an unexplainable variation that correlates with chromosomal banding. Again, this makes no sense under evolution. Why should the chimp-human divergence vary with the banding pattern? Evolutionists have only just-so stories to imagine why this would have happened, and it is another problem for Swamidass to address.

But that's not all.

This supposed divergence rate between chimps and humans is not consistent with the supposed divergence rate between the mouse and rat. The mouse-rat divergence is about an order of magnitude greater than the chimp-human divergence. Yet the mouse and rat are much more similar than the chimp and human. It makes no sense under evolution. In fact, before the rat genome was determined, evolutionists predicted it would be highly similar to the mouse genome. As one paper explained:

Before the launch of the Rat Genome Sequencing Project (RGSP), there was much debate about the overall value of the rat genome sequence and its contribution to the utility of the rat as a model organism. The debate was fuelled by the naïve belief that the rat and mouse were so similar morphologically and evolutionarily that the rat sequence would be redundant.

The prediction that the mouse and rat genomes would be highly similar made sense according to evolution. But it was dramatically wrong.

Another approach is to ignore the morphological similarities and reason from the number of generations available to produce the genomic differences between the mouse and rat. The mouse-rat divergence date is estimated by evolutionists to be older than the chimp-human divergence date. Furthermore, the lifespan and generation time for mice and rats are much shorter than for chimps and humans. From this perspective, and given these two effects, one would conclude that the mouse-rat genetic divergence should be much greater -- at least two orders of magnitude greater -- than the chimp-human genetic divergence. But it isn't. It is only about one order of magnitude greater.

So either way the mouse-rat comparison does not help to explain things and is another problem for Swamidass to explain.

Swamidass Explains?

Under evolution, the science makes no sense. If we begin by assuming chimps and humans share a common ancestor, we end up with all kinds of contradictions and failures. So what exactly are Swamidass's arguments and evidences? How is it that he is so certain? What is it in the data that he finds to be so stunning? And most importantly, how does he resolve the above problems?

Well, he doesn't.

Astonishingly, Swamidass doesn't even mention the above problems. It is as though they don't exist. After some stories and claims of high certainty, here is what Swamidass says:

As predicted by common ancestry, human and chimpanzee genomes are extremely similar (greater than 98% similarity in coding regions), much more similar than we would expect without common descent. Remarkably, just as predicted by the fossil record, humans are about 10 times more genetically similar to chimpanzees than mice are to rats.

First, the high chimp-human genomic similarity was not predicted by common ancestry. No such prediction was made and no such prediction is required by common ancestry. Common ancestry would be just fine with very different levels of similarity from 98-99 percent. In fact, this high similarity makes no sense under evolution, for several of the reasons given above.

Swamidass's claim that this evidence is a stunning confirmation of common ancestry is utterly at odds with the science. It is in stark contrast to the scientific facts.

Second, Swamidass's claim that mouse-rat divergence, compared with the chimp-human divergence, is "just as predicted by the fossil record" is also blatantly false. While evolutionists can always combine various explanatory mechanisms to rationalize just about any comparison, that does not make for stunning evidence that is "just as predicted."

Finally, the real strength of Swamidass's argument lies in its metaphysics. The professor states that the chimp-human genome comparison is "much more similar than we would expect without common descent."

Without common descent?

The evolutionist has just made an unbeatable (and unfalsifiable) argument.

This is not science. Swamidass's claim about what is and isn't likely "without common descent" is not open to scientific scrutiny.

Scientists, qua scientists, do not have knowledge of all possible explanations for the origin of life. This is why scientists, qua scientists, make statements about theories, not about the complement of a theory. A scientist cannot know that something is unlikely "without" his theory. That implies knowledge of all other possible theories. And that knowledge does not come from science.

This is the strength of Swamidass's argument. Notice that with this metaphysical knowledge, all of the scientific problems melt away. No wonder he does not address them. They are inconsequential. At worst, they are simply interesting puzzles. The truth of the matter is already known.

If Swamidass is correct then, yes, of course, the genomic data must be strong evidence for common ancestry. But it all hinges on his metaphysics. This is not about science. It never was.

As 'Just so' as it gets II

Rafting Monkeys "Fill a Gap" in Evolutionary Theory?

David Klinghoffer 

Among evolutionary icons -- peppered moth, Darwin's finches, Haeckel's embryos -- arguably the most risible is the rafting monkey. Even Darwinists seem to understand this.

A Washington Post article includes an interview with an author of a new Science paper, "Oligocene primates from China reveal divergence between African and Asian primate evolution," that once again renews the demand for belief in seafaring monkeys. We've covered this paradox before -- monkeys can't swim much less sail. Just last month evolutionary theorizing dodged a bullet by avoiding the spectacle of rafting foxes on the world's oceans.

The researcher, Christopher Beard, explained to reporter Sarah Kaplan how it must be the case that tarsier-like monkeys, evidenced by fossil teeth found in China, sailed on clumps of earth and felled trees, 30-40 million years ago, across an aquatic void separating Asia from Africa, which was then an island:

"It's a little complicated," Beard said, almost sheepishly.

You don't say.

This more convoluted version of our history begins in the Eocene, some 40 million years ago. At this time, Earth's climate was hot and humid, and the continents were just beginning to move into the positions they hold today. India was zooming headlong toward the bottom of Asia (the inevitable collision would one day give rise to the Himalayas). An inland sea flooded the center of the Eurasian land mass. And Africa was an island continent, separated from Asia and Europe by a narrow stretch of ocean.

Early anthropoid (humanlike) monkeys were flourishing in Asia at that time. But they also, somehow, found a way to migrate across the watery barrier to Africa. And since monkeys don't really swim, scientists' best theory about their migration is -- I kid you not -- that they sailed across on rafts made of trees.

"You're laughing," Beard said, "but it's now known that this happened repeatedly. Because of the greenhouse conditions, a lot of monsoons were hitting Asia at the time. When that happens, rivers would flood, riverbanks erode. A half an acre of land with a bunch of trees growing out of it falls into a river and floats out to sea."

"And if there are a bunch of monkeys hanging out in the trees when that happens," he continued, "suddenly those monkeys become sailors."

"I kid you not." "You're laughing, but it's now known that this happened repeatedly." It is "known" not because anyone can picture the scenario without cracking up or feeling "sheepish" but because the theory demands it. See here for Casey Luskin's earlier comments on the "biogeographical conundrum" posed by these Chinese monkeys.

And look here for pictures of how the drifting continents were disposed in the relevant time period between the Oligocene and the Eocene. From Asia to Africa by sea was a considerable distance, and monkeys are supposed to have accomplished this feat while clinging for dear life to bits of earth and tree debris? On Lake Washington near our home, I beg my wife and kids not to row out even close to shore on a store-bought inflatable raft!

Science Daily has additional thoughts from Dr. Beard on the "'mother lode' of a half-dozen fossil primate species." A half-dozen is a "mother lode"? More:

These primates eked out an existence just after the Eocene-Oligocene transition, some 34 million years ago. It was a time when drastic cooling made much of Asia inhospitable to primates, slashing their populations and rendering discoveries of such fossils especially rare.

"At the Eocene-Oligocene boundary, because of the rearrangement of Earth's major tectonic plates, you had a rapid drop in temperature and humidity," said K. Christopher Beard, senior curator at the University of Kansas' Biodiversity Institute and co-author of the report. "Primates like it warm and wet, so they faced hard times around the world -- to the extent that they went extinct in North America and Europe. Of course, primates somehow survived in Africa and Southern Asia, because we're still around to talk about it." Because anthropoid primates -- the forerunners of living monkeys, apes and humans -- first appeared in Asia, understanding their fate on that continent is key to grasping the arc of early primate and human evolution.

Sarah Kaplan's article in the Post speaks more than once of the fossils as "fill[ing] in the gaps":

The fossils "fill a gap," in our understanding of our evolutionary history, Stony Brook University primatologist John Fleagle, who was not involved in the study, told the Christian Science Monitor. They illustrate "a whole aspect of primate evolution that wasn't clearly documented before."

But the value of "filling a gap" lies in reducing the distance you have to leap in order to believe something seemingly far-fetched. More about rafting animals surely makes the challenge for evolution tougher, not easier. I would have said reducing, not increasing, the number of such unlikely sailors would "fill a gap."