On Formalising design detection II

Peer-Reviewed Scientific Paper Develops New Ways of Measuring Complex and Specified Information in Life
Casey Luskin December 28, 2015 11:28 AM

Winston Ewert, Bill Dembski, and Bob Marks have recently published a new peer-reviewed paper in the journal IEEE Transactions on Systems, Man, and Cybernetic: Systems, titled "Algorithmic Specified Complexity in the Game of Life." The purpose of the paper is to develop the concept of algorithmic specified complexity as a new and improved method of measuring biological (and other forms of) information.

They start by observing that "Neither fundamental Shannon nor Kolmogorov information models are equipped" to measure "meaningful" information. As I recently explained, "the purpose of Shannon information is to help measure fidelity of transmission of information. What the transmission says doesn't matter" and:

Kolmogorov information is not necessarily tied to likelihood. In fact, higher Kolmogorov bits could mean more randomness. In that regard, it's not useful for distinguishing functional information from non-functional.
Complex and specified information (CSI) has long been cited as an improved method of measuring the functional meaning of information. But recently the team at the Evolutionary Informatics Lab has developed a new variation on CSI, algorithmic specified complexity (ASC), to measure the degree to which information is meaningful. As they put it:
We propose an information theoretic method to measure meaning. Fundamentally, we model meaning to be in the context of the observer. A page filled with Kanji symbols will have little meaning to someone who neither speaks nor reads Japanese. Likewise, a machine is an arrangement of parts that exhibit some meaningful function whose appreciation requires context. The distinguishing characteristic of machines is that the parts themselves are not responsible for the machine's functionality, but rather they are only functional due to the particular arrangement of the parts. Almost any other arrangement of the same parts would not produce anything interesting. A functioning computational machine is more meaningful than a large drawer full of computer parts.
They explain why Shannon Information and Kolmogorov-Chaitin-Solomonoff (KCS) measures of information don't help measure functionality:
The arranging of a large collection of parts into a working machine is highly improbable. However, any arrangement would be improbable regardless of whether the configuration had any functionality whatsoever. For this reason, neither Shannon nor KCS information models are capable of directly measuring meaning. Functional machines are specified -- they follow some independent pattern. When something is both improbable and specified, we say that it exhibits specified complexity. An elaborate functional machine exemplifies high specified complexity. We propose a model, algorithmic specified complexity (ASC), whereby specified complexity can be measured in bits.
ASC is similar to KCS in that it assumes a computer environment where we can describe some event, object, or scenario in terms of computer programming commands. This can allow, as they put it, a "quantitative measurement of specified complexity." To show how it works, they use Conway's famous "Game of Life."
The "Game of Life" is a computer simulation that's meant to mimic living systems by creating a grid in which some cells on the grid are "alive" and some are dead. A series of rules based upon the number of alive or dead neighboring cells determine whether a given cell will remain alive, remain dead, or come to life, or die, after each successive generation. They describe the rules as follows

1) Under-Population: A living cell with fewer than two live neighbors dies.
2) Family: A living cell with two or three live neighbors lives on to the next generation.
3) Overcrowding: A living cell with more than three living neighbors dies.
4) Reproduction: A dead cell with exactly three living neighbors becomes a living cell.
If you deliberately create certain patterns in the Game of Life, they can do unexpected things, like "gliders" which can move across the screen, or a really complicated pattern called "Gemini" that can make copies of itself every 33.6 million generations. Ewert, Dembski, and Marks use these features of "Game of Life" to apply ASC:
Our goal is to formulate and apply specified complexity measures to these patterns. We would like to be able to quantify what separates a simple glider, readily produced from almost any randomly configured soup, from Gemini -- a large, complex design whose formation by chance is probabilistically minuscule. Likewise, we would like to be able to differentiate the functionality of Gemini from a soup of randomly chosen pixels over a similarly sized field of grid squares.
A highly probable object can be explained by randomness, but it will lack complexity and thus not have specified complexity. Conversely, any sample of random noise will be improbable, but will lack specification and thus also lack specified complexity. In order to have specified complexity, both components must be present. The object must exhibit a describable functioning pattern while being improbable.

They find that some of these patterns in the Game of Life are "simple enough that they arise from random configurations of cell space," but "[o]thers required careful construction." They measured the ASC in these patterns, and then asked whether the patterns are known to appear randomly, or whether they require intelligent design. Their model predicts that high ASC patterns would arise only by design, and that patterns that are known to appear randomly would always have low ASC. They found that their method is generally a good predictor of whether low ASC patterns can appear at random or require design:
We have merely calculated the probability of generating the pattern through some simply random process not through the actual Game of Life process. We hypothesized that it was close enough to differentiate randomly achievable patterns from one that were deliberately created. This appears to work, with the exception of the unix pattern. However, even that pattern was less than an order of magnitude more probable than the bound suggested. This suggests the approximation was reasonable, but there is room for improvement.
We conclude that many of the machines built in the Game of Life do exhibit significant ASC. ASC was able to largely distinguish constructed patterns from those which were produced by random configurations. They do not appear to have been generated by a stochastic process approximated by the probability model we presented.

In other words, many of the high ASC patterns that appear in Game of Life don't appear at random. But is that surprising? After all, the Game of Life is a computer program created by intelligent agents that's designed to mimic living systems -- systems that also have high ASC. As they conclude, "Our work here demonstrates the applicability of ASC to the measure of functional meaning."

Image credit: aussiegall (Laceflower abstract) [CC BY 2.0], via Wikimedia 

On formalising design detection.

Peer-Reviewed Paper Successfully Measures Specified Complexity in Computer Images:
Casey Luskin December 29, 2015 11:31 AM 

A new peer-reviewed article in the journal IET Computer Vision, "Measuring meaningful information in images: algorithmic specified complexity," by Winston Ewert, William A. Dembski, and Robert J. Marks II, again attempts to apply the concept of algorithmic specified complexity (ASC) as a measure of meaning vs. randomness in a dataset. In a previous article I noted that the team at the Evolutionary Informatics Lab tried to apply algorithmic specified complexity (ASC) to successfully predict random patterns in Conway's Game of Life versus those that were constructed by a programmer. In this paper the authors try to distinguish between "images which contain content from those which are simply redundancies, meaningless or random noise." They begin by asking:

Is information being created when we snap a picture of Niagara Falls? Would a generic picture of Niagara Falls on a post card contain less information than the first published image of a bona fide extraterrestrial being?
They attempt to answer these questions by stating:
For an image to be meaningfully distinguishable, it must relate to some external independent pattern or specification. The image of the sunset is meaningful because the viewer experientially relates it to other sunsets in their experience. Any image containing content rather than random noise fits some contextual pattern. Naturally, any image looks like itself, but the requirement is that the pattern must be independent of the observation and therefore the image cannot be self-referential in establishing meaning. External context is required. If an object is both improbable and specified, we say that it exhibits "specified complexity."
So how can we detect whether there is such a complex and specified pattern?
The more the image can be described in terms of a pattern, the more compressible it is, and the more specified. For example, a black square is entirely described by a simple pattern, and a very short computer programme suffices to recreate it. As a result, we conclude that it is highly specified. In contrast, an image of randomly selected pixels cannot be compressed much if at all, and thus we conclude that the image is not specified at all. Images with content such as sunsets take more space to describe than the black square, but are more specified than random noise. Redundancy in some images is evidenced by the ability to approximately restore groups of missing pixels from those remaining.
The black square might be compressible and specified, but that does not mean it is complex. As they note, "The random image is significantly more complex, whereas the solid square is much less complex."
But these are relatively simple cases. They then try to tackle more complex cases, such as a photograph of Louis Pasteur with increasing amounts of random noise added. As ASC predicts, they find that the more noise is added to the image, the lower the ASC. Similarly, as you resize an image of Einstein so that it loses some of its clarity, it also loses ASC. This is all as their model predicts.

But what about the case of a picture of "stick men on a sea of noise"? They found that ASC was still able to detect the presence of a complex and specified feature even when it was surrounded by noise. They conclude that ASC is an effective methodology for distinguishing random image data from meaningful images:

We have estimated the probability of various images by using the number of bits required for the PNG encoding. This allows us to approximate the ASC of the various images. We have shown hundreds of thousands of bits of ASC in various circumstances. Given the bound established on producing high levels of ASC, we conclude that the images containing meaningful information are not simply noise. Additionally, the simplicity of an image such as the solid square also does not exhibit ASC. Thus, we have demonstrated the theoretical applicability of ASC to the problem of distinguishing information from noise and have outlined a methodology where sizes of compressed files can be used to estimate the meaningful information content of images.

The applicability in the context of intelligent design is clear: If ASC is a useful tool for distinguishing designed images from random ones, then perhaps it can be applied to biological systems or other natural structures to detect design there as well.

The Twilight zone is closer than you think.

Another failed Darwinian prediction II

The cell’s fundamental molecules are universal:

In addition to the DNA code, there are other fundamental molecular processes that appear to be common to all life. One intriguing example is DNA replication which copies both strands of the DNA molecule, but in different directions. Evolution predicts these fundamental processes to be common to all life. Indeed this was commonly said to be an important successful prediction for the theory. As Niles Eldredge explained, the “underlying chemical uniformity of life” was a severe test that evolution passed with flying colors. (Eldredge, 41) Likewise Christian de Duve declared that evolution is in part confirmed by the fact that all extant living organisms function according to the same principles. (de Duve, 1) And Michael Ruse concluded that the essential macromolecules of life help to make evolution beyond reasonable doubt. (Ruse, 4)

But this conclusion that the fundamental molecular processes within the cell are common to all species was superficial. In later years, as the details were investigated, important differences between species emerged. For example, key DNA replication proteins surprisingly “show very little or no sequence similarity between bacteria and archaea/eukaryotes.” (Leipe) Also different DNA replication processes have been discovered. These results were not what were expected:

In particular, and counter-intuitively, given the central role of DNA in all cells and the mechanistic uniformity of replication, the core enzymes of the replication systems of bacteria and archaea (as well as eukaryotes) are unrelated or extremely distantly related. Viruses and plasmids, in addition, possess at least two unique DNA replication systems, namely, the protein-primed and rolling circle modalities of replication. This unexpected diversity makes the origin and evolution of DNA replication systems a particularly challenging and intriguing problem in evolutionary biology. (Koonin)

Some evolutionists are reconsidering the assumption that all life on Earth shares the same basic molecular architecture and biochemistry, and instead examining the possibility of independent evolution, and multiple origins of fundamentally different life forms. (Cleland, Leipe)

References

Cleland, Carol. 2007. “Epistemological issues in the study of microbial life: alternative terran biospheres?.” Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 38:847-861.

de Duve, Christian. 1995. Vital Dust. New York: BasicBooks.

Eldredge, Niles. 1982. The Monkey Business. New York: Washington Square Press.

Koonin, E. 2006. “Temporal order of evolution of DNA replication systems inferred by comparison of cellular and viral DNA polymerases.” Biology Direct 18:1-39.

Leipe, D., L. Aravind, E. Koonin. 1999. “Did DNA replication evolve twice independently?.” Nucleic Acids Research 27:3389-3401.

Ruse, Michael. 1986. Taking Darwin Seriously. New York: Basil Blackwell.

A clash of Titans III

Evolution or Revolution?

In a few short centuries, the Yakutian horse has gained a large body and long, mammoth-like shaggy hair, allowing it to survive truly harsh conditions

• By Jane Palmer

28 December 2015 Local legend has it that when the god of creation flew around the world to distribute riches, he dropped all of his treasures when he arrived in the Yakutian region of Siberia. His hands were simply numb with cold.
The myth is an attempt to explain why Yakutia has such an abundance of precious diamonds, but it is easy to see why the story developed. This republic of Russia gets very cold indeed. Temperatures can dip to -70 °C (-94 °F) and its capitol, Yakutsk, is the coldest city in the northern hemisphere.
There is life in the freezer though, including a population of stocky, shaggy steeds known as Yakutian horses. The Yakuts would undoubtedly have perished if not for these beasts. Locals relied on the horses for transportation, food in the form of horsemeat, and clothing made from horse hides. Horses have played a central role in the region's economy for hundreds of years.
It turns out that these horses adapted to the extreme Siberian climates with astonishing speed.
Averaging about 150cm, the Yakutian stands a little smaller than most horses. Its winter hair can reach about 10cm in length and it has a thick bushy tail and long mane that, like a shawl, covers both its neck and shoulders.

We could really track the whole temporal line

In short, its appearance is a little like the woolly mammoth version of a horse. It is clearly well suited to the brutal and enduring Siberian winters.
But how long has it taken the Yakutian horses to adapt to this extreme environment? Are they ancient natives to the region, like the now-extinct mammoths? Or did the Yakuts bring them to the area when they fled Mongolia in the 13th or 14th Century to escape Genghis Khan?
To answer such questions, scientists recently turned to genome sampling.
"We wanted to take horses from today, horses from after the 13th century, and from prior to the 13th century," says Ludovic Orlando of the University of Copenhagen in Denmark, the lead author of the study. "Because that way, we could really track the whole temporal line and see whether or not those population of horses are actually the same through time."
The team sampled the genomes of nine modern day Yakutian horses, one genome from an early 19th Century horse, and another from a horse that lived in the region 5,200 years ago. The scientists then compared the genomes to one another and to existing sequences for dozens of domestic horses, wild Przewalski's horses that are native to the steppes of central Asia, and ancient horses.

They have adapted to their new environment in just 800 years

The findings of the study were unequivocal. In the genomes of the modern Yakutian horses the researchers found a strong signal of a "founder effect": a reduction in genetic variation that results when a small population is used to establish a new colony. The precise level of genetic variation indicates that the small founding population of horses arrived in the Yakutian region about 800 years ago, in the 13th Century.
"We can exclude the possibility that the Yakutian horses descended from the horses that existed in Yakutia in ancient times," Orlando says.
The team's analyses placed the nine modern-day Yakutian horses and the Yakutian horse from the 19th century within the "evolutionary tree" of domesticated horses. They fall closest to the Mongolian, Fjord and Icelandic horses, with the Mongolian horses their most likely ancestors.
But the Yakutian horses differ significantly in appearance to these Mongol horses. They have adapted to their new environment in just 800 years.
"This is blink-of-an-eye evolution," says Doug Antczak, a veterinarian and equine scientist at Cornell University in Ithaca, New York. "What really captures peoples' imaginations from this research is the evidence for rapid adaption to the environment – in this case a cold, harsh, dry environment."

It shows that there are only so many ways a mammal can get adapted to such environments

Focusing on the variation in the Yakutian horse genome, the team identified the key biological functions involved in the adaptive process: those that modified the morphology, hormones and metabolism of the horses. They found variations in the gene pathways involved in hair development, limb length and body size, explaining the Yakutian horses' unique appearance.
Icelandic and Fjord horses are also squat and fat with thick hair coats, whereas horses that live in the desert, such as Arabian horses, have shorter and finer hair coats. "There's an infinite gradation between the horses that have fine hair coats and the Yakutian horses," Antczak says.
The geneticists also found genes associated with the metabolism of sugars including glucose, which can have anti-freezing properties in the blood.
In July 2015, a team of scientists compared the genomes of ancient woolly mammoths to those of elephants to determine the features that contributed to the mammoth's appearance and ability to withstand extreme cold. The researchers found similar variations in hair growth, metabolism and stature.
"It shows that there are only so many ways a mammal can get adapted to such environments," Orlando says.
But typically, a mammal would take millennia to reach the level of hardiness that Yakutian horses exhibit today.
"It is amazing that in just 800 years, which is only about a hundred generations for horses, you can get from a regular horse, a type of Mongolian horse, to the Yakutian horses we have today," Orlando says. "It tells you how fast evolution can go."

Ice Age ABCs?

Why Are These 32 Symbols Found In Ice Age Caves Across Europe?

7 December, 2015 by Maiya Pina-Dacier

 

Archaeologist Genevieve von Petzinger has made an incredible discovery.

There’s something about caves that draws you in; as soon as you cross their threshold, you enter a surreal and shadowy alternative world. Back when Europe was deep in the Ice Age something drew people in then too; and they left their marks all over the walls.
Archaeologist Genevieve von Petzinger has been studying these marks, which are not only among some of the world’s oldest art, but also some of the most famous. Who can say they have not been impressed by the paintings of Lascaux or Altamira? But, says von Petzinger in a landmark TED talk, we’ve been so caught up by the beautiful, flowing artistry of these painted animals, that we’ve missed something even more remarkable.

Don’t let the animals distract you…

Among the elaborate horses, bulls, bears and hunters, there are some other rather less captivating designs – small geometric motifs, etched onto the walls. Until now, they’ve not received much attention. But as it turns out, these humble designs conceal a much more intriguing mystery.
Von Petzinger and her photographer-husband visited 52 caves across Europe recording every instance of these symbols that they could see. They found new, undocumented examples at 75% of the caves they visited, and found the symbols far outnumbered the human and animal images. But the amazing thing was that however many caves they visited, they found the same 32 shapes being used again and again and again.

Ice Age alphabet?

The fact that the same 32 symbols are repeated across sites that span 30,000 years and an entire content is nothing less than mindblowing. But what do they actually mean?
The oldest written texts appear well over 5,000 years ago, and these symbols appear some 25,000 years earlier than that, but they don’t quite seem to form a written language – there are neither enough characters to represent all their spoken words, nor do they repeat often enough to be some sort of alphabet.
Nevertheless, they clearly meant something to whoever created them and von Petzinger concludes that whatever that meaning was, these symbols changed the course of human communication; no longer confined to spoken words, or gestural movements, 25,000 years ago human communication finally became graphic too.

Yet more on reality's AntiDarwinian bias.II

Peer-Reviewed Article on Transposable Elements Cites "Irreducible Complexity" and Other "Teleologic" Factors
Casey Luskin December 24, 2015 1:07 PM

A new peer-reviewed article in Wiley's eLS, "Transposons in Eukaryotes (Part B): Genomic Consequences of Transposition," reviews the role of transposable elements (TEs). Plant geneticist Wolf-Ekkehard Lönnig argues that "irreducibly complex" structures may defy explanation by TEs or other Darwinian factors:

A general difficulty to be mentioned in this context (but not inherent in the selfish DNA hypothesis) is that mutation and selection may not be the full explanation for the origin of species; that is, the factors of the neo-Darwinian scenario may find their limits, for example, in the generation of 'irreducibly complex structures' (Behe, 2006, 2007). This is a term used to describe structures that, according to Behe, cannot be explained by a piecemeal production via intermediate steps. Among the examples discussed by Behe are the origins of (1) the cilium, (2) the bacterial flagellum with filament, hook and motor embedded in the membranes and cell wall and (3) the biochemistry of blood clotting in humans. Moreover, the traps of Utricularia (Lönnig, 2012) and some other carnivorous plant genera as well as several further apparatus in the animal and plant world appear to pose similar problems for the modern synthesis (joints, echo location, deceptive flowers, the reproductive system of the Australian gastric brooding frog Rheobatrachus silus, the mechanical gears of the nymph stage of the leaf hopper Issus coleoptratus etc.). Up to now, none of these systems has been satisfactorily explained by neo-Darwinism. Whether accelerated TE activities with all the above named mutagenic consequences can solve the questions posed remains doubtful in the eyes of the critical observer. Moreover, natural selection itself may not have the stringency usually ascribed to it (for details, see ReMine, 1993; Lönnig, 2001, 2012, 2014).
(Wolf-Ekkehard Lönnig, "Transposons in Eukaryotes (Part B): Genomic Consequences of Transposition," In: eLS. John Wiley & Sons, Ltd: Chichester. DOI: 10.1002/9780470015902.a0026265 (August 2015).)

While unguided mutational processes involving TEs seem incapable of producing irreducibly complex structures, the article notes that some believe there may be "teleologic benefits" from TE activities:
Concerning the totally unexpected and extraordinarily high level of current DNA transposition activities in bats in clear contrast to near extinction or absence of such elements in all other mammals, Huang et al. (2012) give sympathetic consideration to 'teleologic benefits' (among others) promoting active DNA transposons in the order Chiroptera (perhaps via HT; Tang et al., 2015). A 'pacemaker proponent' sensu lato may perhaps ask whether teleologic benefits could also be involved in an independent origin of the Transip TEs and the immune system of jawed vertebrates (not to mention teleology in the sense of Behe, 2006, 2007).
The article cites ID scientists including Jonathan Wells and Richard Sternberg while noting that they and other researchers think that non-coding DNA is largely functional:
In the wake of the ENCODE (encyclopedia of DNA elements) project, several authors are even favouring positions that almost approach the assumption of 100% functional DNA in all genomes, that is, there is no junk DNA in the genomes of plants and animals at all (Shapiro and von Sternberg, 2005;Wells, 2011).
The article concludes by observing that "several lines of evidence" including "irreducibly complex systems" challenge current evolutionary models and should spur us to follow the evidence unswervingly:
[S]everal lines of evidence concerning the origin of life forms, possibly from irreducibly complex systems such as the bacterial flagellum to Darwin's 'abominable mystery' of the origin of angiosperms as well as the Cambrian explosion (for the latter cf. Erwin and Valentine, 2013) may surpass our present knowledge of the causes and factors involved in variation so far known (including TEs) -- this, as well as the strongly divergent opinions on TEs and evolution -- should be a powerful incentive for further efficient empirical and theoretical research wherever it may lead.

"Wherever it may lead..." That sounds like good advice.

File under "well said" XVII

"Well done is better than well said."
Benjamin Franklin

The Fourth horseman is getting deadlier.

Tinkerer V. Artist

Why Would Evolution Produce Non-Essential Genes?
Evolution News & Views December 22, 2015 2:09 PM

Recent papers have tried to identify the subset of all genes in a genome that are essential for viability. In "The Indispensable Genome," Science Magazine considers this capability a turning point in biology:

Game-changing moments in functional genomics often reflect the development and application of powerful new reagents and methods to provide new phenotypic insight on a global scale. Three independent studies describe systematic, genome-scale approaches to defining human genes that are indispensable for viability, which collectively form the essential gene set. On pages 1092 and 1096 of this issue, Blomen et al. (1) and Wang et al. (2), respectively, report a consistent set of ~2000 genes that are indispensable for viability in human cells. Moreover, very similar results were obtained by Hart et al. (3). For the first time, we now have a firm handle on the core set of essential genes that are required for human cell division. This opens the door to studying the roles of essential genes, how gene essentiality depends on genetic and tissue contexts, and how essential genes evolve. [Emphasis added.]

This achievement follows on the heels of yeast studies where researchers found only 1/6 of its 6,000 genes to be essential. That's an astonishingly low fraction. What functions do essential genes perform?

The yeast essential genes encode proteins that drive basic cellular functions such as transcription, translation, DNA replication, cell division cycle control, and fundamental metabolism. Moreover, the yeast essential genes share several attributes that reflect their critical role in cellular life. For example, they are often conserved and evolutionarily constrained, are highly expressed, and encode abundant proteins that tend to form stable complexes and thus are rich in protein-protein interactions.

The landscape of essential genes in human cells can now be explored using the conceptual framework established in yeast.

All three studies on human cells found only 10 percent of the 20,000 genes in the human genome are essential. What is the other 90 percent doing?

Boone and Andrews, authors of the review, indicate that patterns in the human essential genome are similar to those in the yeast essential genome:

All three groups found that human essential genes are highly conserved, and much like yeast, they encode abundant proteins that engage in protein-protein interactions. The core set of human cell essential genes also tend not to be duplicated and appear to have increased evolutionary constraints, as they evolve slowly and are associated with fewer deleterious single-nucleotide polymorphisms. Although many essential genes are involved in fundamental biological processes including transcription, translation, and DNA replication, a substantial fraction remains functionally uncharacterized. Indeed, each analysis prioritized a wealth of uncharacterized genes whose essential roles are waiting to be explored.

That leaves about 18,000 "non-essential" genes to explore. One possibility is that they really are essential, too, when partnered with other genes. Yeast cells, for instance, can survive two non-lethal single mutations, but die when both occur together. This is called "synthetic lethality." Researchers have identified hundreds of thousands of these synthetic lethal interactions in yeast, they say. Initial studies in humans show the following pattern (notice the use of the phrase "functional information"):

Blomen et al. begin to address the extent of synthetic lethal interactions in human cells by screening a set of five nonessential genes with roles in secretion for synthetic lethal negative genetic interactions. They discovered an average of ∼20 synthetic lethal double-mutant interactions for a given nonessential gene, and these interactions tend to occur with functionally related genes. Even this relatively small genetic network suggests that the properties of the extensive genetic networks mapped for yeast are conserved and can now be mapped efficiently in human cells. The genetic network described by Blomen et al. ought to catalyze large-scale, collaborative efforts to map genetic interactions in human cells. Such an effort promises to enable functional annotation of the human genome, because genetic interaction profiles are rich in functional information and provide a quantitative measure of gene function.

These discoveries have the effect of raising the number of essential genes. If a cell can't survive a double hit on two interacting genes (a "synthetic lethal" condition), this indicates functionality even if each gene can take a hit on its own.

The studies of Blomen et al., Wang et al., and Hart et al. reveal the core essential gene set for human cells, setting the stage for the next wave of new genetic and chemical-genetic science that will take place directly in human cells. A future challenge will be to develop genetic tools, such as conditional alleles of essential genes, for exploring the terminal phenotypes and the various molecular mechanisms underlying the lethality associated with perturbation of different essential functions.

How often do double mutants occur in non-essential genes? If infrequent, synthetic lethals will be invisible to purifying selection. A non-essential gene can mutate and life will go on. Wang et al. say as much:

Essential genes should be under strong purifying selection and should thus show greater evolutionary constraint than that of nonessential genes. Consistent with this expectation, the essential genes found in our screens were more broadly retained across species, showed higher levels of conservation between closely related species, and contain fewer inactivating polymorphisms within the human species, as compared with their dispensable counterparts (Fig. 2, E to G). Essential genes also tend to have higher expression and encode proteins that engage in more protein-protein interactions.

Blomen et al. claim similar findings: essential genes show more conservation. They claim that "old" essential genes "emerged in premetazoans." But then, to their surprise, they found new essential genes incorporated into old existing functional genes:

Remarkably, the products of "new" essential genes are more often connected with old rather than other new essential gene products, suggesting that they largely function within ancient molecular machineries (fig. S9, B and C).

In PNAS, Rubin et al. looked for "The essential gene set of a photosynthetic organism." They identified "718 putative essential genes" for the photosynthetic lifestyle of a cyanobacterium.

There are certain limitations to the essentiality information determined here. Although we identified genes that are essential to the organism when individually mutated, they do not represent a minimal gene set. Essential processes for which there are redundant genes will not be discovered using an approach based on single mutants. In S. elongates, however, this complication is of lesser concern than in most other cyanobacteria because of its small genome size, which at a streamlined 2.7 Mbp, harbors little redundancy. In addition, the findings of essentiality reported here apply only to the specific laboratory conditions used and are likely to be different for a subset of genes under other growth conditions. Finally, because ncRNAs, regulatory regions, and other intergenic regions are much smaller, on average, than protein-coding genes, the essentiality calls for these regions are inherently of lower confidence than those made for protein-coding genes. Therefore, conclusions of essentiality for non-coding loci and to a lesser extent, protein-coding genes must be validated by targeted mutation before definitive statements can be made about their essentiality.

In short, the count of essential genes will vary by lab and researcher. This is definitely a work in progress, so measures of essential genes will need refinement with more study.

Contrasting Predictions

Let's integrate this information by contrasting the predictions of design and Darwinism about essentiality. The distinctions are not clear cut. On the one hand, Darwinians would like to see purifying selection acting to eliminate non-essential genes because, for large populations like yeast, they incur a metabolic cost. On the other hand, Darwinians have historically appealed to "junk DNA" and "vestigial organs" to explain things that do not appear essential, pointing to the weakness of purifying selection to eliminate mutations.

Design advocates, too, maintain competing expectations in tension. They would like to find functions for all gene activity to falsify the junk-DNA myth. But they would like to allow for functions beyond mere survival: functions that a designer with an artistic taste would create for beauty and pleasure.

So who's winning this debate on essentiality? It's too early to tell. Not enough is known yet. Based on experience with ENCODE and modENCODE, it seems likely that more functions will be found for everything in the genome (barring neutral or near-neutral mutations), but they will not always be essential for survival. There is a wealth of phenotypic evidence to support this: the beautiful spirals of a conch shell, elaborate patterns in fur and feathers, and other cases of elegant design that seem to go beyond the requirements for reproduction. Animals could satisfy Darwin's criteria by being all gray and just getting by till they have offspring, but life is incredibly vibrant with "useless" beauty. One suspects that genotypic evidence will follow suit.


Boone and Andrews point to "a wealth of uncharacterized genes whose essential roles are waiting to be explored." Who is better prepared to explain what the "substantial fraction" of genes that remain "functionally uncharacterized" do -- those who start with the assumption that "if it works, it's not happening by accident" or those who expect cobbled-together bits of junk?

On our neighbours' minds.

Furry, Feathery, and Finny Animals Speak Their Minds 
Denyse O'Leary December 22, 2015 3:27 AM 

Much research on animal minds is rooted in Darwinian naturalist assumptions -- a long slow continuum of intelligence from somewhere just north of cytoplasm to humans. These assumptions may have set us back. First, just being a life form includes a drive to survive and an ability to adapt for that purpose, which we do not find in rocks. Many life forms can also communicate for those purposes. But, so far as we know, they lack consciousness or sentience, the ability to feel things. There is no slow ascent; there is a steep cliff.
At the other end of the spectrum are apes, who belong to the same order of life as ourselves. Discussions of their intelligence often assume that they are entering a "Stone Age" (such as the Lascaux cave artists lived in, 20 000 years ago). However, while apes tend to be more intelligent than most mammals, they are not becoming like humans. And smart birds give apes serious competition, when tested.

So what can we learn from other vertebrate life forms, forms that show intelligence but are not closely related to us, do not seem much like us, and are not apparently heading in our direction?

Can Animal Mind Be Explained by "Instinct"?

At one time, it was supposed that most animals were simply born with instincts about what to do. The term is not used much now because it mainly meant that we do not know the source of the animal's information. We are now learning many of these sources.

We have recently discovered, for example, that migrating birds can use the mineral magnetite, embedded above their beaks, to use Earth's magnetic fields for direction.

We learned in recent decades how young birds "know" that they should follow their mother: As Spark Notes explains, following the work of animal behaviorist Konrad Lorenz (1903-1989):

Johnson and Bolhuis identified two independent neural systems that control filial imprinting in precocial birds. Newly hatched chicks will follow almost anything that has eyes and moves. After the chick follows something, another part of the brain, analogous to the frontal cortex, recognizes and imprints on the individual being followed. These mechanisms are independent. There is an instinct for chicks to follow, and then they learn what they are following.
But the "follow her" system is not strictly genetic:

It might seem odd that being able to identify and follow a mother does not have a genetic mechanism. Yet with a neural rather than genetic mechanism, the chick gains flexibility that might help in survival. If a chick's mother dies, the chick can then be adopted by another family member or conspecific.
Yes indeed. Famously, the young bird may follow a psychology student, a stick, or a cat, with varying results. Bird rescuers use hand puppets of bird faces when caring for nestlings, to return them later to a natural setting. Clearly, not all we need to know about an organism is in its genes.

How then does the male weaverbird know how to build a nest? That's apparently not simply a genetic program either; the birds must learn some of the techniques by experience.

Genetics, neural networks, and experience all make animal learning much more complex and information-rich than the concept of "instinct" implied. But we are not yet in the realm of "intelligence." The migrating and nest-building birds access existing solutions to longstanding problems; they do not come up with new ones.

Both birds and mammals can learn to solve new problems presented to them. Let's look at some recent finds in mammals first, bearing in mind that we have only really begun to look at their intelligence seriously. It is early days yet, so some sketchiness is inevitable.

Mammals' Unexpected Intelligence

We find intelligence where we did not expect it. Pigs, for example (despite their reputation), are "socially complex as other intelligent mammals, including primates" (Natural History Magazine). That is surprising because pigs don't usually form close relationships with humans, as dogs do. And hog farming operations don't encourage intelligence.

We know more about the intelligent animal we are close to. In terms of communication, horses' surprisingly varied facial expressions are more similar to those of humans on one measurement than those of chimps are:

The Equine Facial Action Coding System (EquiFACS), as devised by the Sussex team in collaboration with researchers at the University of Portsmouth and Duquesne University, identified 17 "action units" (discrete facial movements) in horses. This compares with 27 in humans, 13 in chimps and 16 in dogs.
That might account for the human-horse bond (there seems no similar chimp-horse bond).

Horses', dogs', and cats' tail communications are also easy to read (they are intended to be). So just as dogs can understand finger pointing even though they don't have fingers, humans can understand some dog messages even though we don't have tails. The habit of co-operative communication can overcome physical barriers.

Thus, one understudied question is whether and when mammal intelligence changes on account of association with humans. Let us say that an indoor domestic dog or cat is freed from the need to hunt, protect herself, or raise offspring. Consequently, she enjoys a vastly increased life expectancy. Some such animals focus on status issues with respect to people and other dogs/cats, etc., generating layers of social complexity that are unlikely in a wilderness environment. She shows no progress toward human intelligence, but her human environment may determine how much canine or feline intelligence she lives to display.

"Feathered Primates" without Primate Brains?

Ravens can match or beat chimpanzees on some accepted tests of animal intelligence. Some researchers call crows "feathered primates." New Zealand crows' causal understanding (within limits) is said to rival that of 5-7 year old children. Or 7- to 10-year old children.

Some New Caledonian crows can use three tools in succession to reach food, and can also enact Aesop's fable by dropping stones into a jar of water till floating food rises.

It's not just crows. Pigeons' ability with numbers up to nine is "indistinguishable from that displayed by monkeys." Even the intelligence of the chicken "startles," according to Scientific American ("communication skills on par with those of some primates").

But how do we understand bird intelligence, given that bird brains show significant differences from mammal brains? And we can hardly fall back on common ancestry.

Language ability is an uncertain guide. Some birds are popularly held to be intelligent because they can imitate the human voice. This ability may be related to structural features of those bird species' brains:

In addition to having defined centers in the brain that control vocal learning called "cores," parrots have what the scientists call "shells," or outer rings, which are also involved in vocal learning.
That "shell" structure may be related to some parrots' ability to dance to music as well. But these birds probably don't know what they are saying or doing apart from the fact that, like the bicycling cockatoo, they are typically rewarded for doing it.

Alex the parrot (1976-2007), possibly the most famous "intelligent bird" personality, could use human language to communicate needs. However, he had only typical parrot needs. Alex was not achieving more human-like intelligence--as his researcher and patron Irene Pepperberg acknowledged:

"I avoid the language issue," she said. "I'm not making claims. His behavior gets more and more advanced, but I don't believe years from now you could interview him." She continued: "What little syntax he has is very simplistic. Language is what you and I are doing, an incredibly complex form of communication."
Put another way, if an intelligent dog had "vocal cords" (a syrinx) like a parrot, he could tell a human in words that he needs to go outside or have his water dish refilled. But he does not go on to express interest in things that do not naturally concern a dog.

One interesting thing we learned recently about smart crows is that they don't depend much on learning from each other (social learning):

Logan and colleagues found that the crows don't imitate or copy actions at all. "So there goes that theory," she said. ...
Even if one crow is at an apparatus and tries unsuccessfully to open the door, if he or she sees another crow on the second apparatus actually solving the problem correctly, the first crow doesn't use that information. "The social learning attracts them to a particular object and then they solve it through trial and error learning after that," Logan said.

The crows' pattern of learning seems different from human learning, and may be related to an inability to grasp or convey abstract information. Which brings us to the recent claim that crows fear death because many crows purposefully avoid places where other crows have died:

And this fear of a potential deadly situation stays with them. Even six weeks later more than a third of 65 pairs of crows continued to respond this way.
But, like the claim that chimpanzees mourn their dead, this one is founded on a misunderstanding: "Death" -- unlike danger or loss, which are experienced viscerally -- is a pure abstraction, like the number 23. An intelligent life form must understand not merely nature but the nature of nature to know what "death" means.

So we come to a culturally unexpected conclusion: Bird intelligence is a respectable competitor on a continuum with primate intelligence. But, like theirs, it is on a different track from that of humans.

Then There Are Those Cold-Blooded Reptiles and Fish...

A number of recent marketing strategies promise sales through appealing to a customer's "self-centered" reptilian brain. But that piece of business folk wisdom is based on a myth:

It is the idea that we have three brains: a reptilian one, the paleomammalian one and the mammalian one. The story goes that these were acquired one after another during evolution. The details differ with the writer. But it is all a myth based on an idea from the '70s of Paul MacLean which he republished in 1990. Over the years in has been popularized by Sagan and Koestler among others.
The brain is hardly so simple. Reptiles lack certain brain structures found in mammals, but like birds they sometimes use the ones they have for purposes that apparently display intelligence: Crocodilians (alligators and crocodiles) are reported to use sticks as decoys, play, and work in teams. Tortoises may well be smarter than once believed, though here we rely mainly on anecdotes, not formal studies, for now.

Even fish have shown signs of what seems like intelligence. We are told that pairs of rabbitfishes "cooperate and support each other while feeding":

While such behaviour has been documented for highly social birds and mammals, it has previously been believed to be impossible for fishes. ... "We found that rabbitfish pairs coordinate their vigilance activity quite strictly, thereby providing safety for their foraging partner," says Dr Simon Brandl from the ARC Centre of Excellence for Coral Reef Studies.
Why don't reptiles and fish appear intelligent? Here is a possible clue: Anole lizards were found as capable as tits (birds) in a problem-solving test for a food reward. But the anoles, being exothermic, don't need much food -- which hinders research. When reptiles and fish need to solve problems, they often use the brain structures available to them quite effectively. The rest of the time they may be comfortably inert. If so, the relationship between brain structure and intelligence is more complex than we have supposed.

Factors That May Promote Intelligence in Vertebrates

We have seen that, while brain structure is not the absolute limitation once supposed, cold-bloodedness (exothermic metabolism) may reduce the need for intelligence without actually preventing it. Conversely, living with humans may promote intelligence by creating systematic rewards for achievement. Nature, it is true, rewards intelligence, but not systematically, like a dedicated trainer seeking a response. So there are rough general trends in intelligence, as in evolution, but they appear to be patterns, not laws.

Do the patterns relate in some way to anatomy? Can we say, for example, that intelligence requires a multicellular life form that has a spinal column and a brain? What can the vast world of invertebrates tell us about that?

Who is hearer of prayer?:The Watchtower Society's commentary.

Should We Pray to Jesus?:

A RESEARCHER recently polled over 800 youths from more than a dozen religious denominations, asking whether they believed that Jesus answers prayers. Over 60 percent said that they firmly believe that he does. However, one youth crossed out the name Jesus on the survey and wrote “God” instead.

What do you think? Should we address our prayers to Jesus or to God?* To find the answer, first let us consider how Jesus taught his disciples to pray.

TO WHOM DID JESUS TEACH US TO PRAY?:
Jesus praying to his Father[Picture on pages 14, 15]
In praying to his heavenly Father, Jesus set an example for us to follow
HIS TEACHING: When one of his disciples asked Jesus, “Lord, teach us how to pray,” Jesus replied: “Whenever you pray, say: ‘Father.’” (Luke 11:1, 2) Further, in his famous Sermon on the Mount, Jesus urged his listeners to pray. He said: “Pray to your Father.” He also reassured them by saying: “Your Father knows what you need even before you ask him.” (Matthew 6:6, 8) On his final night as a human, Jesus told his disciples: “If you ask the Father for anything, he will give it to you in my name.” (John 16:23) Jesus thus taught us to pray to the one who is both his Father and our Father, Jehovah God.—John 20:17.

HIS EXAMPLE: In line with the way he taught others to pray, Jesus personally prayed: “I publicly praise you, Father, Lord of heaven and earth.” (Luke 10:21) On another occasion, “Jesus raised his eyes heavenward and said: ‘Father, I thank you that you have heard me.’” (John 11:41) And as he was dying, Jesus prayed: “Father, into your hands I entrust my spirit.” (Luke 23:46) In praying to his heavenly Father—the “Lord of heaven and earth”—Jesus set a clear example for all to follow. (Matthew 11:25; 26:41, 42; 1 John 2:6) Is that how Jesus’ early disciples understood his instructions?

TO WHOM DID THE EARLY CHRISTIANS PRAY?


Within weeks of Jesus’ return to heaven, his disciples were being harassed and threatened by their opposers. (Acts 4:18) Of course, they reached out in prayer—but to whom did they turn? “They raised their voices with one accord to God,” praying that he would continue helping them “through the name of [his] holy servant Jesus.” (Acts 4:24, 30) So the disciples followed Jesus’ guidelines on prayer. They prayed to God, not to Jesus.

Years later, the apostle Paul described the manner in which he and his associates prayed. Writing to fellow Christians, he said: “We always thank God, the Father of our Lord Jesus Christ, when we pray for you.” (Colossians 1:3) Paul also wrote to his fellow believers about “always giving thanks to our God and Father for everything in the name of our Lord Jesus Christ.” (Ephesians 5:20) From these words, we see that Paul encouraged others to pray to his “God and Father for everything”—but, of course, in Jesus’ name.—Colossians 3:17.

Like the early Christians, we can show our love for Jesus by heeding his advice on prayer. (John 14:15) As we pray to our heavenly Father—and to him alone—the words of Psalm 116:1, 2 will become ever more meaningful to us: “I love Jehovah because he hears my voice . . . I will call on him as long as I live.”*

According to the Scriptures, God and Jesus are not equal. For more information, see chapter 4 of the book What Does the Bible Really Teach? published by Jehovah’s Witnesses.

In order for our prayers to be acceptable to God, we must sincerely endeavor to live up to his requirements. For more information, see chapter 17 of the book What Does the Bible Really Teach?

Did They Pray to Jesus?:

The Bible records a few occasions when faithful humans spoke to the heavenly Jesus—and sometimes to angels. (Acts 9:4, 5, 10-16; 10:3, 4; Revelation 10:8, 9; 22:20) But were those men praying to these heavenly creatures? No. In all such instances, the heavenly creatures initiated the communication. Faithful men and women reserved prayer for God alone.—Philippians 4:6.

The Biblical deluge global or local?:The Bible's answer

We can begin our examination of this issue with God's proclamation to the prophet Noah.Genesis6:13 ASV "And God said unto Noah, The end of all flesh is come before me; for the earth is filled with violence through them; and, behold, I will destroy them with the earth." Genesis6:17ASV"And I, behold, I do bring the flood of waters upon this earth, to destroy all flesh, wherein is the breath of life, from under heaven; everything that is in the earth shall die." Points to note here: the wickedness of man has become,in the eyes of the creator,a global problem requiring a global response. Later the apostle Peter invokes the historical account as a warning to those who doubt Jehovah God's ability/willingness to act decisively to bring an end to the present corruption of our global civilisation 2Peter3:5,7.As you read Peter's words recorded at the cited passage do you get the impression that he thought of the flood as a local event?
Another consideration would be the preparations that Noah were instructed to make.Genesis6:14-16ASV"Make thee an ark of gopher wood; rooms shalt thou make in the ark, and shalt pitch it within and without with pitch. 15And this is how thou shalt make it: the length of the ark three hundred cubits, the breadth of it fifty cubits, and the height of it thirty cubits. 16A light shalt thou make to the ark, and to a cubit shalt thou finish it upward; and the door of the ark shalt thou set in the side thereof; with lower, second, and third stories shalt thou make it." Thus the creator outlined decades of work for his servants.Much of which seems superfluous if we understand the deluge as a local event.Why not simply have Noah and his family migrate from the targeted locale?The local fauna esp.the birds could likewise evacuate the area.
Finally we can examine the Bible's description of the event itself:
Genesis7:17NASB"Then the flood came upon the earth for forty days, and the water increased and lifted up the ark, so that it rose above the earth. 18The water prevailed and increased greatly upon the earth, and the ark floated on the surface of the water. 19The water prevailed more and more upon the earth, so that all the high mountains everywhere under the heavens were covered. 20The water prevailed fifteen cubits higher, and the mountains were covered. 21All flesh that moved on the earth perished, birds and cattle and beasts and every swarming thing that swarms upon the earth, and all mankind; 22of all that was on the dry land, all in whose nostrils was the breath of the spirit of life, died. 23Thus He blotted out every living thing that was upon the face of the land, from man to animals to creeping things and to birds of the sky, and they were blotted out from the earth; and only Noah was left, together with those that were with him in the ark. 24The water prevailed upon the earth one hundred and fifty days." Points to note:The flood is described as covering all of earth's tallest mountains by at least twenty two feet.The flood brings and end to all terrestrial life outside of the ark.The waters of this flood kept rising for one hundred and fifty days,very unlike any local flood in recorded history.Genesis8:5NASB"The water decreased steadily until the tenth month; in the tenth month, on the first day of the month, the tops of the mountains became visible." This is after eight months.
Interestingly there are flood legends native to cultures globally many of which bear such uncanny parallels to the Bible's account that in would be unreasonable to postulate an independent origin to them,rather it seems more likely that in these we have echoes of a spectacular event etched in humankind's collective memory.This too seems to point to a global event.

On the "logic" of the abyss.

Assessing the "Logic" of Legalized Euthanasia

Wesley J. Smith December 17, 2015 1:59 PM 

ournalist Andrew Coyne has written some of the best critiques of legalized euthanasia of which I am aware. He has another A+ effort out in Canada's National Post, reacting to the recommendations of an ethics panel for implementing that country's Supreme Court order to allow euthanasia. From "The Absurd Logic of Assisted Suicide":

When dispatching a patient by lethal injection, would a doctor be obliged to sterilize the needle?

I think they almost certainly would. Old habits die hard, you should pardon the expression, and the unconscious need to shroud an act that at time of writing remains illegal under the Criminal Code as a routine medical procedure would make it unthinkable to do otherwise, however nonsensical it may be.

That's the thing about normalizing suicide. It requires us to set aside all prior assumptions except the most absurd ones. It rushes past all sorts of distinctions that might once have seemed important -- between killing yourself and killing someone else, for example -- yet clutches wildly at others, as if they were any more likely to withstand the momentum of its logic.

Exactly. Once you accept euthanasia's premise, your mindset turns 180 degrees: Up becomes down, in becomes out, compassion becomes killing. Coyne's conclusion shows exactly where Canada -- and the U.S., if we keep following the same path (albeit, more slowly) -- are heading:

Advocates see suicide...as a release from suffering; not as an evil to be prevented, but as a service to be provided (indeed, the panel recommends it be done at public expense).

This presents the right to die, not as a limited one, such as the right to drive, but as an unlimited one, inhering in all persons -- rather like the right to life. And, it has to be said, it is by far the more coherent of the two arguments.

For if assisted suicide is a right to be released from suffering, how can that be restricted to adults? Are we to condemn children to endless torment, where we would not an adult?

Likewise for the mentally incompetent: Are we really so indifferent to their pain as to allow their disability to stand in the way of its alleviation? If they are unable to consent to their own death, should they not be assisted, intellectually, in the same way as those physically unable to kill themselves are to be assisted?

This is not some dire prophecy. It is, as the panel reminds us, the logic of assisted suicide. By making it lawful to euthanize children, we would only be following where Belgium and the Netherlands have led; by applying it to the mentally ill, we would be doing no more than Switzerland has already done.

If that is where we want to go, so be it. But let us at least be clear that that is what is really at stake.

Indeed. The lure of death is becoming like a black hole from which little light escapes. Or as Coyne put it so well several years ago in the wake of widespread public support for a father who murdered his 12-year-old daughter because she had cerebral palsy:

A society that believes in nothing can offer no argument even against death. A culture that has lost its faith in life cannot comprehend why it should be endured.

I fear we are devolving into that nihilistic society. It is still not too late to stop the slide. But we had better do that quickly, or we will soon be over the cliff.