At the feet of the original artist/technologist.

A Designer Encourages Scientists to Think Like Designers:

Evolution News & Views January 2, 2016 3:54 AM

Recently Live Science had a reflective piece by Ayse Birsel, an award-winning designer, co-founder of Birsel + Seck, and author of the book, Design the Life You Love. The title of the article is eye-catching: "The Art of Science: Why Researchers Should Think Like Designers." That's an unusual headline for a science site that generally takes the anti-ID position whenever it can.

Birsel's article is not about intelligent design theory or the intelligent design movement. It is, however, very much about "design" -- exploring how designers think. (It's hard to fathom any good designer not being intelligent; "evolutionary design" is an oxymoron, like "unguided purpose" or "aimless goal.")

Ayse Birsel describes her own design process in four stages: (1) Deconstruction, (2) Point of View, (3) Reconstruction, and (4) Expression. Let's see what these mean and what they have to teach about intelligent design in science.

"Deconstruction is breaking the whole apart to see what it's made of," she says. We see this aspect in the upwardly trending science of biomimetics. The "bioneers" movement is focused on deconstructing living designs to understand their design principles, with the goal of designing applications based on those principles. Birsel adds, "You can even deconstruct something very familiar, like science, to see what goes into it." She did that herself, defining science in a quadrant of (a) emotion of science, (b) physical of science, (c) intellect of science, and (d) spirit of science. Her holistic approach exalts science above intellectual drudgery and puts the A (art) back in STEM, producing STEAM (science, technology, engineering, art, and math). The "A," by the way, refers to "Art and Design," she points out.

"Point of View" refers to shifting your point of view intentionally. "In design," she says, "you want to shift from what you know to what you can imagine." Who would ever think, for instance, of creating a carnival dunk tank that engulfs the victim in flames instead of water? Someone actually designed a "Dunk Tank Flambé" at a carnival to teach people about science. "Luckily for John, he is wearing a super-flame-retardant suit," she hastens to add for gasping viewers of a photo of her friend John on fire in the contraption. It's an effective way to shock people out of the rut of the familiar. Certainly in the ID movement, we see the importance of helping people break out of the often-unchallenged Darwinian point of view.

"Reconstruction," Birsel continues, is the other side of Deconstruction. "It is about putting the subject back together again, knowing that you cannot have everything." This means understanding your constraints as a designer, and making choices that to optimize your effort. ID proponents have seen optimization as an example of design-based science. They have used it to answer ID critics who toss up supposed examples of bad design, showing that optimization provides the best compromise between competing trade-offs. What can Reconstruction do for science? It will undoubtedly give biomimetics engineers a new appreciation for biological designs when they try to reconstruct the design principles they encountered in the "Deconstruction" stage. Any scientist taking apart a cell and trying to reassemble it will likely find Darwinian thinking quite unhelpful.

"Expression," finally, is "giving your idea form." Scientists as well as product designers need to do this. "You build on the foundation of your new idea, and you express it as a unique prototype, a product, a strategy, a mathematical formula or a hypothesis." Clearly all five of those things require intelligent design. A scientist thinking like a designer, furthermore, can involve lay people's creativity and optimism to solve problems together. We're seeing progress in this direction, as social media breaks down the walls of stodgy scientific institutions, inviting scientists out into the sunshine of the Internet. More and more, scientists can pre-publish their hypotheses and have them tested by large communities of scientists out in the open, rather than by faceless reviewers behind journal paywalls.

Whether or not one agrees with Birsel's particular analysis, it is encouraging to see Live Science give good press to "design thinking" as a serious proposal for helping scientists improve their work:

Since I often work closely with engineers, I've come to realize that the design process has uncanny similarity to the scientific and engineering processes, yet it differs in key ways. By understanding the design process I use, everyone, including scientists, can gain insight into solving complex problems that they might want to think differently about ... including how to live a complete life. [Emphasis added.]

Birsel's "spirit of science" quadrant includes the words "Honest, Truth, Humanist, Persevering, Universal, Illuminating" -- each of which presupposes a creative and moral human mind with free will. Can science even operate without these? Notice, too, the subtext of human exceptionalism.


It's time to bring the designing mind back into the spotlight. Darwinian thinking has diminished the spirit of science, relegating the human mind to the end product of impersonal, unguided natural processes. "Thinking like a designer" will put STEAM back into the engine of scientific progress.

A thousand words 43 years thence.

Russia needs to allow JWs to speak for themselves.

Experts Object to Russia’s Banning of JW.ORG:

ST. PETERSBURG, Russia—On July 21, 2015, the Russian Federation banned jw.org, the official website of Jehovah’s Witnesses, making it a criminal offense to promote it from within the federation. Russia is the only country in the world to ban jw.org.

Religious studies specialist and professor at the Academy of Labor and Social Relations in Moscow, Yekaterina Elbakyan, comments on jw.org: “I think the website is necessary because it contains objective information directly from Jehovah’s Witnesses about their organization rather than third-party opinions. . . . Not only are its members interested in the website, but also those who are simply interested in various religions. And I’m not only speaking about professional religious scholars like myself but also journalists and publicists who write about religion.”

“I think the website is necessary because it contains objective information directly from Jehovah’s Witnesses”—Yekaterina Elbakyan, Professor, Academy of Labor and Social Relations, Moscow
A legal expert at the Human Rights Institute in Moscow, Lev Levinson, puts this action by the government in historical context: “Twenty-first century Russia has a constitution that guarantees freedom of religion and equality of religious associations before the law. However, as in the 19th century, Russia is again restricting the freedom of sharing one’s religious views by confiscating literature and banning websites. And this is all being done by judges and experts who apply unlawful regulations under the guise of counteracting extremism.”

The ban is the latest development in a legal battle stretching back to 2013. On August 7 of that year, a Russian district court declared the website “extremist” during a secret trial, but that decision was reversed by a regional court on January 22, 2014. However, a Deputy of the Prosecutor General of the Russian Federation appealed to the Supreme Court of the Russian Federation to reinstate the trial decision. On December 2, 2014, the Supreme Court heard the prosecution’s appeal without the Witnesses present to defend themselves, as they were not properly notified of the hearing. The Supreme Court reinstated the trial decision, declaring the entire website “extremist” although the court conceded that the website no longer contained any religious material prohibited by the Russian authorities. The Witnesses contested the decision and appealed to the chairman of the Supreme Court, but without success. As a result of that decision, on July 21, 2015, the Ministry of Justice of the Russian Federation added the website to the Federal List of Extremist Materials, banning the website throughout Russia.

Yaroslav Sivulskiy, a spokesman for Jehovah’s Witnesses in Russia, comments on the impact of the ban: “We are disappointed that the Russian authorities have taken this unwarranted action. This ban curtails the worship of over 170,000 in this country who are Jehovah’s Witnesses. But when you consider that some 285,000 people in Russia accessed the website every day, it is clear that even those who are not members of our faith have been deprived of an excellent resource for Bible study.”

Speaking from the Witnesses’ world headquarters in Brooklyn, New York, J. R. Brown, an international spokesman for Jehovah’s Witnesses, states: “Our official website, jw.org, hosts award-winning videos, publications for Bible study in hundreds of languages, and the two most widely distributed magazines in the world, The Watchtower and Awake! It has been featured in some of the largest international book fairs and has even been used extensively in schools. It has benefited many communities around the world and was widely used in Russia. Really, this is a website that should be promoted.”

Media Contact(s):

International: J. R. Brown, Office of Public Information, tel. +1 718 560 5000


Russia: Yaroslav Sivulskiy, tel. +7 812 702 2691

The Watchtower Society's commentary on Joy.

JOY:

The emotion excited by the acquisition or expectation of good; state of happiness; exultation. The Hebrew and Greek words used in the Bible for joy, exultation, rejoicing, and being glad express various shades of meaning, different stages or degrees of joy. The verbs involved express the inner feeling and the outward manifestation of joy and variously mean “be joyful; exult; shout for joy; leap for joy.”

Jehovah God and Jesus Christ. Jehovah is called “the happy God.” (1Ti 1:11) He creates and works with joy for himself and his creatures. What he brings about makes him joyful. (Ps 104:31) He wants his creatures likewise to enjoy his works and to enjoy their own work. (Ec 5:19) Since he is the Source of all good things (Jas 1:17), all intelligent creatures, both mankind and angels, can find their chief enjoyment in coming to know him. (Jer 9:23, 24) King David said: “Let my musing about him be pleasurable. I, for my part, shall rejoice in Jehovah.” (Ps 104:34) He also sang: “The righteous one will rejoice in Jehovah and will indeed take refuge in him; and all the upright in heart will boast.” (Ps 64:10) The apostle Paul urged Christians to take joy at all times in their knowledge of Jehovah and his dealing with them, writing to them: “Always rejoice in the Lord [“Jehovah,” in several versions]. Once more I will say, Rejoice!”—Php 4:4.

Jesus Christ, who was the intimate one of Jehovah, knows him best (Mt 11:27), and he is able to explain Him to his followers. (Joh 1:18) Jesus is therefore joyful, being called “the happy and only Potentate.” (1Ti 6:14, 15) Out of love for his Father, he is eager to do always the things that please Him. (Joh 8:29) Therefore, when there was set before him the task of coming to earth, suffering, and dying in order that he might clear his Father’s name of reproach, “for the joy that was set before him he endured a torture stake, despising shame.” (Heb 12:2) He also had great love for and joy in mankind. The Scriptures, personifying him in his prehuman existence as wisdom, represent him as saying: “Then I came to be beside [Jehovah] as a master worker, and I came to be the one he was specially fond of day by day, I being glad before him all the time, being glad at the productive land of his earth, and the things I was fond of were with the sons of men.”—Pr 8:30, 31.

Jesus desired his followers to have the same joy, telling them: “These things I have spoken to you, that my joy may be in you and your joy may be made full.” The angels had joy at the creation of the earth. (Joh 15:11; 17:13; Job 38:4-7) They also view the course of God’s people, taking joy in their faithful course and especially exulting when an individual turns from his sinful ways to the pure worship and service of God.—Lu 15:7, 10.

What makes God joyful. Jehovah’s heart can be made glad by his servants because of their faithfulness and loyalty to him. Satan the Devil has constantly challenged the rightfulness of God’s sovereignty and the integrity of all those serving God. (Job 1:9-11; 2:4, 5; Re 12:10) To them apply the words: “Be wise, my son, and make my heart rejoice, that I may make a reply to him that is taunting me.” (Pr 27:11) Jehovah’s people in the earth can cause God to rejoice by faithfulness and loyalty to him.—Isa 65:19; Zep 3:17.

A Fruit of the Spirit. Since Jehovah is the Source of joy and he desires joyfulness for his people, joy is a fruit of his holy spirit. Joy is named immediately after love in the list at Galatians 5:22, 23. The apostle wrote to the Christians at Thessalonica: “You became imitators of us and of the Lord, seeing that you accepted the word under much tribulation with joy of holy spirit.” (1Th 1:6) Accordingly, Paul counseled the Christians at Rome that the Kingdom of God “means righteousness and peace and joy with holy spirit.”—Ro 14:17.

True joy is a quality of the heart and can affect the whole body for good. “A joyful heart has a good effect on the countenance,” and “a heart that is joyful does good as a curer [or, “does good to the body”],” says the wise writer of Proverbs.—Pr 15:13; 17:22, ftn.

Joy in God’s Service. What Jehovah asks of his servants is not burdensome. (1Jo 5:3) He wants them to enjoy his service. His people Israel were to enjoy the seasonal festivals that he arranged for them, and they were to rejoice in other aspects of their life and worship of God. (Le 23:40; De 12:7, 12, 18) They were to speak out about God joyfully. (Ps 20:5; 51:14; 59:16) If they did not serve with joy of heart, there was something wrong with their hearts and their appreciation of his loving-kindness and goodness. Therefore he warned what would take place if they became disobedient and took no joy in serving him: “All these maledictions will certainly come upon you . . . because you did not listen to the voice of Jehovah your God by keeping his commandments and his statutes . . . And they must continue on you and your offspring . . . due to the fact that you did not serve Jehovah your God with rejoicing and joy of heart for the abundance of everything.”—De 28:45-47.

The Christian, no less, should enjoy his service to God. Otherwise, something is lacking in heart appreciation. (Ps 100:2) “The joy of Jehovah is your stronghold,” said one of God’s faithful servants. (Ne 8:10) The good news the Christian proclaims was announced by God’s angel as “good news of a great joy that all the people will have.” (Lu 2:10) Jehovah’s name upon his witnesses and the truth as found in the Bible should themselves be a joy to them. The prophet Jeremiah said: “Your word becomes to me the exultation and the rejoicing of my heart; for your name has been called upon me, O Jehovah God of armies.”—Jer 15:16.

Moreover, Jehovah’s just, right judicial decisions put into effect in the Christian congregation and in the lives of Christians are cause for joy, especially in a time when the world has thrown justice and righteousness to the ground. (Ps 48:11) Then, too, the marvelous hope ahead surely gives strong ground for joyfulness. (“Rejoice in the hope”; Ro 12:12; Pr 10:28.) Their salvation is a basis for joy. (Ps 13:5) Additionally, there is the joy that the servant of God has in those whom he aids in coming to the knowledge and service of Jehovah. (Php 4:1; 1Th 2:19) Meeting together and working together with God’s people is one of the greatest joys.—Ps 106:4, 5; 122:1.

Persecution a cause for joy. For the Christian who guards his heart, even persecution, though not in itself enjoyable, should be viewed with joy, for endurance of it with integrity is a victory. God will help the faithful one. (Col 1:11) Additionally, it is proof that one is approved by God. Jesus said that when reproach and persecution come, the Christian should “leap for joy.”—Mt 5:11, 12; Jas 1:2-4; 1Pe 4:13, 14.

Other Joys Provided by God. Jehovah has provided many other things that mankind may enjoy day by day. Some of these are marriage (De 24:5; Pr 5:18), being father or mother of a righteous and wise child (Pr 23:24, 25), food (Ec 10:19; Ac 14:17), wine (Ps 104:14, 15; Ec 10:19), and the multitudinous things of His creation (Jas 1:17; 1Ti 6:17).

False or Nonlasting Joys. Jesus speaks of some who would hear the truth and receive it with joy but without getting the real sense of it. Such do not cultivate the implanted word in their hearts and, as a consequence, soon lose their joy by being stumbled when tribulation or persecution arises on account of the word. (Mt 13:20, 21) Joy based on materialism is a false joy that is in error and will be short-lived. Also, a person rejoicing over the calamity of another, even of one who hates him, must account to Jehovah for his sin. (Job 31:25-30; Pr 17:5; 24:17, 18) A young man is foolish to think that enjoyment of life requires that he give in to following “the desires incidental to youth.” (2Ti 2:22; Ec 11:9, 10) Similarly, love of merriment will bring one into a bad situation. (Pr 21:17; Ec 7:4) Even the Christian who exults in comparing himself with others is in error. Rather, he should prove what his own work is and have cause for exultation in himself alone.—Ga 6:4.

Everlasting Joy. Jehovah promised to restore his people Israel after their exile in Babylon. He did bring them back to Jerusalem in 537 B.C.E., and they greatly rejoiced when the temple foundation was laid. (Isa 35:10; 51:11; 65:17-19; Ezr 3:10-13) But Isaiah’s prophecy (65:17) has a greater fulfillment in the establishment of “a new heaven and a new earth,” in which arrangement all mankind will have joy forever under the “New Jerusalem.”—Re 21:1-3.


Under present conditions, wickedness, sickness, and death prevent full and undiminished joy. But in harmony with the Bible rule, “A wise king is scattering wicked people,” Jesus Christ as King will bring an end to all enemies of God and of righteousness. (Pr 20:26; 1Co 15:25, 26) Thus all obstacles to complete joy will be removed, for even “death will be no more, neither will mourning nor outcry nor pain be anymore.” (Re 21:4) Sorrow for those who have died will be completely gone, removed by the resurrection of the dead. This knowledge comforts Christians even today, who, on this account, do not “sorrow just as the rest also do who have no hope.”—1Th 4:13, 14; Joh 5:28, 29.

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?