What's this,the human brain is extremely sophisticated?(Who knew?)

Brain connections “more sophisticated than thought” (straight face here)

Hello, base, do we have a connection? The human brain is said by many to be the most sophisticated known item in the universe.

Never mind, from ScienceDaily::


Inhibitory connections between neurons act as the brain’s brakes, preventing it from becoming overexcited. Researchers thought inhibitory connections were less sophisticated than their excitatory counterparts because relatively few proteins were known to exist at these structures. But a new study overturns that assumption, uncovering 140 proteins that have never been mapped to inhibitory synapses. Some of the proteins have already been implicated in autism, intellectual disability and epilepsy, suggesting new treatment avenues. – Akiyoshi Uezu, Daniel J. Kanak, Tyler W.A. Bradshaw, Erik J. Soderblom, Christina M. Catavero, Alain C. Burette, Richard J. Weinberg, and Scott H. Soderling. Identification of an Elaborate Complex Mediating Postsynaptic Inhibition. Science, September 2016 DOI: 10.1126/science.aag0821 Paper. (paywall) More.

Memo to the new atheists from one of their own:don't open the champagne just yet.

Atheism is doomed: the contraceptive Pill is secularism's cyanide tablet

 
 
 The 1960s counterculture slogan “make love, not war” could have been invented for the Hutterites, a conservative, pacifist Anabaptist community in the US and Canada. Numbering 400 at the end of the 19th century, when they moved to Dakota on the point of extinction, there are almost 50,000 Hutterites today, despite conversion being extremely rare (they speak an archaic form of High German and live in the middle of nowhere, which makes it unlikely they’ll turn up at your doorstep with a funny grin).

They are not alone. The Mormons continue to grow by 40 per cent every decade, largely thanks to a high birth rate, so much so that by 2080 there will be anywhere between 63 and 267 million Mormons, depending on whether that figure falls to 30 per cent or 50 per cent.

And Evangelical Christians now account for two thirds of white American Protestants, while the ultra-Orthodox account for 17 per cent of British Jewry, but 75 per cent of children.

Across the western world the fertility rate of religious conservatives far outstrips that of non-believers, so much so that modern liberal secularism is endangered. That, anyway, is the thesis of Shall the Religious Inherit the Earth?, a fascinating new book by Eric Kaufmann of Birkbeck University, which is published later this month. It may well be one of the most significant books of our era.

It used to be taken for granted that, just as liberal democracy meant the end of history, so it also meant the end of religion. Once people became rich, educated and sexually liberated, they left irrational beliefs and other such nonsense behind.

Christianity declined steadily from the mid-19th century but it wasn’t until the 1960s that European societies were able to fully abandon the emotional baggage of their civilisation’s infancy, and especially its repressive attitude to sex.

But if what Kaufmann is saying is true – and the demographic data suggests it is – then the contraceptive Pill was not so much secular Europe’s liberation as its cyanide tablet.

The good news is that Europe will not become Islamicised (although Kaufmann’s estimate of 20 or 25 per cent is Islamic enough). The bad news (for some) is that it will become Evangelical Protestant instead. This will at least be encouraging for Israel, although whether it will be the same progressive, secular Israel where gays can serve in the military is another matter, as by the second half of the century the ultra-Orthodox will be the majority.

New Atheists comfort themselves with the idea that religious people will continue to drift their way, like rustics to the city, but the figures do not bear this out. It is true that liberal religious people continue to embrace atheism at a rate that alarms the Roman Catholic, Anglican and Methodist Churches, and Reform synagogues. Once religions start to accept secularism and rationality, their young people usually reach the logical conclusion of doubt – unbelief.

More conservative religions do not have that problem. Only 5 per cent of the more traditional Amish leave the faith, and when a community’s birth rate outstrips the national average by 200 or 300 per cent they can easily afford to lose one in 20 of the flock.

While the likes of Richard Dawkins aim their bile at traditional Christianity, fundamentalists are largely immune to their attacks, and become only stronger as the more committed members of the established churches head their way. Those religions that survive will become more conservative.

God alone knows what will happen to the Church of England this century, but we can safely say that the Catholic Church will become smaller but more committed. It will continue to exist at the margins of an atheist-dominated Europe ruled by an increasingly intolerant secular Left.

Widespread anti-religious feeling will only get more intense as the coming demographic changes outlined by Kaufmann appear to ring true, and as Evangelical Christians start to become more significant in, for example, the British Conservative Party.

But that smaller, more orthodox Catholic Church will have a huge inbuilt advantage – what French Canadian Catholics used to call “revenge of the cradle”. Many orthodox Catholics I know have 3 or 4 children – that’s not a recklessly high number, but in a society where the atheist fertility rate is around 1 child per woman, that advantage will show over a few decades, especially since orthodox Catholics have a far smaller drop-off rate than their liberal brethren.

Much as this will anger the New Atheists, which is a plus, Kaufmann’s thesis is disturbing. Personally I prefer Tel Aviv to Jerusalem, and Anglican civilisation to some of the wackier strains of Evangelical Christianity. As for fundamentalist Islam…

It’s happened before: Kaufmann believes that Christianity’s rise from 40 followers to 6 million within three centuries had less to do with conversions that with higher birth rates, since the Christians rejected such pagan practises as polygamy and infanticide.

Today we view the ancient world’s attitude to infanticide as barbaric and incomprehensible, but perhaps future generations will look at our attitudes to abortion in the same way – that's not because pro-lifers would have won the argument, simply that (in addition to the effect of the Pill) abortion is killing the atheists of tomorrow.

Why chirality remains a problem for origin of life science.

Tagish Lake Meteorite Does Not Solve the Homochirality Problem
Evolution News & Views


Amino acids, the building blocks of proteins, share a puzzling feature. All amino acids used in making proteins are "left-handed" amino acids.

In chemistry, we call molecules "left-handed" or "right-handed" based on how things attach to a carbon atom. Imagine the palm of your hand is a carbon atom, and your fingers are different molecules attached to the carbon (e.g., a hydrogen, an amine, a carboxylic acid). Notice that both of your hands have the same "things" attached to it, but in a different order such that your hands are mirror images of each other. My right and left hands both have a pinky finger, a thumb, and an index finger, but the arrangement is different. The same thing happens to carbon atoms that have different things attached to it; you can get molecules that are mirror images of each other. These mirror images are mostly chemically equivalent. (See here and here for more on homochirality.)

The interesting part of this is, when we try to make amino acids in the lab, we always end up with a 50/50 mixture of right- and left-handed amino acids. But when scientists try to construct proteins from this 50/50 mixture, the proteins do not function properly. Right-handed amino acids do not work. So the big question is: How did nature make only left-handed amino acids? Or was there a 50/50 mixture and nature somehow isolated only the left-handed ones to make proteins?

Scientists from the Goddard Astrobiology Analytical Laboratory believe their recent studies on a Tagish Lake (British Columbia) meteorite sample may provide an answer to this question. (See here for the press release. The research paper is still in press). They found that the Tagish Lake sample has an excess of left-handed aspartic acid, one of the 20 amino acids used in protein construction. They also noted, however, that the sample contains only a slight left-handed excess (8% greater) of alanine, another one of those 20 amino acids. They, therefore, conclude that the amino acids on the meteorite sample are not from biological contamination from Earth, but were formed in space. Furthermore, the excess left-handed aspartic acid must have formed and been isolated somehow inside the meteorite, as opposed to being exposed to certain types of radiation that may cause a slight excess of one hand of amino acids over another.

The Tagish Lake meteorite has many unique properties that have made its classification difficult. It has been a subject of interest since January 2000 when it landed. For a look at some of the unique features of the Tagish Lake meteorite, see here. Importantly, the meteorite contained many more organic compounds than just amino acids.

The Goddard Astrobiology Analytical Laboratory researchers conclude that the amino acids must have formed within the meteorite, and the left-handed excess of aspartic acid is likely due to crystallization that occurs in the presence of water. Alanine, on the other hand, does not crystallize in the same way. This is why there was only a left-handed excess of aspartic acid but a minimal excess of alanine. They speculate that perhaps the early Earth formed left-handed amino acids in a similar way -- by forming crystals in the presence of water.

The fact that a particular handedness can be isolated through crystallization is not news. Chemists do this in the lab when they want to isolate a left- or right-handed molecule. This only works if the molecule can form crystals that only contain one hand. Not all molecules form crystals and not all molecules form crystals that are purely left- or purely right-handed. Alanine is not a good candidate for isolating one form using crystallization because alanine crystals form from combinations of left- and right-handed molecules, giving the chemist crystals that are 50/50 left- and right-handed.

So what makes this finding so interesting? The researchers reason that because they have found a left-handed excess of aspartic acid that formed naturally, they speculate that nature could do this on Earth or perhaps the early Earth was seeded from amino acids that traveled on a meteorite similar to this one.

Unfortunately, this does not quite solve the left-handed (or "homochirality") problem. You see, in order to form left-handed crystals of aspartic acid, there needs to be a slight abundance of left-handed molecules in the first place. In other words, crystals do not form from a true 50/50 mixture. There must be a slight excess of left-handed molecules to form pure left-handed crystals. Given the alanine observation (an 8% excess of left-handed molecules), we might conclude that something caused a slight excess, such as polarized light interacting with the amino acids. This is a possibility, but of the amino acids found on the meteorite, only aspartic acid and alanine are mentioned, meaning that whatever caused the slight excess did not affect all of the amino acids.

Another glaring problem is, while crystallization may be an explanation for how some left-handed amino acids were isolated in nature, it does not explain all of the amino acids. Not all of the amino acids form homochiral crystals. So were there two different mechanisms that happened to isolate only left-handed versions of all 20 of the predominant amino acids? This seems to be a bit of a stretch, and does not solve the mystery of why nature prefers left-handed amino acids.

The NASA report ends, as much origin-of-life research ends, with more speculation and storytelling than actual findings or viable conclusions:

This process only amplifies a small excess that already exists. Perhaps a tiny initial left-hand excess was created by conditions in the solar nebula. For example, polarized ultraviolet light or other types of radiation from nearby stars might favor the creation of left-handed amino acids or the destruction of right-handed ones, according to the team. This initial left-hand excess could then get amplified in asteroids by processes like crystallization. Impacts from asteroids and meteorites could deliver this material to Earth, and left-handed amino acids might have been incorporated into emerging life due to their greater abundance, according to the team. Also, similar enrichments of left-handed amino acids by crystallization could have occurred on Earth in ancient sediments that had water flowing through them, such as the bottoms of rivers, lakes, or seas, according to the team." [emphasis added]
All of these statements are speculative and do not necessarily follow from the actual findings in the meteorite. The meteorite shows that aspartic acid, which we already know forms homochiral crystals, formed homochiral crystals while alanine, which we know forms crystals with a 50/50 composition, had a slight left-handed excess. This says nothing about how these amino acids could have formed on the early Earth.

Furthermore, the Tagish Lake sample contained multiple organic compounds, not just amino acids, so if these meteorites provide a naturalistic example of possible origin-of-life mechanisms, we need to consider the presence of other compounds that nature apparently did not "choose" to employ. These findings, therefore, do not help us understand why nature builds proteins from 20 particular organic compounds that are specifically left-handed or where those 20 amino acids came from.

Christendom's theologians are finding that commonsense is a bit more resilient than they previously thought.

New Poll Finds Evangelicals’ Favorite Heresies
Kevin P. Emmert




Jesus, Almost as Good as His Father?
Almost all evangelicals say they believe in the Trinity (96%) and that Jesus is fully human and fully divine (88%).

But nearly a quarter (22%) said God the Father is more divine than Jesus, and 9 percent weren’t sure. Further, 16 percent say Jesus was the first creature created by God, while 11 percent were unsure.

No doubt, phrases like “only begotten Son” (John 3:16) and “firstborn of all creation” (Col. 1:15) have led others in history to hold these views, too. In the fourth century, a priest from Libya named Arius (c.250–336) announced, “If the Father begat the Son, then he who was begotten had a beginning. … There was a time when the Son was not.” The idea, known as Arianism, gained wide appeal, even among clergy. But it did not go unopposed. Theologians Alexander and Athanasius of Alexandria, Egypt, argued that Arius denied Christ’s true divinity. Christ is not of similar substance to God, they explained, but of the same substance.

Believing the debate could split the Roman Empire, Emperor Constantine convened the first ecumenical church council in Nicaea in A.D. 325. The council, comprising over 300 bishops, rejected Arianism as heresy and maintained that Jesus shares the same eternal substance with the Father. Orthodoxy struggled to gain popular approval, however, and several heresies revolving around Jesus continued to spread. At the second ecumenical council in Constantinople in 381, church leaders reiterated their condemnation of Arianism and enlarged the Nicene Creed to describe Jesus as “the only-begotten Son of God, begotten of the Father before all worlds, Light of Light, very God of very God, begotten, not made, being of one substance with the Father, by whom all things were made.”


In other words, the Son is not a created being, nor can he be less divine than the Father.

The Holy Spirit: May the Force Be with You?
But if evangelicals sometime misunderstand doctrines about Jesus, the third member of the Trinity has it much worse. More than half (51%) said the Holy Spirit is a force, not a personal being. Seven percent weren’t sure, while only 42 percent affirmed that the Spirit is a person.

And 9 percent said the Holy Spirit is less divine than God the Father and Jesus. The same percentage answered “not sure.”


Like Arianism, confusion over the nature and identity of the Spirit dates to the early church. During the latter half of the fourth century, sects like Semi-Arians and Pneumatomachi (Greek for “Spirit fighters”) believed “in the Holy Spirit”—as the First Council of Nicaea (A.D. 325) taught—but said the Spirit was of a different essence from the Father and the Son. Some said the Spirit was a creature, and others understood the Spirit to be a force or power, not a person of the Trinity.

More on Darwinism and racism.

Human Zoos, Award-Winning Documentary, Will Premiere in Houston on April 18

David Klinghoffer | @d_klinghoffer

Eugenics and racist pseudoscience are not safely confined to history. They’re very much with us today, as Steve Fuller, among others, has pointed out.

To understand the present situation, however, you need to understand the past. That includes shameful times in our own country, not so very long ago, that have been swept under the memory carpet. John West’s new documentary, Human Zoos, is a reminder of a particularly vicious episode in U.S. history: the display of an African pygmy, Ota Benga, at the Bronx Zoo in 1906. That much was known to me, but not that many others — thousands! — were similarly displayed as “missing links” connecting apes to more “advanced” humans, per Darwinian theory. This is amazing stuff.

The 55-minute film will receive its premiere in Houston, TX, on April 18. Please join us for this FREE event! More information is here, and don’t forget to REGISTER to reserve your space. See the trailer here:

Yes, this was the consensus science, the prestige science of its day. It was taught to young people, and the smart set in academia and the media readily endorsed it. To adopt today’s favored terminology, speaking out against eugenic dogma or Darwinian racism would have made you a crank and a science-denier. Yet some did speak out:

Human Zoos tells the shocking story of how thousands of indigenous peoples were put on public display in America in the early decades of the twentieth century. Often touted as “missing links” between man and apes, these native peoples were harassed, demeaned, and jeered at.

Their public display was arranged with the enthusiastic support of the most elite members of the scientific community, and it was promoted uncritically by America’s leading newspapers. This award-winning documentary explores the heartbreaking story of what happened, shows how African-American ministers and other people of faith tried to push back, and reveals how some people today are still drawing on Social Darwinism in order to dehumanize others. The film also explores the tragic story of eugenics in America, the effort to breed humans beings based on Darwinian principles.

Congratulations to our colleagues John West and Rachel Adams for their outstanding work on Human Zoos, which has already accumulated a range of awards and recognitions including: “Best in Show” (Cinema Worldfest Award), “Best Editing” (Oregon Documentary Film Festival), and “Awards of Excellence” (Hollywood International Independent Documentary Awards, Impact DOCS Awards).

Dr. West will answer questions from the audience afterward via Skype. Other regional premieres are upcoming. See you in Houston!

More on the re-privileging of our home world.

New Geochemical Discoveries Reaffirm Earth as a Privileged Planet (Updated)

Evolution News | @DiscoveryCSC

Each gas component in our atmosphere has a “partial pressure.” The partial pressure of carbon dioxide (CO2) in the atmosphere is represented as pCO2. You could think of it as the percentage of CO2 in the atmosphere compared to the total amount of gas.

If you believe that pCO2 has a major influence on Earth’s surface temperature, then a new PNAS paper has revealed a significant new fine-tuning parameter for Earth. The paper argues that although CO2 is released into the atmosphere through outgassing (volcanos), thereby increasing Earth’s surface temperature, chemical weathering of continental and seafloor rock into the oceans (where carbon is precipitated out as carbonate rock) serves as a natural sink of CO2. That is, the oceans remove CO2 from the atmosphere, thereby decreasing temperature. All of this serves to keep Earth’s temperature stable:

Continental and seafloor weathering buffer Archean surface temperatures to 0–50 °C. This result holds for a broad range of assumptions about the evolution of internal heat flow, crustal production, spreading rates, and the biotic enhancement of continental weathering.

Many origin-of-life theorists hope that the early Earth’s atmosphere was rich in methane so that organic molecules could be produced. But this new fine-tuning parameter removes an argument that methane must have been present on the early Earth to keep the climate warmer:

The seafloor weathering feedback is important, but less dominant than previously assumed. Consequently, the early Earth would not have been in a snowball state due to pCO2 drawdown from seafloor weathering. In principle, little to no methane is required to maintain a habitable surface climate, although methane should be expected in the anoxic Archean atmosphere once methanogenesis evolved.

What’s really interesting is that they say this fine-tuning parameter is not just for Earth but for any rocky planet located within the circumstellar habitable zone. If they’re right, we’re not looking at Earth being a “privileged planet” but Earth living in a “privileged universe.”

The latter extrapolation deserves some serious skepticism, however. Most likely this is just a “privileged planet” argument. Why?

Their model uses so many particulars of Earth (e.g., Earth’s mantle composition, ocean composition, continental crustal composition, oceanic crustal composition, weathering patterns, and carbonate deposition patterns) that it’s highly premature to conclude that any rocky planet in the habitable zone would be so privileged to enjoy this same temperature-buffering mechanism. For example, Earth seems peculiar due to its high water content — something that geology still struggles to explain.

Would other rocky planets enjoy the same? Nobody knows. Until we discover rocky planets out there in the habitable zone that are very, very, very Earthlike, the extrapolation is unwarranted.

Indeed, another article, out today, reports that Earth is so unique in its high phosphorous content that it may be unlikely that extraterrestrial life exists anywhere else in the universe:

Amid efforts to find alien life, scientists have not yet confirmed the existence of an extraterrestrial civilization. Findings of a new study suggest this has something do with the element phosphorus lacking in the cosmos. … Astronomers have been hunting for phosphorus in the universe because of the role it plays in life on Earth. If the element is lacking in other parts of the cosmos, it could be difficult for alien life to exist.

A new study presented at the European Week of Astronomy and Space Science meeting now suggests that life as we know it is more unusual than previously thought because the universe substantially lacks phosphorus.

Despite this general lack of phosphorous in the universe, it is the 11th most abundant element on Earth, and it’s vital for life. Remember CHONPS — the acronym you learned in high school to remember the elements most important for life? In case you forgot, the “P” stands for phosphorus, which is vital for the construction of DNA and RNA in every life form, and is also an indispensable component of the energy-carrying molecule in all living things, ATP. Phosphorylation, the addition of a phosphoryl group (PO32-), is also necessary for the function of most enzymes, as well as numerous other biomolecules. Yet our home planet is strangely and almost inexplicably rich in phosphorous.

The study proposes that Earth got its phosphorus due to its proximity to a supernova explosion. Perhaps, but although phosphorous is common on Earth (making up 0.07 percent of our planet), it’s only a trace element in the solar system   as a whole. If Earth was close to that supernova explosion, so was the rest of our solar system, and you’d expect it to be rich in phosphorus as well. But it isn’t. Earth is special even within our solar system for its high phosphorus content, and this richness in life-giving phosphorus is very difficult to explain.

As we’ve said many times before, Earth is a indeed  privileged planet.

Analysis of a Darwinian own goal

Read Your References Carefully: Paul McBride's Prized Citation on Skull-Sizes Supports My Thesis, Not His

Casey Luskin August 31, 2012 1:01 PM

While Paul McBride's response to my Chapter 3, "Human Origins and the Fossil Record," in Science and Human Origins ignores most of my arguments, one area where he does attempt a substantive rebuttal pertains to the history of hominin skull sizes. Even here, however, he again ignores some of my most important points regarding skull size in Homo, and cites a paper which supports my thesis rather than his.

There's a reason why McBride focuses his response so heavily on skull sizes -- it's a rare characteristic for which there's some consistent kind of a trajectory over time. But as we'll see, the technical literature finds there is a "rapid change in hominin brain size," with "punctuated changes" and a "saltation" in skull size that occurred with the appearance of the genus Homo. Believe it or not, that language came from a paper McBride cited in response to me. As one might surmise, that paper supports my thesis rather than his.

True to his civil tone, McBride "cordially" invited me to address cranial capacities, and this is what I hope to do in this article. I just wish he would also invite his fellow evolution bloggers like Nick Matzke and Richard B. Hoppe to behave in a "cordial" manner when discussing these issues. (Another double-standard?)

First, some preliminary matters.

Ignoring Authorities Backing My Arguments on Habilis

McBride writes: "Luskin, in fact, appears to reject that H. habilis belongs in Homo, referring to habiline specimens separately from 'true members of Homo'." McBride correctly describes my view, but he writes as if I invented this position arbitrarily to suit my wishes. That's hardly the case, as this position is held by a number of other scientists. In that regard, McBride makes no mention of the strong authorities I cited in Science and Human Origins which support this view. Were it not for these papers and these authorities, I would never hold this position. Thus, my Chapter 3 cites a major review article in the journal Science by leading paleoanthropologists Bernard Wood and Mark Collard which suggested that habilis should be classified as a member of Australopithecus rather than Homo. They surveyed six traits and found that for each one, habilis fell within the australopithecines rather than Homo. A table summarizing their analysis is below:

Other credible sources I cited agree that habilis was unlike Homo. One paper from the Journal of Human Evolution found the skeleton of habilis was more similar to living apes than were other australopithecines like Lucy, and concluded: "It is difficult to accept an evolutionary sequence in which Homo habilis, with less human-like locomotor adaptations, is intermediate between Australopithecus afaren[s]is ... and fully bipedal Homo erectus." Likewise a paper from Nature I cited states: "Phylogenetically, the unique labyrinth of [the habilis skull] represents an unlikely intermediate between the morphologies seen in the australopithecines and H. erectus." Again, McBride ignores these citations, and neither mentions nor addresses any of my reasons for arguing that habilis doesn't belong in Homo.

One-Dimensional Thinking: The Pitfalls of Using Regression Lines to Claim "Gradual" Evolution

In arguing about skull sizes, McBride's main approach is to rehash an old blog post by Nick Matzke from 2006, where Matzke was commenting on a paper I had published on human origins in 2005. Citing a paper by Henneberg and de Miguel (2004), Matzke noted that there's an increase in the average size of hominin brain sizes over the past few million years. The paper had concluded that "all hominins appear to be a single gradually evolving lineage" with respect to cranial capacity. This got Matzke quite excited. Using the kind of rhetoric we've come to expect from Panda's Thumb, Matzke argued that "creationists should be embarrassed and ashamed about the huge mass of evidence they ignore every time they fail to mention the stunning, overwhelming, transitional, gradual, nature of the hundreds of ancient fossil skulls that have been discovered." He boasts that this is "an astonishing confirmation of evolution." What was this "stunning" evidence? Matzke put up a chart showing hominin cranial capacities over the last few million years, with a nice, smooth regression line fit to skull sizes plotted against time. According to Matzke, this is supposed to show hominin cranial capacity increasing in a "gradual" fashion.

Matzke's mistake is that a regression line can be fit to many types of data sets -- including data that shows "gradual" change, but also including data that shows abrupt, rapid, and/or punctuational change. Sang-Hee Lee and Milford Wolpoff make this point compellingly in a 2003 article in Paleobiology, writing that "although changes in cranial capacity may be plotted against time, a trend line fitted to the bivariate distribution on the basis of regression is misleading." Why is it misleading? Precisely because a trend line alone -- the kind that Matzke waves triumphantly -- doesn't tell you whether the change in cranial capacity was gradual or punctuated:

However, whether brain size increased with statistical significance is not at issue here: there is no question that brain size increased over time. What we want to know is whether there was a change in the underlying process of change, and this cannot be answered with statistical rigor by fitting a single linear model for all the data points over time. For example, regression cannot be relied on to distinguish between a pattern of punctuated equilibrium and a gradual, constant change, because both of these could produce best-fitting trend lines with similar statistical attributes. This prevents us from using a regression method to fit one line for all the data points in answer to our question about process.

(Sang-Hee Lee and Milford H. Wolpoff, "The pattern of evolution in Pleistocene human brain size," Paleobiology, Vol. 29 (2): 186-196 (2003) (emphasis added).)

Godfrey and Jacobs (1981) also warn against using a regression line approach because it can miss "punctuational" change. Their critique of other authors who used regression line analyses led to the following noteworthy warning about how these methods assume, rather than test for, gradual evolution:

those that are inclined to reject the punctuational hypothesis for human evolution should not design mathematical "tests" of punctuationalism that have gradualist conclusions predicated by gradualist a priori assumptions!

(Laurie Godfrey and Kenneth H. Jacobs, "Gradual, Autocatalytic and Punctuatlonal Models of Hominid Brain Evolution: A Cautionary Tale," Journal of Human Evolution, Vol. 10: 255-272 (1981).)

Thus, papers like Henneberg and de Miguel (2004) used a flawed analysis and do not conclusively show "gradual" change.

Godfrey and Jacobs come to the conclusion that there is evidence for punctuational change, whereas Lee and Wolpoff believe hominin brain size changes in a "gradual" manner. Clearly, there are different opinions out there on this question. The recent reanalysis by Shultz et al. (2012) investigates why there are different opinions, noting that when one reviews the literature, you see there have been "different inferences made about the process of hominin brain size changes" due to the "different methodologies have been used." The authors write:

A number of proponents support gradualism, whereas others argue that there have been long periods of stasis in brain size followed by bursts of change, or that rates of change vary over time and space.

(Susanne Shultz, Emma Nelson and Robin I. M. Dunbar, "Hominin cognitive evolution: identifying patterns and processes in the fossil and archaeological record," Philosophical Transactions of The Royal Society B, Vol. 367:2130-2140 (2012) (internal citations removed).)

Shultz et al. (2012) conclude that "One conclusion that all methods agree upon is that brain size has increased, but the tempo of those changes remains unresolved." I'll discuss this paper further below, since it shows a "rapid change in hominin brain size," with "punctuated changes" and a "saltation" in skull size when Homo abruptly appeared.

Paul McBride's response to me usually tried to maintain an objective tone. But he got so caught up in Matzke's strong rhetoric about skull sizes--"creationists should be embarrassed and ashamed about the huge mass of evidence they ignore every time they fail to mention the stunning, overwhelming, transitional, gradual, nature of the hundreds of ancient fossil skulls that have been discovered"--that McBride called Matzke's arguments "breathtaking." I suppose that's a fitting word when you realize that the regression line which so excited Matzke doesn't tell you anything about whether the data shows gradual change.

So What if There Are Skulls of Intermediate Size?

I never found Matzke's original 2006 Panda's Thumb post to be worth much of a reply because it in turn responded to so little of my 2005 paper, and anyone who read my prior paper would see that this objection about the existence of intermediate skull sizes was addressed. I also discussed it in my recent chapter on the hominin fossil record in Science and Human Origins.

First, my chapter acknowledges that there are plenty of skulls of intermediate size -- and that skull size increased abruptly about 2 my. As I wrote:

A 1998 article in Science noted that at about 2 mya, "cranial capacity in Homo began a dramatic trajectory" that resulted in an "approximate doubling in brain size."103 Wood and Collard's review in Science the following year found that only one single trait of one individual hominin fossil species qualified as "intermediate" between Australopithecus and Homo: the brain size of Homo erectus.104

So yes, there are lots of skulls of different sizes -- some might call many of them "intermediate." In fact according to some leading paleoanthropologists, this is the only trait for which there are intermediate examples in the hominin fossil record. As seen in Table 1 above, Wood and Collard's review looked at six traits -- and you can score brain size as the one trait for which they find fossils with intermediate characters. So instead of the score being 6 to nothing against Darwinian evolution, I suppose the score now is only 5 to 1. This is nothing new and I fully acknowledge it in my paper.

But how important is brain size as an intermediate trait? Though McBride tries to brush it off, my article addresses this topic as well:

However, even this one intermediate trait does not necessarily offer any evidence that Homo evolved from less intelligent hominids. As they explain: "Relative brain size does not group the fossil hominins in the same way as the other variables. This pattern suggests that the link between relative brain size and adaptive zone is a complex one."105

Likewise, others have shown that intelligence is determined largely by internal brain organization, and is far more complex than the sole variable of brain size. As one paper in the International Journal of Primatology writes, "brain size may be secondary to the selective advantages of allometric reorganization within the brain."106 Thus, finding a few skulls of intermediate size does little to bolster the case that humans evolved from more primitive ancestors.

[...]

Figure: Got a big head? Don't get a big head. Brain size is not always a good indicator of intelligence or evolutionary relationships. Case in point: Neanderthals had a larger average skull size than modern humans. Moreover, skull size can vary greatly within an individual species. Given the range of modern human genetic variation, a progression of relatively small to very large skulls could be created by using the bones of living humans alone. This could give the misimpression of some evolutionary lineage when in fact it is merely the interpretation of data by preconceived notions of what happened. The lesson is this: don't be too impressed when textbooks, news stories, or TV documentaries display skulls lined up from small sizes to larger ones.

McBride vaguely alludes to this discussion but frames it in the context of my supposed motives rather than actually evaluating the arguments and evidence I provide in support of my view.

In short, you shouldn't be too impressed when Nick Matzke or someone else posts a graphic showing that skull size increased over the last couple million years. Definitely don't be impressed by regression lines presented in the absence of any deeper analysis.

And what about the upward trendline? This too is as unimpressive as it is unsurprising. After all, between 2 and 4 million years ago, the primary hominins running around were small-brained australopithecines. Homo didn't exist before 2 million years ago, but sometime after that it appeared abruptly, and thus after that time we see much larger brain sizes dominating the fossil record -- much larger than the australopithecines which dominated before that time. So it's no surprise that the average size of skulls increased. (And as we'll see below, when it does increase, it occurs in "rapid" and "punctuated" fashion which implies "saltation.") But the point is that when you look at the overall story of human evolution, it's a lot more complicated than the sole dimension of skull size increasing steadily in one direction. There is an entire suite of traits that, taken together, uniquely characterize the first members of Homo, and skull size is just one of many. So finding that a single trait changes smoothly doesn't really tell you much about whether Homo itself appeared in a gradual manner.

Again, my article addressed this point and showed that many complex traits characterized the revolution that occurred with the appearance of Homo:

[A] study of the pelvic bones of australopithecines and Homo proposed "a period of very rapid evolution corresponding to the emergence of the genus Homo."107 In fact, a paper in the Journal of Molecular Biology and Evolution found that Homo and Australopithecus differ significantly in brain size, dental function, increased cranial buttressing, expanded body height, visual, and respiratory changes and stated: "We, like many others, interpret the anatomical evidence to show that early H. sapiens was significantly and dramatically different from... australopithecines in virtually every element of its skeleton and every remnant of its behavior."108

McBride (and Matzke's) objections to my chapter on this point are very unsophisticated. Evolution is much more complex than the sole dimension of brain size, and that dimension itself is of uncertain importance in determining intelligence. Yes it increases over time, but early Homo differed from the australopithecine apes by a lot more than just brain size. When Homo appears, it appears with a bang. As my chapter explains:

Noting these many changes, the study called the origin of humans, "a real acceleration of evolutionary change from the more slowly changing pace of australopithecine evolution" and stated that such a transformation would have included radical changes: "The anatomy of the earliest H. sapiens sample indicates significant modifications of the ancestral genome and is not simply an extension of evolutionary trends in an earlier australopithecine lineage throughout the Pliocene. In fact, its combination of features never appears earlier."109

These rapid, unique, and genetically significant changes are termed "a genetic revolution" where "no australopithecine species is obviously transitional."110 For those not constrained by an evolutionary paradigm, what is also not obvious is that this transition took place at all. The lack of fossil evidence for this hypothesized transition is confirmed by Harvard paleoanthropologists Daniel E. Lieberman, David R. Pilbeam, and Richard W. Wrangham, who provide a stark analysis of the lack of evidence for a transition from Australopithecus to Homo:

Of the various transitions that occurred during human evolution, the transition from Australopithecus to Homo was undoubtedly one of the most critical in its magnitude and consequences. As with many key evolutionary events, there is both good and bad news. First, the bad news is that many details of this transition are obscure because of the paucity of the fossil and archaeological records.111

As for the "good news," they still admit: "[A]lthough we lack many details about exactly how, when, and where the transition occurred from Australopithecus to Homo, we have sufficient data from before and after the transition to make some inferences about the overall nature of key changes that did occur."112

In other words, the fossil record provides ape-like australopithecines, and human-like Homo, but not fossils documenting a transition between them.

In the absence of fossil evidence, evolutionary claims about the transition to Homo are said to be mere "inferences" made by studying the non-transitional fossils we do have, and then assuming that a transition must have occurred somehow, sometime, and someplace.

Again, this does not make for a compelling evolutionary account of human origins. Ian Tattersal also acknowledges the lack of evidence for a transition to humans:

Our biological history has been one of sporadic events rather than gradual accretions. Over the past five million years, new hominid species have regularly emerged, competed, coexisted, colonized new environments and succeeded -- or failed. We have only the dimmest of perceptions of how this dramatic history of innovation and interaction unfolded...113

Likewise, evolutionary biologist Ernst Mayr recognized our abrupt appearance when he wrote in 2004:

The earliest fossils of Homo, Homo rudolfensis and Homo erectus, are separated from Australopithecus by a large, unbridged gap. How can we explain this seeming saltation? Not having any fossils that can serve as missing links, we have to fall back on the time-honored method of historical science, the construction of a historical narrative.114

As another commentator proposed, the evidence implies a "big bang theory" of the appearance of our genus Homo.115

McBride (and Matzke) don't really engage with any of this evidence for the abrupt appearance of the new body plan represented by Homo other than to say (my paraphrase): "Well, we've got a skulls of intermediate sizes and can see skull sizes increasing over time, therefore I can ignore all this evidence of the abrupt appearance of Homo." I supposed Matzke would add I should be "embarrassed and ashamed." I'm not here to shame anyone. But critics need to deal with the fact that Homo represented a new type of hominin that had many distinct features, and a highly distinct combination of features, and that when it appeared, it appeared abruptly, without similar precursors. Simplistic diagrams or references to increases in the sole dimension of brain size don't answer my argument.

Read Your Citations Carefully

As we saw, Nick Matzke got excited over Henneberg and de Miguel (2004) because it claimed "all hominins appear to be a single gradually evolving lineage" with respect to cranial capacity. This citation is also very important to McBride -- but in an "Update" at the end of his review of my Chapter 3, he brandishes a new paper in Philosophical Transactions of the Royal Society B -- the aforementioned paper by Shultz et al. (2012).

It's ironic that McBride positively cites Shultz et al. (2012), because McBride would seemingly disagree with the paper. McBride maintains there is a "lack of discontinuity" in the fossil record regarding hominin cranial capacity, but Shultz et al. (2012) finds evidence for "punctuational changes," "saltation," and "rapid change in hominin brain size." The paper finds there was an abrupt increase in brain size in hominins corresponding to the origin of the genus Homo. This supports my thesis, not McBride's.

Shultz et al. (2012) reviews many other papers that have investigated cranial capacity over time, and observes: "One conclusion that all methods agree upon is that brain size has increased, but the tempo of those changes remains unresolved." The paper's analysis is quite thorough and would seem to refute the strictly "gradual" interpretation of Henneberg and de Miguel (2004). The paper's abstract then notes that a more sophisticated analysis reveals punctuated changes in cranial capacity:

Using both absolute and residual brain size estimates, we show that hominin brain evolution was likely to be the result of a mix of processes; punctuated changes at approximately 100 kya, 1 Mya and 1.8 Mya are supplemented by gradual within-lineage changes in Homo erectus and Homo sapiens sensu lato.

(Susanne Shultz, Emma Nelson and Robin I. M. Dunbar, "Hominin cognitive evolution: identifying patterns and processes in the fossil and archaeological record," Philosophical Transactions of The Royal Society B, Vol. 367:2130-2140 (2012).)

Thus, there's a "punctuated change" in skull size associated with the appearance of Homo about 1.8 mya. The abstract uses the word "gradual" but we learn later that this is not the normal trend for changes in brain size. As the paper states:

The consistent signal for step changes suggests that hominin brain expansion is not a single, gradual process but is rather characterized by step changes.

At one point the paper even characterizes these "step changes" as being equivalent to "saltations."

Reading the rest of this paper, we find that there are periods of "rapid change in hominin brain size" -- one of which corresponds to the appearance of the genus Homo. The paper states: "The first two step changes coincide with the appearance of early Homo," and then offers this thesis statement at the beginning of the Discussion section:

We revaluated patterns of hominin brain size change and demonstrate that, rather than being a monotonic increase, hominin brain size increase is dominated by step changes with limited evidence for long-term gradual increases.

So this Shultz et al. (2012) actually argues that hominin brain size is "dominated by step changes" and while there is some gradual increase in cranial capacity, that evidence for longterm gradual increases is said to be "limited."

If this paper had been published before our book was written, I surely would have cited it as another example of the abrupt appearance of a trait associated with the origin of Homo. In essence, this paper shows the opposite of what McBride is arguing -- it shows that there is an abrupt increase in cranial capacity corresponding to the appearance of Homo.

In his haste to post an "Update," McBride seemingly failed to read the citation carefully. And what of the "gradual and continous" change mentioned by this paper? Is this important for showing humans evolved from ape-like precursors? I'll discuss that in the next section.

Small Homo erectus Skulls? Please Don't Throw Me in That Briar Patch!

At one point in his review, McBride criticizes me for citing a lower-bound for Homo erectus cranial capacities which is higher than he thinks it should be, stating: "The average cranial volume of early Georgian H. erectus, dating to about 1.7 Mya, is 700cc (see Anton, 2003). Luskin's source does not even acknowledge such small sizes, giving the lower bound for H. erectus as 850cc."

I appreciate that McBride is checking my sources. That great if he found a source saying that there are erectus skulls that are a mere 150 cc smaller than the smallest erectus skull size I was aware of. I was just citing the sizes I found in my source -- an authoritative textbook on human variation by Washington University of St. Louis anthropologist Stephen Molnar, Human Variation: Races, Types, and Ethnic Groups. If McBride found a skull size that was slightly smaller, that wouldn't surprise me a bit since I also cited a credible scientific paper stating that modern humans can have cranial capacities as small as 800 cc -- lower than the smallest size I found for H. erectus. In light of that fact, what should we make of the following comment from McBride?

For reference, modern humans have a cranial capacity averaging close to twice the average Georgian specimen.

McBride's comment means very little. As I document in the book, there are modern humans with skull sizes ranging from 800 to 2200 cc. So we could easily rewrite McBride's statement to say "some modern humans have a cranial capacity averaging close to three times of other modern human specimens."

Does that mean some humans are evolutionary intermediates in lines that led to others? Does it mean some humans are less intelligent and represent evolutionary precursors to others? No, it means none of that. What it means is that there's lots of diversity in skull size among modern humans, and skull size is a poor predictor of intelligence or evolutionary importance. This singular dimension is also a poor predictor of what species you belong to. So the fact that McBride found an erectus skull with 700 cc doesn't do anything to bolster an evolutionary story.

But McBride apparently thinks otherwise. He ups the rhetoric when he writes:

This certainly leaves substantial ground to infer vast differences between us and early Homo in the one area most precious to Luskin. The problem for Luskin is there is no discontinuity in the fossil record between us and early Homo. Hence, we must conclude -- contra Luskin -- that there is no evidence of discontinuity in the fossil at the point where humans are singularly most likely to have acquired our truly modern humanness.

As we already saw, Shultz et al. found evidence of a discontinuity with regard to cranial capacity corresponding to the emergence of Homo. That aside, McBride's comments are puzzling. He must think I tremble at the thought of hominin skulls in the range of 600-800 cc. He suggests I would be "uncomfortable" with such evidence. That's both amusing and wrong. If he'd read my chapter more carefully, not only would he see that I fully acknowledges that cranial capacity is the one single trait for humans where we clearly find intermediates, but he'd also understand why I argued that that fact is of limited importance.

And as we saw above, when we look at average skull size over time, there are significant discontinuities in the fossil record -- including a major one corresponding to the emergence of Homo. This is much more significant than finding a few skulls of intermediate size. There's so much variation in this trait that one can always find skulls of intermediate sizes in the fossil record -- perhaps there is even some limited evidence of gradual trajectories within species. But when you look at the record over time, you see abrupt jumps in average skull size -- indicating that Homo had a starkly different average skull size which came on the scene abruptly, without gradual transitions from other forms. This evidence supports my thesis, not McBride's.

Intelligent Homo erectus?

Finally, regarding the emergence of Homo, McBride writes, "An intellectually lacking H. erectus would seriously challenge all of what he has been trying to establish here -- that there is an important discontinuity between humans (in the thoughtful, artful sense) and all else." Largely inferred from tools presumed to have been fashioned by Homo erectus, our knowledge of the true intelligence of erectus is uncertain. However, as I recently discussed, there is intriguing evidence that erectus was capable of boatbuilding and seafaring over significant distances of water. Articles that have covered this story offer intriguing suggestions that erectus was highly intelligent:

"To accomplish any seafaring journeys, Dr. Karl Wegmann of North Carolina State University says, 'They had to have used some sort of boat, though we will probably never find preserved evidence of one.' He acknowledges that this discovery weakens the idea that earlier hominids were landlocked. 'We all have this idea that early man was not terribly smart. The findings show otherwise -- our ancestors were smart enough to build boats and adventurous enough to want to use them.'" (Jørn Madsen, "Who was Homo erectus," Science Illustrated (July/ August 2012), p. 23.)

"Many researchers have hypothesized that the early humans of this time period were not capable of devising boats or navigating across open water. But the new discoveries hint that these human ancestors were capable of much more sophisticated behavior than their relatively simple stone tools would suggest. 'I was flabbergasted,' said Boston University archaeologist and stone-tool expert Curtis Runnels. 'The idea of finding tools from this very early time period on Crete was about as believable as finding an iPod in King Tut's tomb.'" (Heather Pringle, "Primitive Humans Conquered Sea, Surprising Finds Suggest," National Geographic (February 17, 2010).)

We can only speculate about the intelligence of Homo erectus, but the likelihood remains that he was highly intelligent.

Conclusion

This has been a long article, but I hope it is instructive in showing how evolutionists deal with the fossil hominin evidence. As we've seen, multiple authorities recognize that our genus Homo appears in the fossil record abruptly with a complex suite of characteristics never-before-seen in any hominin. And that suite of characteristics has remained remarkably constant from the time Homo appears until the present day with you, me, and the rest of modern humanity. The one possible exception to this is brain size, where there are some skulls of intermediate cranial capacity, and there is some increase over time. But even there, when Homo appears, it does so with an abrupt increase in skull-size. And the earliest forms of Homo -- Homo erectus -- had an average skull size, and even a range of skull sizes, that are essentially within the range of modern human genetic variation. Citing smaller skull-sizes doesn't change the fact that skull-size is of uncertain importance for determining intelligence.

The complex suite of traits associated with our genus Homo appears abruptly, and is distinctly different from the australopithecines which were supposedly our ancestors. There are no transitional fossils linking us to that group. If a few skulls of intermediate size is enough to convince McBride that humans shared a common ancestor with apes, so be it. But for me it's insufficient--especially when there are so many other traits (possibly including skull size) which appear abruptly in a unique Homo body plan. My Chapter 3 in Science and Human Origins cites a wealth of scientific articles, books, and papers backing up my arguments -- most of which are ignored by McBride. The lesson, I think, is that the gap in brain-size between Homo and the australopithecines will not be bridged by one-dimensional thinking.

Modern scientific discoveries put reductionism on the ropes.

A "Mechanical" Philosophy for the 21st Century
Evolution News & Views November 8, 2015 4:51 AM

In Francis Bacon's day, it was easy to oversimplify nature. Elizabethan scientists began to conceive of a world that ran like a machine. Robert Boyle was a strong proponent of the mechanical philosophy. Soon, Isaac Newton's clockwork heavens reinforced the notion that all the Creator had to do was wind it up, and let it run all by itself. From Boyle to Babbage, the Newtonian revolution showed the way for scientific progress: just uncover the natural laws that make the universe run.

By the late 18th century and into Victorian times, mechanical philosophy was sufficient unto itself. An original Designer could be conceived of, perhaps, but as science progressed, the Prime Mover had less and less to do. Some argued that it was an insult to the Watchmaker to suggest he needed to intervene and fix the watch.

Then molecular biology arrived, and we found out the clocks are real. Literal machines made of molecules make life run. Simultaneously, the computer age dawned and we learned a bit about programming. Now, robotics is here. We're going to need a new philosophy: one that can handle realities the Elizabethans and Victorians could never have imagined.

It's important to note that we're not speaking of mechanistic or reductionist philosophy. See Jay Richards's clarification. We seek an explanation for how natural machinery can operate without continuous intervention.

Real Clocks

Paley's "watch on a heath" was only an analogy in 1805. Now, we can see real biological clocks of amazing design and precision in the cells of life. Current Biology talks about "unexpected biochemical cogs" in a cyanobacterium, freely using the word "clock" as well as "oscillator," "regulator," and "switch." The circadian clock runs on a much slower schedule than most cellular reactions. It's calibrated to the 24-hour day-night cycle, and keeps constant time even when the temperature changes. It would have been astonishing to Paley or Bacon to learn that a three-protein oscillating machine is found in such a tiny organism. In higher vertebrates, biological clocks are even more elaborate.

Real Engines

Is this the little engine that could? Penn State News finds that "little engines" of kinesin (see our animation) can do more than thought on their microtubule tracks. These little walking robots, one ten-thousandth the diameter of a human hair, not only walk the tracks but help them grow. When kinesin-5 pauses at the end of a microtubule, it "generates pushing forces, which slide the microtubules apart and essentially allow the motor to grow the microtubules." [Emphasis added.]

Real Solar Panels, Quality Control, and Recycling

The Salk Institute calls chloroplasts "solar panels" and reveals how the cell monitors them with a "quality control check" that can "recycle" the parts of damaged chloroplasts. Notice the mechanical word: they uncovered "how plants thrive using a natural mechanism to recycle chloroplasts."

Real Stress Management

Another "fundamental biological mechanism" is described by bioscientists at the University of Heidelberg. In a common lab plant, they found that proteins are "further adapted" after they are manufactured "for their specific jobs." In one case they studied, chemical tags regulate the stress response to drought by closing the stomata and lengthening the primary root.

Real Coordinated Timing and Assembly

Scientists at Virginia Tech found that, during development, "timing is indeed everything." They use music as an analogy:

Everyone who has played in a band or orchestra knows that playing in time creates music, while playing out of time creates cacophony. In an orchestra, each player may be out of tune when warming up, but eventually, all players must reach the same pitch, rhythm, and timing to produce a viable piece of music.

They found something similar in dividing cells. Just as live musicians can compensate for other players' changes in tempo, "cells modulate the exact timing of when crucial cellular events happen, slowing down or speeding everything up to make sure everything is playing its proper part at the right time." They were "astonished to see how greatly the starting conditions for each cell could differ and still lead to the same outcome," the article says.

Is it just an analogy to call a ribosome a "protein-making factory"? Ask the researchers at Rockefeller University, who think "factory" is an appropriate description:

Ribosomes, the molecular factories that produce all the proteins a cell needs to grow and function, are themselves made up of many different proteins and four RNAs. And just as an assembly line must be built before it can manufacture cars, these tiny factories must be constructed before they can put proteins together.

Real Mobile Factories

Rockefeller is not alone in using the word factory -- only the one they found escaped detection till now. "Salk Scientists Discover Protein Factories Hidden in Human Jumping Genes," a news item from Salk Institute says. Researchers found a third Open Reading Frame (ORF0) in certain jumping genes known as LINE-1 elements.

"Jumping genes with ORF0 are basically protein factories with wheels," they said. The fact that they consider "evolution" to be the driver of the bus does not negate the fact that they are real machines that must function properly, otherwise it could cause disease. And there are 3,500 of these "factories with wheels" in the human genome.

Real Repair Stations

The nuclear membrane gained new respect from scientists at the University of Southern California when they found that it's a lot more than "just a protective bubble" around the nuclear material. A team at USC has documented "how broken strands of a portion of DNA known as heterochromatin are dragged to the nuclear membrane for repair." At the inner wall of the nuclear membrane, "a trio of proteins mends the break in a safe environment, where it cannot accidentally get tangled up with incorrect chromosomes." (The discovery was made in fruit flies.)

As for heterochromatin, this "mysterious part of the genome" composed of repetitive elements has been promoted from "junk DNA" to superhero (watch the word "mechanism"):

The reason why we don't experience thousands of cancers every day in our body is because we have incredibly efficient molecular mechanisms that repair the frequent damages occurring in our DNA. But those that work in heterochromatin are quite extraordinary.

Real Repair Machines

We see "mechanism" also used to describe a "new class of DNA repair enzyme" found by researchers at Vanderbilt University. This adds to the same work that earned a Nobel Prize earlier this year. This enzyme has some "remarkable properties," they said, such as the ability to find damage indirectly without actually contacting the lesion, and the ability to fix bulkier lesions than other repair mechanisms can.

"Our discovery shows that we still have a lot to learn about DNA repair, and that there may be alternative repair pathways yet to be discovered. It certainly shows us that a much broader range of DNA damage can be removed in ways that we didn't think were possible," said Eichman. "Bacteria are using this to their advantage to protect themselves against the antibacterial agents they produce. Humans may even have DNA-repair enzymes that operate in a similar fashion to remove complex types of DNA damage.

Real Shaping Machinery

Nonsense-mediated mRNA decay (NMD) is described in Nature Reviews: Molecular Cell Biology as "an intricate machinery that shapes transcriptomes." The abstract mentions "intricate steps" in this process, "cellular quality control," and the ability of NMD to "dynamically adjust their transcriptomes and their proteomes to varying physiological conditions."

Real Packaging

A grad student at MIT is studying how cells pack two meters' worth of DNA into a cell nucleus. It's like "trying to fit 24 miles of string into a tennis ball," Abe Weintraub says. He's intrigued by the fact that "DNA gets packed tightly in organized loops, rather than being haphazardly crammed into cell nuclei." The specific 3-D organization appears to affect its functionality, because mistakes cause cancer and other diseases.

Philosophical Implications

Those are a few recent examples of the "machine talk" pouring out of labs around the world. This is not just metaphorical language for "nature" like the Victorians used. It's observation and description of realities the early mechanical philosophers could not have imagined. And it's everywhere. Machine talk is driving an explosion of discovery in science.

The old mechanical philosophy is hopelessly inadequate for these realities. The reason? We know from our experience that unguided natural law does not produce machinery, factories, and quality control. Something else is required: information.

The Santa Fe Institute identifies this critical part of the new 21st century philosophy. A working group met to discuss the question, "What physical principles predict life?" They put the question into stark perspective:

We are immersed in life here on Earth, but life isn't found on the Moon. Nor has it arisen, so far as we know, anywhere else in the solar system. Why do some physical environments precipitate life, and why don't others?

It's not enough to say that the moon has no water:

If the Earth really does use sunlight to convert a disorderly lump of mass and energy into organized living things, why can't the Moon, Earth's nearest neighbor, do something similar using different mechanisms?

This implies that "natural laws" alone are insufficient to account for the difference. David Wolpert was on hand to share an important suggestion:

One part of the answer, Wolpert says, might lie in information theory. In addition to being central to modern biologists' understanding of evolution, information theory overlaps heavily with thermodynamics, the area of physics concerned with how the different kinds of internal energy of a system (such as heat and stored chemical energy) might be affected by the outside world.

In a video clip Wolpert elaborates on this theme. Apparently many others in the working group felt it was a promising avenue of thought.

"In many talks and discussions, the nature of information flow between different scales of organization emerged as an important theme and open question," says O'Dwyer. "We look forward to future collaboration on each of these ideas."

Willaim Dembski's latest book, Being as Communion, would serve as a fine discussion starter. Wolpert comes so close, but is still so far from explaining what he set out to explain: why the moon differs from the earth. He talks about information flow through the system, but the moon gets exactly the same sunlight the earth does. And he never defines what information is, or where it comes from. Here is where intelligent design can offer real, substantive insight.

Information is the key to a "mechanical" philosophy for the 21st century. We know, because we have a great deal of experience producing information and imposing it on matter. We build computers. We make robots. We make clocks and trucks and factories. Indeed, we can even make machines that make other machines, and robots that increasingly look and act like us.

Our machines can run like clockwork, not because we shined sunlight on a "disorderly lump" and waited for natural laws to take their unguided course, but because we infused the lumps with information. And since we know that intelligence was the true cause that resulted in those lumps of raw material becoming Steinway pianos, Toyota robotic assembly lines, and New Horizons spacecraft, it's a fair inference that intelligence is the true cause behind atoms that become kinesins, ribosomes, and circadian clock proteins.