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March 06, 2014

"Answers for Creationists"

I would hope that none of my readers need this. But maybe you know some people who do. Short, effective, and good-natured.

(That the "Second Law of Thermodynamics" question persists is a serious indictment of our educational system. It's also another reminder that a little learning is a dangerous thing.)


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Not sure why you had to slam creationists here. If you think the article deserves consideration, why would you phrase your introduction to insult everyone you're trying to convince?

By the way, some of this guy's answers might be the beginning of a interesting conversation, but others are just stupid. Mainly this one: "I don't need religion to know murder is wrong." Of course not! He lives in a culture with a Judeo-Christian heritage that has known that for hundreds of years. It's like saying, "Well, obviously, disease is caused by germs." It's easy to say that now, but it wasn't obvious back in the day. And without that religious heritage, murder might not be so obviously wrong. (And indeed, murder is not as "obviously wrong" to everyone as it used to be. Abortion & euthanasia continue to gain acceptance. It's usually the religious who stand against these.)

I'm still a creationist, but I didn't "need this." I'm not looking to be convinced or unconvinced.


I was having a similar conversation w/ my 12yo daughter last night who attends a catholic middle school. My point to her was that God gave us a mind and the ability to reason. It is with this gift that we can try to understand the miracles of the universe that are his creation. Science and religion should never conflict. Science is based on observable evidence while religion is based on faith.

Do I believe in the Big Bang Theory? Yes, because the evidence strongly supports it. Do I believe in evolution? Yes again, because the evidence supports it. Do I also believe that these things are the creation of God? Yes, because I have faith. When I see the wonders of the universe explained through math, that is when I see the hand of God.

I also told my daughter that she should apply that same critical thinking in her Religion class as she does in Science. Knowledge is truth and always good. In the end, I want her to develop her own relationship with God and not just take mine.


Good job on generating some comments if that was your goal. Creationism / evolution will always get people to come out of the woodwork. There are very few topics that create as much uneducated response and vigor from both sides of the argument.

I do find this quote to be an amusing example of a difference without a distinction:

"Scientists don't believe in evolution; we trust that it's the best way to describe how we came to be. And we do that because it's earned that trust."


In 8, the author reveals as much of his own ignorance of the Bible and Christianity as many creationists do when asking that thermodynamics debunks evolution.


"It was partly by chance, but it wasn’t random."

This is rank nonsense. The answer to the question "If God did not create everything, how did the first single-celled organism originate? By chance?” is quite plainly a resounding "YES".


"If this question is an argument to allow creationism to be taught in schools, that’s a violation of the First Amendment anyway."

Is a false statement. And the only reason it even has any validity at all is because of the government imposing its monopoly on the indoctrination, I mean education system.

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... several key problems faced by most theories on the origins of life are related to the different ways in which chemical and living systems deal with thermodynamic constraints. Even the simplest microorganisms known on Earth are breathtakingly complex. Indeed, the probability that a random sequence of physicochemical events would lead to a bacterium by spontaneous self-organization of biomolecules is negligibly low. This would also be the case if we tried to imagine the spontaneous synthesis of relatively simpler, nonautonomous replicative entities, such as viruses or viroids. The whole process of molecular self-organization toward protoliving or living systems seems to be against the second law of thermodynamics, although we know that an open system can generate ordered cycles at the expense of its increasingly disordered environment, that is, in continuous matter–energy flow conditions.(19, 20) The organization of living beings is much more intricate than any other known spontaneously generated pattern of spatial/temporal order, as in the so-called “dissipative structures”.(21) Life manages to stay far from equilibrium due to molecular mechanisms that are much more diverse, complex, and also based on quasi-equilibrium structures. Living beings are therefore able to combine self-organization and self-assembly processes,(22) keeping many of the resulting molecular ensembles (i.e., polymers, membranes, etc.) just at the edge of a transition phase, so that their behavior can be more easily adjusted to changes in the surrounding conditions. -- "Prebiotic Systems Chemistry: New Perspectives for the Origins of Life", Chemical Reviews


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Both hypotheses run counter to scenarios in which organisms evolve to be increasingly complex. In one, a complex nervous system and muscles were lost in the sponges. In the other, the sponges had the genetic capability for complex features but stayed simple, while a more primitive group, the comb jellies, acquired brains and muscles that help them chase down prey. Furthermore, the idea that complex parts like a brain and nervous system -- including nerve cells, synapses, and neurotransmitter molecules -- could evolve separately multiple times perplexes evolutionary biologists because parts are gained one at a time. The chance of the same progression happening twice in separate lineages seems unlikely -- or so biologists thought. "Traditional views are based on our dependence on our nervous system," says Ryan. "We think the nervous system is the greatest thing in the world so how could anything lose it," he says. "Or, it's the greatest thing in the world, so how could it happen twice." -- Evolution, You’re Drunk, DNA studies topple the ladder of complexity

Keep your arrogance (and your ignorance) to yourself.

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... life seemingly did not choose its twenty building blocks randomly ... "We found that chance alone would be extremely unlikely to pick a set of amino acids that outperforms life's choice." -- Stephen J. Freeland, NASA Astrobiology Institute at the University of Hawaii

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Does maths exist without human beings to observe it, like gravity? Or have we made it up in order to understand the physical world?

I argue, as others have done before me, that mathematical concepts and ideas exist objectively, outside of the physical world and outside of the world of consciousness. We mathematicians discover them and are able to connect to this hidden reality through our consciousness. If Leo Tolstoy had not lived we would never have known Anna Karenina. There is no reason to believe that another author would have written that same novel. However, if Pythagoras had not lived, someone else would have discovered exactly the same Pythagoras theorem. Moreover, that theorem means the same to us today as it meant to Pythagoras 2,500 years ago.

So it's not subject to culture?

This is the special quality of mathematics. It means the same today as it will a thousand years from now. Our perception of the physical world can be distorted. We can disagree on many different things, but mathematics is something we all agree on.

The only reason the theory means the same is that it describes the reality of the physical world, so mathematics must need the physical world.

Not always. Euclidian geometry deals with flat spaces, such as the three-dimensional flat space. For millennia people thought we inhabited a flat, three-dimensional world. It was only after Einstein that we realised we lived in a curved space and that light doesn't travel in a straight line but bends around a star. Pythagoras' theorem is about geometric shapes in an idealised space, a flat Euclidian plane which, in fact, is not found in the real world. The real world is curved. When Pythagoras discovered his theorem there were, of course, inferences from physical reality, and a lot of mathematics is drawn from our experience in the physical world, but our imagination is limited and a lot of mathematics is actually discovered within the narrative of a hidden mathematical world. If you look at recent discoveries, they have no a priori bearing in physical reality at all.

The naïve interpretation that mathematics comes from physical reality just doesn't work. The other interpretation that mathematics is a product of the human mind also has serious issues, because it seems clear that some of these concepts transcend any specific individual.

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Evolutionary scientists have long argued that species that live together must evolve in different ways in order to avoid direct competition with each other, but new research published Sunday in the journal Nature suggests otherwise.

A team of researchers led by Dr. Joe Tobias of Oxford University’s Department of Zoology studied ovenbirds, one of the most diverse families of birds in the world, in order to conduct an in-depth analysis of the processes that result in the evolution of species differences.

They found that even though bird species that occurred together were typically more varied than those that lived apart, this was “simply an artifact of species being old by the time they meet,” the researchers said. Once differences in the age of species was accounted for, they found that coexisting species tended to be more similar than those types of birds that evolved separately – the opposite of what Charles Darwin claimed in Origin of Species.

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"Once you have identified an enzyme that has some weak, promiscuous activity for your target reaction, it's fairly clear that, if you have mutations at random, you can select and improve this activity by several orders of magnitude," says Dan Tawfik at the Weizmann Institute in Israel. "What we lack is a hypothesis for the earlier stages, where you don't have this spectrum of enzymatic activities, active sites and folds from which selection can identify starting points. Evolution has this catch-22: Nothing evolves unless it already exists."

Overall, what the field of protein evolution needs are some plausible, solid hypotheses to explain how random sequences of amino acids turned into the sophisticated entities that we recognize today as proteins. Until that happens, the phenomenon of the rise of proteins will remain, as Tawfik says, "something like close to a miracle."

I hope that none of your readers need this explained to them.

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Scientists have long wondered how atoms first came together to make up the three crucial molecular components of living organisms: RNA, DNA and proteins.

The molecules that combined to form genetic material are far more complex than the primordial "pre-biotic" soup of organic (carbon-based) chemicals thought to have existed on the Earth more than three billion years ago, and RNA (ribonucleic acid) is thought to have been the first of them to appear.

Simply adding energy such as heat or light to the more basic organic molecules in the "soup" does not generate RNA. Instead, it generates tar.

RNA needs to be coaxed into shape by "templating" atoms at the crystalline surfaces of minerals.

The minerals most effective at templating RNA would have dissolved in the oceans of the early Earth, but would have been more abundant on Mars, according to Prof Benner.

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"Underlying the central dogma and conventional views of genome evolution was the idea that the genome is a stable structure that changes rarely and accidentally by chemical fluctuations or replication errors. This view has had to change with the realization that maintenance of genome stability is an active cellular function and the discovery of numerous dedicated biochemical systems for restructuring DNA molecules ... Genetic change is almost always the result of cellular action on the genome. These natural processes are analogous to human genetic engineering ... Genome change arises as a consequence of natural genetic engineering, not from accidents. Replication errors and DNA damage are subject to cell surveillance and correction. When DNA damage correction does produce novel genetic structures, natural genetic engineering functions, such as mutator polymerases and nonhomologous end-joining complexes, are involved. Realizing that DNA change is a biochemical process means that it is subject to regulation like other cellular activities. Thus, we expect to see genome change occurring in response to different stimuli and operating nonrandomly throughout the genome, guided by various types of intermolecular contacts ... If we are to give up the outmoded atomistic vocabulary of 20th-Century genetics, we need to develop a new lexicon of terms based on a view of the cell as an active sentient entity, particularly as it deal with the genome. The emphasis has to be on what the cell does with and to it's genome, not what the genome directs the cell to execute ..." -- James A. Shapiro, Revisiting the Central Dogma in the 21st Century, 2009

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[T]here has arisen a curious consilience between the findings of modern cosmology and some traditional understandings of the creation of the universe. For example, theists have noted that the model known as the Big Bang has a certain consistency with the Judeo-Christian notion of creation ex nihilo, a consistency not seen in other cosmologies that postulated an eternally existent universe. (In fact, when the astronomer-priest Georges Lemaître first postulated the theory, he was met with such skepticism by proponents of an eternal universe that the name "Big Bang" was coined by his opponents -- as a term of ridicule.) Likewise, many cosmologists have articulated various forms of what is known as the "anthropic principle" -- that is, the observation that the basic laws of the universe seem to be "fine-tuned" in such a way as to be favorable to life, including human life.

(Austin L. Hughes, "The Folly of Scientism," The New Atlantis (Fall, 2012):32-50.)

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The earliest large life forms may have appeared on land long before the oceans filled with creatures that swam and crawled and burrowed in the mud.

This story is told from fossils that date from before an extraordinary period in Earth history, called the Cambrian explosion, about 530 million years ago. That's when complex life suddenly burst forth and filled the seas with a panoply of life forms.

Paleontologists have found fossil evidence for a scattering of fossil animals that predate that historic moment. These mysterious organisms are called Ediacarans.

Many scientists have assumed Ediacarans were predecessors of jellyfish, worms and other invertebrates. But Greg Retallack at the University of Oregon says he always had his doubts.

Retallack has been building the case that Ediacarans weren't in fact animals, but actually more like fungi or lichens. And if that idea weren't enough of a departure from standard theory, he now argues in a paper in the journal Nature that Ediacarans weren't even living in the sea, as everyone has assumed. He says he has reanalyzed some Australian rock where they're found and concluded that it's ancient soil, not marine mud.

These early life forms were landlubbers. ...

This is an audacious idea. But Retallack is not alone in entertaining this possibility.

Paul Knauth at Arizona State University has been pondering this same possibility.

"I don't have any problem with early evolution being primarily on land," says Knauth, a professor in the School of Earth and Space Exploration at Arizona State University. "I think you can make a pretty good argument for that, and that it came into the sea later. It's kind of a radical idea, but the fact is we don't know." ...

"The idea that Ediacaran fossils were marine invertebrates is so deeply entrenched, it's in all the textbooks," he says. When someone (namely him) comes along and says that's not so, "it's going to be treated like a death in the family. It's going to go through all the phases of grief, starting with denial."

It remains to be seen whether the story ends with acceptance of Retallack's provocative proposal.

But you knew all of this, right?

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"The big problem for neo-Darwinian evolution is that they must show that the probability of getting the right mutations at the right time is large enough to make evolution work. We know the mutation rates (approximately) but we don't know what fraction of them will be adaptive in any particular situation. It turns out that if we assume the fraction is large enough to make evolution work, then there are too many evolutionary pathways to allow convergent evolution." -- Lee Spetner, MIT PhD and author of Not by Chance!: Shattering the Modern Theory of Evolution

Of course, he's not one of your readers, is he?

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"A team of psychology researchers has found that, despite years of scientific training, even professional chemists, geologists, and physicists from major universities such as Harvard, MIT, and Yale cannot escape a deep-seated belief that natural phenomena exist for a purpose."


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This is the issue I have with neo-Darwinists: They teach that what is generating novelty is the accumulation of random mutations in DNA, in a direction set by natural selection. If you want bigger eggs, you keep selecting the hens that are laying the biggest eggs, and you get bigger and bigger eggs. But you also get hens with defective feathers and wobbly legs. Natural selection eliminates and maybe maintains, but it doesn't create. ... [N]eo-Darwinists say that new species emerge when mutations occur and modify and organism. I was taught over and over again that the accumulation of random mutations led to evolutionary change-led to new species. I believed it until I looked for evidence. ...

What you'd like to see is a good case for gradual change from one species to another in the field, in the laboratory, or in the fossil record--and preferably in all three. Darwin's big mystery was why there was no record at all before a specific point [dated to 542 million years ago by modern researchers], and then all of the sudden in the fossil record you get nearly all the major types of animals. The paleontologists Niles Eldredge and Stephen Jay Gould studied lakes in East Africa and on Caribbean islands looking for Darwin's gradualchange from one species of trilobite or snail to another. What they found was lots of back-and-forth variation in the population and then--whoop--a whole new species. There is no gradualism in the fossil record. ...

The critics, including the creationist critics, are right about their criticism. It's just that they've got nothing to offer by intelligent design or "God did it." They have no alternatives that are scientific. ...

Population geneticist Richard Lewontin gave a talk here at UMass Amherst about six years ago, and he mathemetized all of it--changes in the population, random mutation, sexual selection, cost and benefit. At the end of his talk he said, "You know, we've tried to test these ideas in the field and the lab, and there are really no measurements that match the quantities I've told you about." This just appalled me. So I said, "Richard Lewontin, you are a great lecturer to have the courage to say it's gotten you nowhere. But then why do you continue to do this work?" And he looked around and said, "It's the only thing I know how to do, and if I don't do it I won't get grant money." So he's an honest man, and that's an honest answer.

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Does the universe care about life? Intelligent design is one answer. Indeed, a fair number of theologians, philosophers, and even some scientists have used fine-tuning and the anthropic principle as evidence of the existence of God. For example, at the 2011 Christian Scholars’ Conference at Pepperdine University, Francis Collins, a leading geneticist and director of the National Institutes of Health, said, “To get our universe, with all of its potential for complexities or any kind of potential for any kind of life-form, everything has to be precisely defined on this knife edge of improbability…. [Y]ou have to see the hands of a creator who set the parameters to be just so because the creator was interested in something a little more complicated than random particles.”

Intelligent design, however, is an answer to fine-tuning that does not appeal to most scientists. The multiverse offers another explanation. If there are countless different universes with different properties--for example, some with nuclear forces much stronger than in our universe and some with nuclear forces much weaker--then some of those universes will allow the emergence of life and some will not. Some of those universes will be dead, lifeless hulks of matter and energy, and others will permit the emergence of cells, plants and animals, minds. From the huge range of possible universes predicted by the theories, the fraction of universes with life is undoubtedly small. But that doesn't matter. We live in one of the universes that permits life because otherwise we wouldn't be here to ask the question.

This disturbs many physicists who are adjusting to the idea of the multiverse. Not only must we accept that basic properties of our universe are accidental and uncalculable. In addition, we must believe in the existence of many other universes. But we have no conceivable way of observing these other universes and cannot prove their existence. Thus, to explain what we see in the world and in our mental deductions, we must believe in what we cannot prove.

Sound familiar? Theologians are accustomed to taking some beliefs on faith. Scientists are not. All we can do is hope that the same theories that predict the multiverse also produce many other predictions that we can test here in our own universe. But the other universes themselves will almost certainly remain a conjecture.

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"In order to be truthful, we must acknowledge that certain questions, like the origins of the first living cells, currently have no credible scientific answer. However, given the historical record of science and technology in achieving the "impossible" (e.g., space flight, telecommunications, electronic computation and robotics), there is no reason to believe that unsolved problems will remain without naturalistic explanations indefinitely." -- James Shapiro

But you have all the answers, don't you?

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In 1995 the Japanese scientists Shigeru Kondo and Rihito Asai applied Turing's equations to the beautiful tropical angelfish Pomacanthus imperator, which displays striking yellow and purple stripes. Turing's model made a surprising prediction: the stripes of the angelfish move along its body (unlike those on an adult zebra, for example, which are fixed).

It seemed wildly unlikely, but when Kondo and Asai photographed specimens of the angel­fish over periods of several months, they found that the stripes slowly migrated across its surface. Moreover, defects in the pattern of otherwise regular stripes, known as dislocations, broke up and re-formed exactly as Turing's equations predicted. They did this because the pigment proteins leaked from cell to cell, drifting from the fish's tail towards its head. (In animals whose stripes are fixed, this does not happen; but once the size of the animal and other factors are known, the maths can predict whether its markings will move.)

Hmm, the material conforms to the non-material.

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ScienceDaily (Feb. 4, 2011) — Researchers have discovered the 100 million-year-old ancestor of a group of large, carnivorous, cricket-like insects that still live today in southern Asia, northern Indochina and Africa. The new find, in a limestone fossil bed in northeastern Brazil, corrects the mistaken classification of another fossil of this type and reveals that the genus has undergone very little evolutionary change since the Early Cretaceous Period, a time of dinosaurs just before the breakup of the supercontinent Gondwana. ...

Although the fossil is distinct from today's splay-footed crickets, its general features differ very little, Heads said, revealing that the genus has been in a period of "evolutionary stasis" for at least the last 100 million years.

100 million years of evolutionary stasis. Please explain.

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THE children of Charles Darwin, whose theories on evolution revolutionised science, may have been genetically blighted themselves — because of generations of inbreeding in his own family.

Reasearchers have linked a series of marriages between cousins from Darwin's family, and that of Emma Wedgwood, who became his wife, to the high levels of infertility and premature death that beset both their wider families as well as their children.

Charles and Emma, who were also first cousins, had 10 children, of whom three died early while three were infertile.

Studies of Darwin's ancestors show a history of intermarriage between the Darwins and Wedgwoods that could have produced multiple genetic defects.

Such marriages were so common in Darwin's family, according to research from James Moore, professor of science history at the Open University, that both of his maternal grandparents and his mother were Wedgwoods. He said: "In Victorian times it was quite common for cousins to marry but the level of intermarriage in these families was unusual even then."

Your idol has feet of clay.

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Inevitably, those of us who aren't professional scientists have to take a lot of science on trust. And one of the things that makes it so easy to trust the standard view of evolution, in particular, is amply illustrated by the legend of the Nasa astronomers: the doubters are so deluded or dishonest that one needn't waste time with them. Unfortunately, that also makes it embarrassingly awkward to ask a question that seems, in the light of recent studies and several popular books, to be growing ever more pertinent. What if Darwin's theory of evolution – or, at least, Darwin's theory of evolution as most of us learned it at school and believe we understand it – is, in crucial respects, not entirely accurate?

Such talk, naturally, is liable to drive evolutionary biologists into a rage, or, in the case of Richard Dawkins, into even more of a rage than usual. They have a point: nobody wants to provide ammunition to the proponents of creationism or "intelligent design", and it's true that few of the studies now coming to public prominence are all that revolutionary to the experts. But in the culture at large, we may be on the brink of a major shift in perspective, with enormous implications for how most of us think about how life came to be the way it is. As the science writer David Shenk puts it in his new book, The Genius in All of Us, "This is big, big stuff – perhaps the most important [discoveries] in the science of heredity since the gene."


Epigenetics is the most vivid reason why the popular understanding of evolution might need revising, but it's not the only one. We've learned that huge proportions of the human genome consist of viruses, or virus-like materials, raising the notion that they got there through infection – meaning that natural selection acts not just on random mutations, but on new stuff that's introduced from elsewhere. Relatedly, there is growing evidence, at the level of microbes, of genes being transferred not just vertically, from ancestors to parents to offspring, but also horizontally, between organisms. The researchers Carl Woese and Nigel Goldenfield conclude that, on average, a bacterium may have obtained 10% of its genes from other organisms in its environment.

To an outsider, this is mind-blowing: since most of the history of life on earth has been the history of micro-organisms, the evidence for horizontal transfer suggests that a mainly Darwinian account of evolution may be only the latest version, applicable to the most recent, much more complex forms of life. Perhaps, before that, most evolution was based on horizontal exchange. Which gives rise to a compelling philosophical puzzle: if a genome is what defines an organism, yet those organisms can swap genes freely, what does it even mean to draw a clear line between one organism and another? "It's natural to wonder," Goldenfield told New Scientist recently, "if the very concept of an organism in isolation is still valid at this level." In natural selection, we all know, the fittest win out over their rivals. But what if you can't establish clear boundaries between rivals in the first place?


Far more than biologists, evolutionary psychologists bought in to the ultra-simple version of natural selection, and so they stand to lose far more from advances in our understanding of what's really been going on. They were always prone to telling "just-so stories" – spinning plausible tales about why some trait might be adaptive, instead of demonstrating that it was – and numerous recent studies have begun to chip away at what evidence there was. (That waist-to-hip ratio finding, for example, doesn't seem to hold up in the face of international and historical research.) And now, if epigenetics and other developments are coming to suggest that environment can alter heredity, the very terms of the debate – of nature versus nurture – suddenly become shaky. It's not even a matter of settling on a compromise, a "mixture" of nature and nurture. Rather, the concepts of "nature" and "nurture" seem to be growing meaningless. What does "nature" even mean if you can nurture the nature of your descendants?


"What all this evidence shows is that we need a much more subtle and nuanced understanding of Darwinism and natural selection," Shenk says. "I think that's inevitably going to happen among scientists. The question is how much nuance will carry over into the public sphere . . . it's really funny how difficult it is to have this conversation, even with a lot of people who understand the science. We're stuck with a pretty limited way of viewing all this, and I think part of that comes from the terms" – such as nature and nurture – "that we have."

Among the arsenal of studies at Shenk's disposal is one published last year in the Journal of Neuroscience, involving mice bred to possess genetically inherited memory problems. As small recompense for having been bred to be scatterbrained, they were kept in an environment full of stimulating mouse fun: plenty of toys, exercise and attention. Key aspects of their memory skills were shown to improve, and crucially so did those of their offspring, even though the offspring had never experienced the stimulating environment, even as foetuses.

"If a geneticist had suggested as recently as the 1990s that a 12-year-old kid could improve the intellectual nimbleness of his or her future children by studying harder now," writes Shenk, "that scientist would have been laughed right out of the hall." Not so now.

Maybe, it's you who should do a little more reading.

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