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Date: Wednesday, 16 Apr 2014 02:19

Or is it the same crossroads, circumnavigated any number of times?

File:Calabi yau.jpg

5 dimensions in 2

Scientific American’s May edition will feature “Supersymmetry and the Crisis in Physics”:

For decades physicists have been working on a beautiful theory that has promised to lead to a deeper understanding of the quantum world. Now they stand at a crossroads: prove it right in the next year or confront an epochal paradigm shift – By Joseph Lykken and Maria Spiropulu More. (paywall)

This seems to be a way of getting around to saying now what Peter Woit at Not Even Wrong (and others) have been saying for at least a decade: These new cosmologies are not supported by evidence and are not advancing our understanding.

Betting here is: They won’t really confront any “epochal paradigm shift” no matter what happens because the standard is subtly changing. In cosmology, evidence matters less now and conformity with other naturalist theories matters more. If that were not so, this stuff would have been abandoned a while back. It’s always about to be abandoned, and then they remember.

See also: Multiverse cosmology: Assuming that evidence still matters, what does it say?

and

In search of a road to reality

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Date: Wednesday, 16 Apr 2014 02:02

A friend sent us this:

“I said it was a terrible, terrible paper and they university should not be endorsing it,” Myers said.

But attorneys for the student newspaper are alleging Myers broke the law when they say he wrote a blog post on his personal blog urging people to throw away the publication.

The Alliance Defending Freedom has accused Myers, an associate professor in the school’s biology program, of encouraging people to steal and throw away a copy of the November 22nd edition of the newspaper. More.

But students, why are you reading the paper anyway? Just ask PZ, Sage of Morris, Minnesota, what to think. That’s why you went to university in the first place. Right?

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Author: "News" Tags: "Darwinism, Intellectual freedom, Media, ..."
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Date: Tuesday, 15 Apr 2014 23:08

The fallacious results of the Avida computer simulation were used in the infamous Kitmiller vs. Dover trial to argue in favor of Darwinian evolution. Using the evidence from the Avida simulation and other testimony, Judge Jones ruled that it is illegal to contest Darwinism for all time. Prosecution witness Robert Pennock claimed in sworn testimony that Avida solved the problem of Irreducible Complexity (IC).

Unfortunately the incompetent defense team wasn’t privy to later discoveries by me and Richard Hoppe, namely, that Avida offers solutions to the OOL problem and predicts the possibility of a Zombie Apocalypse through cosmic radiation. It would have been read more


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Author: "scordova" Tags: "Cybernetics and Mechatronics, Humor, New..."
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Date: Tuesday, 15 Apr 2014 20:31
File:Lightmatter lab mice.jpg

lightmatter lab mice/Aaron Logan

Evidence that parents’ exposure to trauma can be inherited (apart from exposure to the parents’ psychology later) has often been dismissed as superstition.

A strictly Darwinian understanding of genetics—one gene one protein was the central dogma, remember?—ruled. If it couldn’t fit into that explanation, it couldn’t be true.

Fast forward. In a recent mouse study, reported in Nature:

In the new study, Isabelle Mansuy, a neuroscientist at the University of Zurich, Switzerland, and her colleagues periodically separated mother mice from their young pups and exposed the mothers to stressful situations — either by placing them in cold water or physically restraining them. These separations occurred every day but at erratic times, so that the mothers could not comfort their pups (termed the F1 generation) with extra cuddling before separation.

When raised this way, male offspring showed depressive behaviours and tended to underestimate risk, the study found. Their sperm also showed abnormally high expression of five microRNAs. One of these, miR-375, has been linked to stress and regulation of metabolism.

The F1 males’ offspring, the F2 generation, showed similar depressive behaviours, as well as abnormal sugar metabolism. The F1 and F2 generations also had abnormal levels of the five microRNAs in their blood and in the hippocampus, a brain region involved in stress responses. Behavioural effects persisted in the F3 generation as well.

To rule out the possibility that the effects of stress were transmitted socially, the researchers also collected RNA from the F1 males’ sperm and injected it into freshly fertilized eggs from untraumatized mice. This resulted in mice with comparable depressive behaviours and metabolic symptoms — and the depressive behaviours were passed, in turn, to the next generation. More.

No wonder some are standing athwart epigenetics and yelling Stop! Apart from the damage such findings could do to current textbook Darwinism as such, if this sort of finding holds up and also proves true for humans, just think of all the assumptions that must be rethought, about the long-term effects of trauma.

If the body itself has memories, we could be hearing less of “Aw never mind. They’ll get over it.”

Here’s the abstract:

Small non-coding RNAs (sncRNAs) are potential vectors at the interface between genes and environment. We found that traumatic stress in early life altered mouse microRNA (miRNA) expression, and behavioral and metabolic responses in the progeny. Injection of sperm RNAs from traumatized males into fertilized wild-type oocytes reproduced the behavioral and metabolic alterations in the resulting offspring. – K. Gapp et al. Nature Neurosci. http://dx.doi.org/10.1038/nn.3695; 2014 (Paywall)

See also: Epigenetics and neuroplasticity: The case of the rewired ferrets

Epigenetics: Inheritance of acquired traits gradually gaining acceptance

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Vid is discussing a study of inherited fear in mice.


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Author: "News" Tags: "Epigenetics, News"
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Date: Tuesday, 15 Apr 2014 19:22

Larry Moran wrote:

If Salvador Cordova can put together an audience of biology students at a reputable university (George Mason?) and get an Intelligent Design Creationist to ask these questions, I’ll be happy to come and answer them.

Some of them are easy to answer. The best answer is “I don’t know.”

That is very kind of you Larry. I will even do one better, I will suggest biology students take your classes. Really I don’t think I have to even make that plug, because I’m sure they probably have to take your classes anyway.

Many of my professors were openly anti ID and have campaigned against ID, such as James Trefil and Robert Ehrlich. Their anti-ID views did not stop me from taking their classes nor would their anti-ID biases hinder me from recommending them as professors for IDist or creationist students. In fact, it was Dr. Ehrlich’s encouragement that eventually inspired me to study physics.

I sense you are a good chem teacher, so I’d have no problem recommending students learn from you because I’m delighted when anyone learns more science. I’d even be delighted that creationist biology students score in the 99th percentile in evolutionary biology.

I will even plug your book here at Uncommon Descent, even though I haven’t read it, because it is a bio chem book written by a Princeton PhD like you teaching at a respectable university in Canada. I figure there will be something to learn by reading your book.

I’m willing to do this to help improve your books Amazon sales ranking at #54 in textbook biochemistry. Currently your book has:

Amazon Best Sellers Rank: #204,423 in Books (See Top 100 in Books)

#54 in Books > Textbooks > Medicine & Health Sciences > Medicine > Basic Sciences > Biochemistry

Principles of Biochemistry

I’m willing to do this because as of right now there is no threat your book will out pace the #10 book in biochemistry on the list of Amazon Best Sellers in Biochemistry. And which book is in the #10 spot?

dbb cover

:-)

PS
Just as a caution, because I didn’t read Dr. Moran’s book, as a matter of conscience, I must point out some of the 1-star reviews at Amazon:

For a beginning biochemistry text they make simple concepts overly complicated and wordy. Important concepts are not easily taken out of the text and they often refer to information in chapters that are much later in the text. The problems are the end of each chapter are extremely confusing and require you to do a search and find to figure out what tables you should refer to since the problem often does not tell you where you will find the information. Sometimes when a problem does refer to a table you go to look for the table and realize that they were all renumbered in the revised edition (though they forgot to change the table references in the problems). There are also numerous spelling and grammatical errors. Nothing about this text is straight forward or easy to understand.

In all my science courses this is probably the worst book I have ever encountered and have resorted to using other sources for learning most concepts as this book does not explain things clearly.

and

I really, really hated this book and it doesn’t help that my professor used it like a crutch. I could read and write notes about a chapter, get to the end of the chapter questions, and not have a clue on how to answer the questions. There also aren’t any examples throughout the chapter on how to solve the problems. All the answers are at the end of the book, but it really didn’t help because there isn’t anyway to find out where they got that answer.

but there was one 3 star review

It is EXTREMELY frustrating to think that a textbook, the supposed pinnacle of education, could contain such a vast number of errors. It really makes it difficult to get through a page knowing that the authors overlooked all of these flaws.


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Author: "scordova" Tags: "Education, News"
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Date: Tuesday, 15 Apr 2014 19:20

Recently I came across some amazing animations of various kinds of engines and other machines at the following Web sites, which I thought I might share with readers:

Here, here, here, here and here.

Two questions to ponder:

(1) How many of these machines have analogues in the world of living things?

(2) What predictions does Intelligent Design theory make regarding which of these machines will be found in organisms?

Enjoy!


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Author: "vjtorley" Tags: "Intelligent Design"
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Date: Tuesday, 15 Apr 2014 18:57

Hornworts/Fay-Wei Li

From ScienceDaily:

During the age of the dinosaurs, the arrival of flowering plants as competitors could have spelled doom for primitive ferns. Instead, ferns diversified and flourished under the new canopy — using a mysterious gene that helped them adapt to low-light environments. Scientists have now pinpointed the curious origins of this gene and determined that it was transferred to ferns from a group of unassuming, mossy plants called hornworts.

If ferns were so “primitive,” how did they manage to do this?

And hornworts? “A hornwort is a flowerless, spore-producing plant – with the spores typically produced in a tapering, horn-like or needle-like capsule which develops from a flattish, green sheet.” It is believed to have parted ways with the ferns about 400 million years ago.

Further:

Only one mechanism could explain how the gene hopped from hornworts to ferns so long after the lineages themselves diverged: horizontal gene transfer. But researchers have only just begun to explore how this occurs in plants.

They have only begun because the decline in Darwinism has only recently made it okay to openly look for non-Darwinian mechanisms.

“We’re actually seeing more and more incidence of horizontal gene transfer in plants, but there’s no definite answer as to what mediates it,” Li said.

In the microbial world, bacteria, fungi and viruses have been shown to mediate horizontal gene transfer wherever bits of genetic material get mixed up in different organisms. It’s a messy affair, but it can have powerful evolutionary consequences — gene transfer is how many bacteria learn antibiotic resistance, for example.

Let the record show that he said that HGT, not Darwinian natural selection, “is how many bacteria learn antibiotic resistance.” And keep that in mind when a science mediabot tells you that if you doubt Darwin, you are impeding antibiotic research.

However neochrome was transferred, it seems to have occurred at just the right moment in ferns’ evolutionary history.

Stare at a point in the far distance, okay?

See also: HGT: Gene from bacteria lets beetle feed only on coffee beans

Why horizontal gene transfer is bad news for Darwinism

Here’s the abstract:

Significance: Despite being one of the oldest groups of land plants, the majority of living ferns resulted from a relatively recent diversification following the rise of angiosperms. To exploit fully the new habitats created by angiosperm-dominated ecosystems, ferns had to evolve novel adaptive strategies to cope with the low-light conditions exerted by the angiosperm canopy. Neochrome, an unconventional photoreceptor that allows ferns to “see the light” better, was likely part of the solution. Surprisingly, we discovered that fern neochrome was derived from a bryophyte lineage via horizontal gene transfer (HGT). This finding not only provides the first evidence that a plant-to-plant HGT can have a profound evolutionary impact but also has implications for the evolution of photosensory systems in plants.

Ferns are well known for their shade-dwelling habits. Their ability to thrive under low-light conditions has been linked to the evolution of a novel chimeric photoreceptor—neochrome—that fuses red-sensing phytochrome and blue-sensing phototropin modules into a single gene, thereby optimizing phototropic responses. Despite being implicated in facilitating the diversification of modern ferns, the origin of neochrome has remained a mystery. We present evidence for neochrome in hornworts (a bryophyte lineage) and demonstrate that ferns acquired neochrome from hornworts via horizontal gene transfer (HGT). Fern neochromes are nested within hornwort neochromes in our large-scale phylogenetic reconstructions of phototropin and phytochrome gene families. Divergence date estimates further support the HGT hypothesis, with fern and hornwort neochromes diverging 179 Mya, long after the split between the two plant lineages (at least 400 Mya). By analyzing the draft genome of the hornwort Anthoceros punctatus, we also discovered a previously unidentified phototropin gene that likely represents the ancestral lineage of the neochrome phototropin module. Thus, a neochrome originating in hornworts was transferred horizontally to ferns, where it may have played a significant role in the diversification of modern ferns.– Fay-Wei Li, Juan Carlos Villarreal, Steven Kelly, et al. Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns. Proceedings of the National Academy of Sciences, April 14, 2014 DOI: 10.5061/dryad.fn2rg

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Date: Tuesday, 15 Apr 2014 15:51

The ID-friendly version of Natural Selection was pioneered by the creationist Blyth. I have also argued that there is credible evidence that Darwin plagiarized and distorted Blyth’s work.

I view Natural Selection as itself a design feature of optimization and search. Whereas Darwinist view natural selection as a mechanism of design, I view natural selection as feature of design. This essay was also partly written to correct and clarify some of my earlier choice of words in Same pattern, different implementations.

When we find designs that cannot be implemented via selection, I consider that strong evidence of design. However, finding possible evidence that selection is a feature of a biological system doesn’t automatically imply there is no Designer. In fact, NS might actually be a design feature. The best example I can think of is in Royal Truman’s essay B Cell Maturation. But here is the gist of his arugment:

Proposed evolutionary processes which supposedly produced first bacteria and eventually humans are assumed to not have been driven by intelligent guidance. We must clearly distinguish between true randomness and a purposeful algorithm to cover a search space to converge on an intended goal.

(A) Where fired shotgun pellets actually impact is only in an incomplete sense “random”. The gun barrel, triggering mechanism, explosive mixture, size and number of pellets, etc. are organized to solve a class of problem. Although the specific target need not be known in advance, the topology of desired outcome (in time and space) is part of the shotgun design. The design covers a constrained range of possibilities: it cannot kill bacteria nor whales (area), nor destroy satellites (distance) and needs a triggering mechanism (time). This permits a non-random outcome, such as killing a bird at a specific time and place with a high probability, with little risk of collateral damage.

The designer of the apparatus need not specify the exact picometer each pellet will end up at. It suffices to ensure within a high probability that when used in the correct context and manner, the “random” behavior of the ensemble of pellets is within the intended tolerance.

(B) Construction workers sometimes throw debris down a chute when repairing a building. One cannot predict the precise trajectories nor final location of every object thrown down. Nevertheless, the range of outcomes is constrained by the design which ensures bystanders aren’t killed.


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Author: "scordova" Tags: "Intelligent Design, News"
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Date: Tuesday, 15 Apr 2014 12:53

400 mya plant/U Cal Berkeley

From ScienceDaily:

Benca described this 400-million-year-old fossil lycopod, Leclercqia scolopendra, and created a life-like computer rendering. The stem of the lycopod is about 2.5 millimeters across.

File:Lycopodium plant.jpg

club moss ( Lycopodiella cernua)/Eric Guinther

Examples of the lycopod or club moss abound today:

Called Leclercqia scolopendra, or centipede clubmoss, the plant lived during the “age of fishes,” the Devonian Period. At that time, lycopods — the group Leclercqia belonged to — were one of few plant lineages with leaves. Leclercqia shoots were about a quarter-inch in diameter and probably formed prickly, scrambling, ground-covering mats. The function of Leclercqia’s hook-like leaf tips is unclear, Benca said, but they may have been used to clamber over larger plants. Today, lycopods are represented by a group of inconspicuous plants called club mosses, quillworts and spikemosses.

They may be “inconspicuous” but they are certainly a durable group. They used to be forests.

File:A small cup of coffee.JPG

Note: Is it correct to refer to a computer animation of a plant?

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Note: Sometimes in nature nothing is what it seems: That thing below isn’t a flower and the thing hanging off it isn’t a stick:


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Author: "News" Tags: "Intelligent Design, Plants, stasis"
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Date: Tuesday, 15 Apr 2014 01:27

A fiddly job but someone at Fermilab is doing it:

Now Chou and his team are down in the dirt, hunting for the universe’s quantum bits. In length terms, these bits are expected to be on the smallest scale of the universe, the Planck scale: 1.6 x 10-35 meters. That’s roughly 10 trillion trillion times smaller than an atom; no existing instrument can directly probe objects that small. If humanity could build a particle collider the size of the Milky Way, we might be able to investigate Planck-scale bits directly.

“Right now, so little experimental data exists about this high-energy scale that theorists are unable to construct any meaningful models other than those based on speculation,” Chou says. “Our experiment is really a mission of exploration—to obtain data about an extremely high-energy scale that is otherwise inaccessible.”

Chou thinks the universe might not be 3D but a 2D hologram.

Actually the 2D idea, in itself, has been done before, in a 19th century novel called Flatland.

What if the universe turns out to be fiction? Can Fermilab still fund the research?

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