Michael J. Behe's Blog, page 583

March 10, 2017

Research group: Up to 85% of medical research funds may be wasted

What’s hot? What’s not?/Niklas Bildhauer, Wikimedia

From University of Plymouth at Eurekalert:

Funders need to take more responsibility for the efficiency of the research they fund

It has been estimated that up to 85% of medical research is wasted because it asks the wrong question, is badly designed, not published or poorly reported. Health research around the world depends heavily on funding from agencies which distribute public funds. But a new study has found that these agencies are not as open as they could be about what they are doing to prevent this waste and that governments responsible for the public money they distribute are not holding them to account.

The findings come in response to a question posed by a letter published on-line today, 9th March 2017, in The Lancet. It asks how transparent the funding agencies are about the policies and procedures they use to reduce waste and support methodological research and research infrastructure, and what they are doing to secure best value for taxpayers. The study was carried out by an international team of researchers led by Dr. Mona Nasser of Plymouth University Peninsula Schools of Medicine and Dentistry.

It arose from challenges laid down in The Lancet’s series on reducing waste and increasing value in medical research, published in 2014. More.

Much of the problem arises from the glorification of science as a special way of knowing truth, irrespective of who is doing it and why. Science journalists bear much of the blame.

One expects media in free countries to be sources of constructive criticism. North American political writers, for example, are generally worth reading, even when they call it wrong (see Brexit and US 2016). At least, one reasonably expects the political hacks will give themselves the right to give themselves a swift kick and get up to speed. They don’t necessarily feel they need to glamorize, let alone worship, their subjects in order to write about them. That fact alone sharpens thinking skills.

But the science writers’ cheerleader attitude (Sci-ENCE! Sci-ENCE!) has delayed efforts to address the huge problems of waste and fraud in research, probably for decades. To ay nothing of failures to even try to replicate findings.

It’s got so bad, it won’t be easy to fix. One must start somewhere. Today is always best.

Resources on research waste reduction. Keep up to date with Retraction Watch

See also: Peer review “unscientific”: Tough words from editor of Nature

and

Science writing in an age when we ran out of pom poms to wave

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Published on March 10, 2017 05:37

March 9, 2017

NASA’s mission to find life on Jupiter’s promising moon, Europa

Artist's rendering shows NASA's Europa mission spacecraft From Eric Berger at Ars Technica:

Thanks to the ominous warning in Arthur C. Clarke’s novel, 2010: Odyssey Two, much of the science and technical community shares Culberson’s fascination with Europa. But for the general public, the icy moon remains largely an unknown. Eight billion dollars to peck at the ice on some moon around Jupiter? What is the sense of that? As he works on his peers in Congress, Culberson will eventually have to convince Joe the Plumber, Ken Bone, and the rest of America about the relevance of Europa, too.

For this mission, he has a secret weapon. During the briefings at JPL, Culberson brought a friend with him, the famed Director James Cameron. The two men share an interest in exploring the depths of oceans, and periodically Cameron peppered the JPL presenters with questions about batteries, the chemistry of Europa’s ocean, and so forth. But mostly, he came as Europa’s storyteller-in-chief. “If you want to talk to the world, this man knows how to do it,” Culberson said of his friend. It’s true in some sense. Titanic and Avatar are the two highest-grossing movies of all time. More.

Why Europa? Underground oceans have long made it a favored site to hunt for life. Anyway, it’s great to see extraterrestrial life come to seem like science again. As opposed to angst about the problems religious people might have with ET and/or they just gotta be OUT THERE! hype (= the heck with evidence, that’s UnCool now).

See also: Rob Sheldon to Europan scientists, last November: Don’t go home before you check the Jobs board

2016: Search for ET life more focused, less aimless conjecture

and

NASA cares what your religion thinks about ET One would expect that those world religions that care much one way or the other if NASA finds bacteria in space could fund their own examination of the question.

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Published on March 09, 2017 08:41

Extinction: Dying woolly mammoths were in genetic meltdown?

From Brian Switek at Nature:

A study1 published 2 March in PLOS Genetics gives a rare insight into how genomes change as a species dies out. Towards the end of the last Ice Age, around 11,700 years ago, woolly mammoths ranged through Siberia and into the colder stretches of North America. But by about 4,000 years ago, mainland mammoths had died out and only 300 remained on Wrangel Island off the Siberian coast.

In order to examine this disappearance at the genetic level, biologists Rebekah Rogers and Montgomery Slatkin at the University of California, Berkeley, compared the complete genome of a mainland mammoth (Mammuthus primigenius) that lived about 45,000 years ago with that of a Wrangel Island mammoth from about 4,300 years ago. The sequences were made available by Love Dalén at the Swedish Museum of Natural History in Stockholm.

“As I looked at the sequence data,” says Rogers, “it became very clear that the Wrangel mammoth had an excess of what looked like bad mutations.” More.

That’s a useful insight for conservation, as the authors point out: One wants genomes from the middle of the stream, not the swampy shallows.

It also raises the question whether mass extinctions, say, of the trilobites or the dinosaurs (when examples of many other classifications of life form survived) had a genetic component.

See also: Extinction: Can New Zealand extirpate invasive species?

Researchers: The dinosaurs died of darkness and cold

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Published on March 09, 2017 07:21

Could the Neanderthals have “won”?

Neanderthal/Photaro

Well, how could they lose? Just recently, they turned up again with documents. From Gaia Vince at Digg:

But by 39,000 years ago, Neanderthals were struggling. Genetically they had low diversity because of inbreeding and they were reduced to very low numbers, partly because an extreme and rapid change of climate was pushing them out of many of their former habitats. A lot of the forested areas they depended on were disappearing and, while they were intelligent enough to adapt their tools and technology, their bodies were unable to adapt to the hunting techniques required for the new climate and landscapes.

…

“It could’ve gone the other way – if instead the climate had got wetter and warmer, we might be Neanderthals today discussing the demise of modern humans.”

Although the Neanderthals, like the Denisovans and other races we are yet to identify, died out, their genetic legacy lives on in people of European and Asian descent. Between 1 and 4 per cent of our DNA is of Neanderthal origins, but we don’t all carry the same genes, so across the population around 20 per cent of the Neanderthal genome is still being passed on. That’s an extraordinary amount, leading researchers to suspect that Neanderthal genes must be advantageous for survival in Europe.

Interbreeding across different races of human would have helped accelerate the accumulation of useful genes for the environment, a process that would have taken much longer to occur through evolution by natural selection. More.

<em>Teapot</em> Cobalt Blue

So the Neanderthals did not “die out”; they just assimilated, to get hold of new technologies?

You know what they say about marrying the boss’s daughter. And who’s to say the Neanderthals don’t still rule? What do you really know about your supervisor’s genome?

See also: Do extinct Neanderthals control human gene expression?

Evidence suggests that there were no separate early human lineages?

and

Neanderthal Man: The long-lost relative turns up again, this time with documents

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Published on March 09, 2017 06:35

Are there really “laws of life”? Maybe, but…

But what are they? From Charles Cockell at Physics Today:

Look at the menagerie of life—for example, as depicted by Jan Brueghel the Elder in the painting to the left. The casual viewer could easily conclude that life is limitless in its scope, that its forms and shapes are constrained only by the imagination. But however trite the observation may be, life must conform to the laws of physics. Science still does not know how many possible solutions there are to building a self-replicating system within those laws, however, or to what extent physics constrains the products of the evolutionary process.

At the scale of organisms, physical laws certainly do limit the engineering solutions to life’s problems. For example, consider locomotion. In a now classic paper,3 Michael LaBarbera addressed a question that has been a favorite at biologists’ café tables since time immemorial: Why doesn’t life use wheels? People use them in a vast diversity of forms of locomotion. Why did biology reject them? Apart from the biomechanical problems of evolving rotating muscles and veins, wheels have an inherent physical problem in that they are limited in the landscapes they can navigate: They cannot overcome obstacles with a height greater than their radius unless they are lifted up.

But life does use wheels:

Whatever the physical laws are life are supposed to be, life always seems to find a way around them. Life continues to ignore what evolution experts say. The world of the extremophiles testifies to that.

Life must be fashioned by the laws of physics. Birds must conform to the principles of aerodynamics, protein folding to thermodynamics, and energy acquisition systems that use electrons to the various energy states of those subatomic particles. What is less clear is the extent to which physics narrows the range of Darwinian possibilities. The physical principles that underlie the construction of life from predominantly C-based molecules instead of Si-based ones have long been understood. More recently, however, scientists have suggested that other choices that once seemed contingent are nonrandom events based on statistical probabilities, energetic considerations, and optimal arrangements for a self-replicating, evolving system. Examples include the structure of proteins or even the 20 amino acids that life chooses from the many hundreds of possibilities to build those proteins. More.

Chances are, the explicit law of physics that life simply cannot get around will turn out to be very few. But that raises the question, why does life so obviously seek to come into existence and stay that way?

See also: Life forms found at abyssal depths

Life continues to ignore what evolution experts say

and

What can we hope to learn about animal minds? (which includes the strivings of life forms without brains)

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Previously believed to be only man-made, a natural example of a functioning gear mechanism has been discovered in a common insect – the plant-hopper Issus – showing that evolution developed interlocking cogs long before we did.

Interlocking cogs are wheels. And we won’t even get into the bacterial flagellumTM.

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Published on March 09, 2017 06:10

March 8, 2017

Free live interactive webinar Saturday with fine-tuning astrophysicist Luke Barnes

Jonathan McLatchie kindly writes to say,

This coming Saturday, at the usual time of 8pm GMT / 3pm EST / 2pm CST /12noon PST, I am going to be hosting another edition of the *Apologetics Academy* live interactive webinar. This week, our guest is astrophysicist Dr. Luke Barnes of the University of Sydney. Dr. Barnes is arguably the world’s leading authority on the fine-tuning evidence for the existence of God. There will be plenty of opportunity to interact and ask questions (you can even do so anonymously!).

Go here and make sure no one sees you install the Zoom software (a minute or two).

See also: Cosmologist Luke Barnes on fine-tuning of the universe

Webinar with Scott Minnich: Reinterpreting long-term evolution experiments

and

Copernicus, you are not going to believe who is using your name. Or how.

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Published on March 08, 2017 13:51

Horizontal gene transfer in bacteria: Numbers surprise researchers

From ScienceDaily:

Gene transfers are particularly common in the antibiotic-resistance genes of Streptococcus pneumoniae bacteria.

When mammals breed, the genome of the offspring is a combination of the parents’ genomes. Bacteria, by contrast, reproduce through cell division. In theory, this means that the genomes of the offspring are copies of the parent genome. However, the process is not quite as straightforward as this due to horizontal gene transfer through which bacteria can transfer fragments of their genome to each other. As a result of this phenomenon, the genome of an individual bacterium can be a combination of genes from several different donors. Some of the genome fragments may even originate from completely different species.

In a recent study combining machine learning and bioinformatics, a new computational method was developed for modelling gene transfers between different lineages of a bacterial population or even between entirely different bacterial species.

…

The study was able to show that gene transfer occurs both within species and between several different species. The large number of transfers identified during the study was a surprise to the researchers. Paper. (public access) – Rafal Mostowy, Nicholas J. Croucher, Cheryl P. Andam, Jukka Corander, William P. Hanage, Pekka Marttinen. Efficient inference of recent and ancestral recombination within bacterial populations. Molecular Biology and Evolution, 2017; DOI: 10.1093/molbev/msx066 More.

We remember when it was all put down to Darwinism (natural selection acting on random mutation) in lineal mother-daughter descent. One wonders how many would-be science majors are still learning that dogma in school.

See also: Horizontal gene transfer: Virus carries DNA of black widow spider toxin

Can parasitic plants use hosts’ genes against them?

Horizontal gene transfer: Researchers believe any two major groups of organisms can share genetic codes

and

Horizontal gene transfer: Sorry, Darwin, it’s not your evolution any more

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Published on March 08, 2017 13:39

Oldest life forms: Extraterrestrial origin or design? Self-organization?

From Nature:

(paywall) Although it is not known when or where life on Earth began, some of the earliest habitable environments may have been submarine-hydrothermal vents. Here we describe putative fossilized microorganisms that are at least 3,770 million and possibly 4,280 million years old in ferruginous sedimentary rocks, interpreted as seafloor-hydrothermal vent-related precipitates, from the Nuvvuagittuq belt in Quebec, Canada. These structures occur as micrometre-scale haematite tubes and filaments with morphologies and mineral assemblages similar to those of filamentous microorganisms from modern hydrothermal vent precipitates and analogous microfossils in younger rocks. The Nuvvuagittuq rocks contain isotopically light carbon in carbonate and carbonaceous material, which occurs as graphitic inclusions in diagenetic carbonate rosettes, apatite blades intergrown among carbonate rosettes and magnetite–haematite granules, and is associated with carbonate in direct contact with the putative microfossils. Collectively, these observations are consistent with an oxidized biomass and provide evidence for biological activity in submarine-hydrothermal environments more than 3,770 million years ago. More.

If the earliest dates hold up, they are an argument either for design or an extraterrestrial origin of life, or both. Or self-organization? Darwinian claims are laughable in so short a period in the absence of evidence.

But will it be possible to have a serious discussion in today’s tenure world?

See also: Earliest evidence of life on Earth found at 3.77 bya?

Origin of life requires “a privileged function?”

and

What we know and don’t know about the origin of life

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Published on March 08, 2017 10:35

Scott Minnich: Reinterpreting long-term evolution experiments

From Jonathan McLatchie, who writes,

Saturday’s webinar with Scott Minnich (U Idaho) was really excellent. He talked about his recent work on long-term evolution experiments with *E. coli *and responded to the various criticisms from Lenski & Blount.

See also: Why microbiologist Scott Minnich acknowledges design in nature

and

Iowa State did it to Gonzalez, Now U of Idaho is doing it to Minnich Note: That was in 2005. Someone must have forgotten to change the batteries in the local Darwinbots.

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In this webinar, pro-ID bacterial geneticist Dr. Scott Minnich (University of Idaho) talks to the Apologetics Academy about his recent research published in the Journal of Bacteriology, in regards to the long-term E. coli evolution experiments of Dr. Richard Lenski (see http://jb.asm.org/content/198/7/1022….)

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Published on March 08, 2017 05:49

“Tully Monster” mystery, from 300 mya, is far from solved?

Tully monster/Nobu Tamura

As recently reported. Worse luck, most of us probably didn’t even know about the Tully Monster. Well, … from ScienceDaily:

Last year, news headlines declared that a decades-old paleontological mystery had been solved. The ‘Tully monster,’ an ancient animal that had long defied classification, was in fact a vertebrate, two groups of scientists claimed. Specifically, it seemed to be a type of fish called a lamprey. The problem with this resolution? According to a group of paleobiologists, it’s plain wrong.

<em>Coffee</em> Tins

“This animal doesn’t fit easy classification because it’s so weird,” said Sallan, an assistant professor in Penn’s School of Arts & Sciences’ Department of Earth and Environmental Science. “It has these eyes that are on stalks and it has this pincer at the end of a long proboscis and there’s even disagreement about which way is up. But the last thing that the Tully monster could be is a fish.”

In a new report in the journal Palaeontology, Sallan and colleagues argue that the two papers that seemingly settled the Tully monster debate are flawed, failing to definitively classify it as a vertebrate. The mystery of the Tully monster, known to scientists as Tullimonstrum gregarium, remains.

…

“You would expect at least a handful of the specimens to have preserved these structures,” Sallan said. “Not only does this creature have things that should not be preserved in vertebrates, it doesn’t have things that absolutely should be preserved.” Paper. (public access) – Lauren Sallan, Sam Giles, Robert S. Sansom, John T. Clarke, Zerina Johanson, Ivan J. Sansom, Philippe Janvier. The ‘Tully Monster’ is not a vertebrate: characters, convergence and taphonomy in Palaeozoic problematic animals. Palaeontology, 2017; DOI: 10.1111/pala.12282 More.

We’ll leave them to it. There have been many strange life forms before and since. Consider the tulip animal from over half a billion years ago:

See also: Cambrian explosion: “Tulip animal” had unique feeding system ““Most interesting is that this feeding system appears to be unique among animals. Recent advances have linked many bizarre Burgess Shale animals as primitive members of many animal groups that are found today, but Siphusauctum defies this trend. We do not know where it fits in relation to other organisms,” said lead author O’Brien.”

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vs.

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Published on March 08, 2017 05:36

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