F Rosa Rubicondior: Physiology
Showing posts with label Physiology. Show all posts
Showing posts with label Physiology. Show all posts

Monday 11 March 2024

Unintelligent Design - RuBisCO Is Slowly Evolving - And Becoming Even More Embarrassing For Any Creationist Who Understands It


The world’s most prolific CO2-fixing enzyme is slowly getting better | University of Oxford

The world’s worst enzyme, ribulose-1,5-bisphosphate carboxylase/oxygenase, or RuBisCo as it is known, has featured in these blog posts several times and it described in my book, The Unintelligent Designer: Refuting the Intelligent Design Hoax as an example of the lack of intelligence in biological systems, and, as such, why it would be a major embarrassment to creationists - if they understood it.

Briefly, RuBisCo is one of the most ancient enzymes known and became an essential component of photosynthesis early on in the history of life on Earth when the first cyanobacteria evolved the ability to use the energy from sunlight to fix the carbon in atmospheric carbon dioxide (CO2) to build the sugar glucose. Eventually, these photosynthesising cyanobacteria became incorporated into plant cells as the chloroplasts to produce the green plants at the base of most food chains. Because it is so inefficient, it quickly became probably the most abundant enzyme on Earth, making up with quantity what it lacked in quality.

But, evolution, unlike good intelligent design, is a one-way, utilitarian process in which whatever works better than preceded it will be retained and will provide the next basis for further evolution, because evolution has no mechanism to scrap a bad design and start again as any backward step will inevitably be worse, so will be quickly eliminated.
Tell me all about RuBisCo and why it's so inefficient. RuBisCo, or ribulose-1,5-bisphosphate carboxylase/oxygenase, is an enzyme crucial for the process of carbon fixation in plants, algae, and some bacteria. It catalyzes the first major step of the Calvin cycle, which is the primary pathway for carbon dioxide fixation in photosynthesis. Despite its importance, RuBisCo is often considered inefficient for several reasons:

Tuesday 5 March 2024

Creationism in Crisis - A Mystery In Plant Evolution - 125 Million Years In The Making In That Long Pre-'Creation Week' History Of Life On Earth



A 'Ginormous' tomato produced by an unregulated CLV3 gene.

An evolutionary mystery 125 million years in the making | Cold Spring Harbor Laboratory

In an example of one of those lovely gaps in the record of the evolution of a species into which creationists try to shoehorn their ever-shrinking and increasingly homeless little god, there is something about the evolution of tomatoes and Arabidopsis thaliana that scientists can't yet explain.

But the problem for creationists is that this gap is somewhere in the evolutionary history of these plants that occurred almost 125 million years before creationism’s god decided to create a small flat planet with a dome over it to keep the water above the sky out, centred on the Middle East, in what creationists like to call 'Creation Week'.

The problem comes from the fact that what creationists think is a science and history text book was written by ignorant people who knew nothing of the world outside their small part of it and who had no idea about the history of the planet or of life on it, so they wrote an imaginative story to fill the gap in their knowledge and understanding, and, quite understandably, got almost every aspect of it complete wrong.

And of course, they would never have imagined that one day someone almost as ignorant as they were, would gather their tales into a book and declare it to be the inerrant word of a god - an idea that would be hilarious if it wasn't taken seriously by adults who can become dangerously violent when their superstition is questions.

The mystery that Cold Spring Harbor Laboratory (CSHL) biologists have uncovered is that sometime during the last 125 million years, tomatoes and Arabidopsis thaliana plants experienced an extreme genetic makeover. Just what happened remains unclear. But the mystery surrounds CLV3, a gene key to healthy plant growth and development.

CLV3 controls the growth of fruit in these plants and, if uncontrolled will result in large, even gigantic, fruits, so there is an evolutionary trade-off between a few large fruits and lots of smaller fruits. The mystery is just how and why this balance was achieved differently in two distantly-related plants.

As the CSHL press release explains:

Saturday 2 March 2024

Unintelligent Design - The Heath-Robinson Workaround For A Design Fault In The Immune System


The “switch” that keeps the immune system from attacking the body - EPFL

A Machine for Testing Golf Drivers - William Heath-Robinson
A characteristic of designs by creationism's putative intelligent designer, is the needless complexity which often arises because earlier solutions were suboptimal and either didn't work very well or tended to cause problems that needed to be mitigated with another layer of (often suboptimal) complexity.

This is also a characteristic of systems 'designed' by a mindless natural process with no power or mechanism for scrapping a suboptimal design and starting again and no ability to predict the future and design for problems which will arise later.

In fact, what creationists think is evidence of a supreme intelligence, more often seems to resemble the designs of the British cartoonist and eccentric designer, William Heath-Robinson, who was famous for his machines designed to solve every-day problem, which were invariably far more complex than they need have been, and which incorporated everyday objects such as umbrellas, full coal-scuttles for counter-weights, lengths of knotted string and stepladders balanced on upright pianos to give them enough height. Take away any of these unlikely components and the whole machine would fail, in an almost perfect metaphor for how evolution can exapt pre-exiting structures from other processes and structures for novel functions, to give the appearance of irreducible complexity.

And yet they work, or at least look as though they would if anyone ever made one.

An example of a Heath-Robinson machine in mammalian 'design' was revealed by a scientists working at the Swiss École polytechnique fédérale de Lausanne (EPFL), who have discovered how the body prevents the immune system from attacking itself.

But, as the very many auto-immune diseases show, this system is far from perfect and frequently fails, sometime with serious, even fatal, consequences.

But the whole immune system is only needed because something designed pathogens such as bacteria, viruses and other parasites, apparently to attack us and make us sick in the first place. Parasites are a source of conflict for creationists who have to believe both that the putative designer god is the only entity capable of designing living things, and that something else created parasites because their god wouldn't do such a thing, and both that their god is omnipotent, but powerless against that other designer.

So, what is this mechanism the EPFL researchers have discovered?

Their findings are the subject of an open access paper in Nature and is explained in an EPFL news release:

Saturday 3 February 2024

Unintelligent Design News - Why Women Are More Prone To Lupus Than Men - Evolution, Or Does Creationism's God Just Hate Women More?


The classic 'butterfly rash' of systemic lupus erythematosus (SLE)
Lupus and other autoimmune diseases strike far more women than men. Now there's a clue why

In my days as an operational paramedic, I once had to move a 26 your old women to hospital because lupus had made her so ill her blood pressure was below the safe level to maintain her renal function.

It was so low I couldn't even sit her up to carry her down stairs without her losing consciousness, so I had to run a couple of units of IV fluid into her to bring it up enough to make it safe to move her. She really was profoundly ill and at death's door. But such was the nature of the profession that, having delivered her safely to hospital and handed her over to the care of doctors and nurses, that was the end of my role in her care, so I never heard the outcome.

The autoimmune condition, lupus erythematosus, is caused by a malfunction of the immune system in which something triggers it to turn against the sufferer's own body instead of the invasive pathogens from which it has evolved to protect us. Although, of course, a creationist would hotly dispute the idea that a system like our immune system evolved at all, and would insist that it was intelligently [sic] designed by their favourite, evidence-free, supernatural deity without whom nothing can be created, presumably because they believe chemistry and physics don't know how to behave without a magic god telling them.

But an intelligently-designed immune system would only malfunction and turn against the person it is supposedly designed to protect if it were either incompetently designed or malevolently designed and is doing what it was designed to do - randomly increasing the suffering in the world. The evidence is that lupus is far more common in women than in men by a ratio of 9:1, which begs the question, does the designer just hate women more than men or was he more diligent when designing men's immune system then when designing women's?

The answer, as anyone who understands anatomy and physiology and particularly, evolution, will tell you, is that as an evolved system, we can expect compromises and a lack of perfection because evolution is a utilitarian process with no foresight and no reverse gear, so we are stuck with a sub-optimal immune system that evolved in an ancient ancestor, maybe even a pre-vertebrate ancestor. Certainly, all known vertebrates have one, and some, like that of bats, is far superior to ours.

Now a team of researchers at Stanford University School of Medicine, Stanford, CA, USA have worked out why lupus is far more common in women than men. Ther results are published, open access, in Cell and explained in a Stanford Medical news release. But first, a little AI background:

Friday 26 January 2024

Closing In On Abiogenesis - How Amino Acids Become Peptides in Water Droplets - No Magic Required


A tripeptide (example Val-Gly-Ala) with green marked amino end (L-valine) and blue marked carboxyl end (L-alanine)
Chemistry professor R. Graham Cooks expands research of water droplet interfaces that offer the secret ingredient for building life - Purdue University Department of Chemistry

One of the puzzles of how the earliest proteins were built from amino acids was that the reaction of joining two amino acids together is a condensation reaction in which a molecule of water is eliminated when the -C-OH of one amino acid binds to the H2N-C- of the other amino acid in what is known as a peptide bond:

-C-OH + H2N-C- → -C-NH-C + H2O;

but how could this happen in an aqueous solution?

In 2022, Professor R. Graham Cooks' team at Purdue University found the answer: It is due to the peculiar properties at the surface of droplets of water. Because of the way electrostatic forces align the water molecules at the surface, it behaves as though it is extremely dry, and highly acidic. These conditions provide the perfect conditions for a condensation reaction to occur, resulting in a peptides.

Droplets of water are everywhere in nature, from the spray of breaking waves, the splash of raindrops, waterfalls, trickling streams to aerosols of water in clouds and fog.

And Professor Cooks's team at Purdue have now shown that these conditions also occur at the macro, centimeter scale as water evaporates on, for example rocks or the margins of hydrothermal pools. They have also shown that these reactions, in the presence of oxazolones (produced by the dehydration of amino acids) preserve the chirality of the peptides so the resulting peptides are 'L' enantiomers, as found in all living organisms.

As the Purdue University press release says:
The study adds to the body of evidence that the surface of water drops represents a uniquely active physical and chemical system. Present are very high electric fields and extreme acidity that drives dehydration of amino acids to form peptides. Studies of the chemistry at water droplet interfaces offer new insights into the early stages of life's chemical evolution.
Significance

This study provides experimental evidence identifying oxazolones as the key intermediates in prebiotic peptide synthesis. These compounds yield the dipeptides upon reaction with water and generate tripeptides in the presence of other amino acids. These key steps in protein formation occur in pure water droplets. Amino acid chirality is preserved in forming the oxazolone and the addition of amino acids during peptide chain extension shows a strong chiral preference, viz. the aqueous droplet chemistry represents a simple route to chirally pure polypeptides. A direct connection between this intermediate and the dipeptide isomer, oxazolidinone, is demonstrated by simple hydration/dehydration. The oxazolone/oxazolidinone-mediated mechanism also occurs in macroscopic wet–dry cycling, establishing a strong connection between macroscopic and microscopic peptide synthesis.

Abstract

Peptide formation from amino acids is thermodynamically unfavorable but a recent study provided evidence that the reaction occurs at the air/solution interfaces of aqueous microdroplets. Here, we show that i) the suggested amino acid complex in microdroplets undergoes dehydration to form oxazolone; ii) addition of water to oxazolone forms the dipeptide; and iii) reaction of oxazolone with other amino acids forms tripeptides. Furthermore, the chirality of the reacting amino acids is preserved in the oxazolone product, and strong chiral selectivity is observed when converting the oxazolone to tripeptide. This last fact ensures that optically impure amino acids will undergo chain extension to generate pure homochiral peptides. Peptide formation in bulk by wet-dry cycling shares a common pathway with the microdroplet reaction, both involving the oxazolone intermediate.

Qiu, Lingqi; Cooks, R. Graham
Oxazolone mediated peptide chain extension and homochirality in aqueous microdroplets
Proceedings of the National Academy of Sciences (PNAS) 121(2). DOI: 10.1073/pnas.2309360120

© 2024 PNAS.
Reprinted under the terms of s60 of the Copyright, Designs and Patents Act 1988.
And so that day that creationist frauds must be dreading, when science finally closes their favourite gap in which to force-fit their ever-shrinking little god finally slams as shut as all the other gaps it used to occupy in the minds of scientifically illiterate believers, gets a little closer. Only yesterday we learned how simple metabolic biochemical cycles can be produced from simple precursors, all of which were present on the pre-biotic Earth and without protein enzymes, and here we see how the proteins that could catalyse and improve those processes could also arise from simple precursors that were also present.

I wonder what disinformation the frauds who feed pseudo-science to the creation cult are preparing for that eventuality.

Ten Reasons To Lose Faith: And Why You Are Better Off Without It

This book explains why faith is a fallacy and serves no useful purpose other than providing an excuse for pretending to know things that are unknown. It also explains how losing faith liberates former sufferers from fear, delusion and the control of others, freeing them to see the world in a different light, to recognise the injustices that religions cause and to accept people for who they are, not which group they happened to be born in. A society based on atheist, Humanist principles would be a less divided, more inclusive, more peaceful society and one more appreciative of the one opportunity that life gives us to enjoy and wonder at the world we live in.

Available in Hardcover, Paperback or ebook for Kindle


What Makes You So Special? From The Big Bang To You

How did you come to be here, now? This books takes you from the Big Bang to the evolution of modern humans and the history of human cultures, showing that science is an adventure of discovery and a source of limitless wonder, giving us richer and more rewarding appreciation of the phenomenal privilege of merely being alive and able to begin to understand it all.

Available in Hardcover, Paperback or ebook for Kindle




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Thursday 25 January 2024

Unintelligent Design - How Ovulation Goes Wrong Because It Wasn't Intelligently Designed


Gene expression atlas captures where ovulation can go awry | Cornell Chronicle

Back in the late 1960s and early 1970, in what seems like a different lifetime now, I was a senior research assistant in the Oxford University/MRC Neuroendocrinology Research Unit, researching the hormonal control of ovulation in guinea pigs. Two of our tools were radioimmunoassays I had adapted for measuring extremely low levels of a hormone in guinea pig anterior pituitary glands known as luteinizing hormone (LH), and another similar assay for measuring the level of the steroid progesterone in guinea pig blood.

Sadly, having worked for close on two years towards producing a research paper with hundreds of assay results, thousands of microscope slides, hundreds of electron micrographs and a freezer full of samples waiting to be assayed, the government pulled the rug from under our feet by withdrawing our research funding, and I was made redundant, so my work was never published. Disillusioned and with a young family to support, I left research and perused a career in the NHS Ambulance Service instead - but that's a different story, and not relevant to the subject of this blogpost, which illustrates how much science has progressed in the last 50-60 years.

Researchers are no longer researching the hormonal control of ovulation but the fine details of the genetic control of the process of ovulation at the cell level, and what they've found is that the process is far from intelligently designed by anything resembling a perfect, omniscient, omnipotent designer. It is a process that is so complex that it can, and does, go wrong. An intelligent designer who didn't want random women to be unable to shed viable eggs, could have designed a less complicated process, but you can depend on creationism's putative intelligent[sic] designer to never do something simple when there is a far more complicated and wasteful way to achieve the same result.

The research, published a few days ago in Proceedings of the National Academy of Sciences, was led by Iwijn De Vlaminck, associate professor of biomedical engineering in Cornell Engineering, and Yi Athena Ren, assistant professor of animal science in the College of Agriculture and Life Sciences. The paper’s lead author is Madhav Mantri, Ph.D., now a postdoctoral researcher at Stanford University.

The team used a form of RNA tagging to map the gene expressions that occur during ovarian follicle maturation and ovulation in mice.

This spatial transcriptomics map depicts the cell types of a mouse ovary undergoing hormone-induced ovulation
The research is explained in a Cornell University Press release:

Monday 1 January 2024

Unintelligent Design - Malevolence or Incompetence? - Why Design A Uterus To Grow Fibroids?


Assistant Professor Stacey Schutte, left, and Research Associate Andreja Moset Zupan study new avenues to treat fibroids in Schutte's biomedical engineering lab in UC's Bioscience Center.

Photo/Andrew Higley/UC Marketing + Brand
Researchers find ways that uterine fibroid cells respond differently from surrounding tissue | University of Cincinnati

Almost 80% of women of child-bearing age will develop uterine fibroids. Although usually not malignant, they can nevertheless be extremely painful, can cause bleeding and can lead to infertility. The economic cost of fibroids has been estimated to be some $9 billion in the USA alone.

Fibroids grow in response to the same hormones, oestragen and progesterone, which cause the endometrium to thicken then breakdown during the menstrual cycle. Now a research team at the University of Cincinnati have shown that cell stretching is also a factor in their growth.

Hormones and uterine stretching as the endometrium thicken and shrinks and during pregnancy and childbirth are, of course part of the normal state of affairs for the uterus that creationists believe must have been designed by their supposedly omniscience, omnipotent designer, so, if we accept that childish notion of magic design by an omniscient supernatural entity, for the sake of argument, we have to assume growing fibroids was all part of the plan, since it is not possible for an omniscient designer to not be aware of the outcome of its design and for it not to design with that outcome in mind.

So, the only alternative, within the creationist paradigm, is that fibroids are the accidental and unforeseen consequences of the design and function of the uterus - which would mean one of three things:
  1. The designer was not omniscient.
  2. The designer was incompetent.
  3. If the designer was both competent and omniscient it must have been malevolent and intended a high percentage of women to suffer the pain and inconvenience of fibroids.
This discovery is the subject of a research paper in the journal F&S Science which, sadly is behind a paywall, but the Abstract in the form of a summary of the paper is available.

Saturday 30 December 2023

Creationism in Crisis - Tears Evolved To Manipulate The Behaviour Of Men, So Where Is The Free Will


Sniffing women’s' tears reduces aggression in men.
Tears without Fears: Sniffing Women’s Tears Reduces Aggression in Men | Weizmann USA

Research by Israeli scientists has shown that sniffing tears can reduce male aggression by almost 44% by lowering the level of testosterone.

The problem for Christianity here is that the entire rationale for the religion is that human free will allowed the mythical founder couple, who were magically created without ancestors, to choose to disobey their magic creator in the so-called 'Fall'.

Because the magic, omnipotent creator has never managed to get over this exercise of the free will it gave them, we need Jesus (the magic creator personified) to help him forgive us, because he had himself sacrificed in a blood sacrifice that everyone knows satiates irascible gods, especially when it's them being sacrificed. (I'm not making this up! Just ask any Christian who Jesus was and what he was born for.)

But, if behaviour is mediated by physiology in the form of hormones and if the levels of those hormones can be mediated by external influences, then external influences can modify behaviour, so where does that leave the notion of free will?

Obviously, the authors of that tale in the Bible knew nothing of hormones and pheromones and how they can modify and influence behaviour.

The research is explained in a press release from the American Committee for the Weizmann Institute of Science:

Friday 15 December 2023

Creationism in Crisis - Human Intelligence Is Not So Much A Matter of Quantity But Of Quality


Human intelligence: how cognitive circuitry, rather than brain size, drove its evolution

Researchers have shown that human intelligence does not depend primarily on the size of our brain - there are animals with bigger brains (elephants, orcas) - but on the cognitive circuitry.

The team, led by Valentin Riedl of the Department of Neuroradiology at Klinikum rechts der Isar, TUM School of Medicine and Health, Technical University of Munich, Munich, Germany, have published their findings, open access, in the journal Science Advances. It is explained in an article in The Conversation by two Cambridge University professors who were not involved in the research.

Their article is reprinted here under a Creative Commons license, reformatted for stylistic consistency:

Thursday 21 April 2022

Evolution News - How Our Gut Biota May Be Dictating What We Eat.

Got food cravings? What’s living in your gut may be responsible | University of Pittsburgh

In a fascinating example of the kind of thing that co-evolution can produce, scientist at Pittsburg University believe they have shown how the gut biota of mice could be controlling the mouse's cravings for particular foods.

If this holds true for humans, it could mean that our gut biota could be telling us what they want us to eat, based not on our nutritional needs, but on theirs. We have, of course, been evolving along with our gut organisms since the first multicellular organisms evolved the first alimentary cannal, and possibly even earlier. More recently, it has proved possible to track the dispersion out of Africa and across the globe by subtle differences in the strains of organisms in our gut biota.

In other words, evolution has had plenty of time to evolve suptle relationships between us and our internal biota and, biologically speaking, we have not been evolving as a single species but as a collony, so any species in the colony could be influencing the evolution of the colony as a whole.

That evolutionary relationship was behind the research by the Pittsburgh Scientists, Assistant professor, Kevin Kohl and Doctor Brian Trevelline, as the Pittsburgh University new release explains:

Monday 8 November 2021

Evolution News - How Brains Evolved From Sponges' Stomachs

Sponge neuroid cell (orange) extends arms that enwrap the feeding apparatus of a sponge digestive cell (green) to create a link for targeted communication. The image was taken using electron microscopy.

Credit: Jacob Musser, Giulia Mizzon, Constantin Pape, Nicole Schieber/EMBL
More than a gut reaction - EMBL.

Brain cells, all 86 billion of them, communicate with one another across microscopic gaps between them called synapses. Communication across this gap is via neurotransmitter substances such as acetyl choline. A similar process is involved at the neuromuscular junction between nerves and muscle cells. This has been well understood for some time but what was a mystery was how this system evolved.

Certainly it happened early in the evolutionary history of multicellularity because all but the most primitive multicellular organisms such as sponges have a nervous system of some sort.

This is the sort of mystery that Creationists latch onto to fool their dupes with the false dichotomy that if science hasn't explained it, the locally popular god must have created it, leaving their scientifically illiterate targets to assume that if science hasn't explained something then science can't explain it and never will.

Now though, scientists working for EMBL have discovered that this method of cell communication evolved in just those primitive organisms, sponges, for an entirely different function - an example of something Creationists hate - evolutionary repurposing, or exaptation, of an existing process or structure for a new function. This is, of course, how apparently irreducibly complex processes and systems such as flagella evolve.

In so doing, the scientists have also solved another mystery - why do sponges have the genes for synaptic control when they don't have a nervous system?

The EMBL news release explains:

Wednesday 15 September 2021

Malevolent Designer News - Leaving Nothing To Chance With Alzheimer's Disease

Plasma and brain concentrations of apo B and Aβ.
(A) In vivo PET detection of amyloid binding was used to confirm cerebral amyloid deposition in HSHA mice and their age-matched WT controls. Representative PET and MRI fusion images (coregistered with MRI templates using conventional Fast Spin Echo Sequence T2-weighted sequence) show scan data at 20 to 40 minutes’ post-intravenous administration of [11C] PiB. Each panel (from left to right) illustrates maximum binding potential for [11C] PiB represented by coronal images at −2, 0, 4, and 6 mm from the bregma; indicated by the vertical bar. Plasma (B) and brain (C) levels of apo B, a surrogate marker of TRLs in HSHA and WT control mice, were determined with ELISA. Data are expressed as mean ± SEM. Human and mouse isoforms of Aβ in plasma (D) and brain (E, F) were measured separately with ELISA kits using antibodies specific to each isoform. The data underlying Fig 2B–2F can be found in S1 Data. Aβ, amyloid beta; apo B, apolipoprotein B; HSHA, hepatocyte-specific human amyloid; MRI, magnetic resonance imaging; PET, positron emission tomography; PiB, Pittsburgh compound; TRL, triglyceride-rich lipoprotein; WT, wild-type.
Synthesis of human amyloid restricted to liver results in an Alzheimer disease–like neurodegenerative phenotype

According to Creationists, everything about biology and human anatomy and physiology especially, is definitely not the result of natural, evolutionary forces and the operation of random chance. Instead, it is all designed by their reputedly omnipotent, omniscient god who knew exactly what it was designing and designed if for the particular purpose which it serves - which means it is responsible for both the good and the bad in its 'designs', of course.

So, playing at Intelligent [sic] Design advocates for a moment, we have in this scientific paper an example of the sheer mendacious nastiness of Creationism's divine malevolence. It shows how, just to make sure it's victims get Alzheimer's disease in later life, it has designed a mechanism in the liver that manufactures one of the proteins which has been implicated in the progress of this ghastly disease which robs the sufferer of their dignity, their memory, their personality and eventually their life.

The study, published open access in PLOS Biology, was carried out by John Mamo of Curtin University in Bentley, Australia, and colleagues.

According to the press release from PLOS:
Deposits of amyloid-beta (A-beta) in the brain are one of the pathological hallmarks of AD and are implicated in neurodegeneration in both human patients and animal models of the disease. But A-beta is also present in periphereral organs, and blood levels of A-beta correlate with cerebral amyloid burden and cognitive decline, raising the possibility that peripherally produced a-beta may contribute to the disease. Testing that hypothesis has been difficult, since the brain also produces A-beta, and distinguishing protein from the two sources is challenging.

In the current study, the authors surmounted that challenge by developing a mouse that produces human a-beta only in liver cells. They showed that the protein was carried in the blood by triglyceride-rich lipoproteins, just as it is in humans, and passed from the periphery into the brain. They found that mice developed neurodegeneration and brain atrophy, which was accompanied by neurovascular inflammation and dysfunction of cerebral capillaries, both commonly observed with Alzheimer's disease. Affected mice performed poorly on a learning test that depends on function of the hippocampus, the brain structure that is essential for the formation of new memories.

The findings from this study indicate that peripherally derived A-beta has the ability to cause neurodegeneration and suggest that A-beta made in the liver is a potential contributor to human disease. If that contribution is significant, the findings may have major implications for understanding Alzheimer's disease. To date, most models of the disease have focused on brain overproduction of A-beta, which mimics the rare genetic cases of human Alzheimer's. But for the vast majority of AD cases, overproduction of A-beta in the brain is not thought to be central to the disease etiology. Instead, lifestyle factors may play a more important role, including a high-fat diet, which might accelerate liver production of A-beta.

Friday 30 April 2021

Another Religion-Based Dogma Falls to Science

Mice form categories to simplify their world. Showing that, researchers identified neurons that encode learned categories.
© MPI of Neurobiology/ Kuhl
Simplifying our world - Mice master complex thinking with a remarkable capacity for abstraction | Max-Planck-Gesellschaft

Yet another religion-based dogma fell to investigation by science recently. The dogma was that there is something unique about humans that sets us apart from the other animals as some sort of special creation - the basis of our belief that we own the planet and everything on and in it, including the other animals, incidentally.

In particular, humans were once thought to be the only sapient, tool-making species. That dogma has been laid to rest many times with many species now known to be capable of logical reasoning, tool-making and use, and problem-solving.

Now here we have evidence, provided by scientists working at the Max Planck Institute of Neurobiology, Martinsried, Germany, that mice can categorise information and think in the abstract - a fundamental of logical reasoning, information processing and learning, and mice use the same parts of their brain to do it with as we use. Their results were published, open access, in Nature recently.

The Max Plank Gesellschaft news release explains:

Saturday 20 March 2021

Evolution News - How to Make a Giraffe Without Using Magic

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Photo credit: Mogens Trolle
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Reticulated Giraffe, Buffalo Springs, Kenya.
Photo credit: Mogens Trolle
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Help Us Stand Tall for Giraffes.
The U.S. is one of the leading importers of giraffe parts. We need your help persuading America’s leaders to protect them before they’re gone.

Photo by Philippe Chantecaille
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"The Last Giraffes on Earth"
Source: The Atlantic
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Image credit: San Diego Zoo
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Giraffes, found throughout sub-Saharan Africa, are susceptible to poaching and habitat loss.

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Giraffes on the Masai Mara National Reserve in Kenya.
Credit: Goran Tomasevic/Reuters
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Reticulated sub-species of Giraffe at Loisaba conservancy in Laikipia, Kenya. As across the rest of African, they have declined steadily in recent decades.
Credit: AFP/Tony Karumba
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Girafffes in the Masai Mara.
Credit: Manoj Shah/Getty
Source: BBC Wildlife
The Trouble of Being Tall – Biologisk Institut - Københavns Universitet

Researchers at the Biologisk Institut, University of Copenhagen, and Northwestern Polytechnical University in China have succeeded in sequencing the whole genome of the giraffe and in doing so have uncovered the mechanisms by which giraffes evolved their unique features.

Evolving a long neck and tall stature presented the giraffe with a number of physiological and anatomical challenges:
  • A very high blood pressure is needed to pump blood up to the brain. The giraffe BP is about twice the normal BP for a mammal and would normally cause severe damage to the cardiovascular system.
  • Standing up from a lying position is difficult, as is bending down to drink, making the giraffe especially vulnerable while sleeping and drinking.
  • At about 5 metres above the ground, there is little role for a sense of smell.
The researchers found a number of evolved genetic features which help giraffes overcome these problems, including a version of the FGFRL1 with seven amino acid substitutions compared with the same gene in other ruminants. When tested in mice, this gene gave them added protection against damage from high blood pressure and more compact, denser bones. The team believe the function of this gene may have application in the treatment of high blood pressure in humans.

As the Biologisk Institut news release explains:

Thursday 7 January 2021

Unintelligent Design News - Science Reveals a Ludicrously Complex System

A human cell is featured during mitosis with its chromosomes (gray areas) aligned. The region known as the kinetochore (colored with yellow, red and cyan markers) is the origin of the checkpoint signal that acts as a safety check against premature cell division and is the focus of UC San Diego researchers’ study.
Wait for Me: Cell Biologists Decipher Signal that Ensures No Chromosome is Left Behind - UC San Diego News Center

News today that scientists have discovered how cells ensure the faithful copying of every last piece of DNA as cells divide to produce the trillions of cells in a multicellular organism.

But why is this highly complex system needed, especially when the process of epigenetics is going to turn most of it off to create cell specialisation on which multicellular organisms depend for the division of labour into functional tissues and specialised organs, and what does this tell us about a hypothetical designer who would come up with something this complex to get around a problem it created earlier?

Firstly, why is this process needed in the first place?

Saturday 20 April 2019

Moral Decisions - No Gods Required

How Do We Make Moral Decisions?

Contrary to Christian apologists' assertions, humans do not get 'objective' morals from a god whose capricious whims determine right and wrong.

No matter how much C.S.Lewis tied himself into knots with his intellectual contortions, trying to prove that because he couldn't tell right from wrong, the god his mummy and daddy believed in must be real, the evidence of other cultures with other gods, and with none, shows that moral codes have broad principles common to all human cultures.

The rule probably most basic to all human cultures is the 'golden rule' - do as you would be done by or, as Christians would say, do unto others as you would have them do unto you. However, why people generally stick to this principle has been the subject of debate. Do they do it because of guilt, because we would feel bad about letting the other person down, or because of an innate sense of fairness where we want the fairest outcome.

Thursday 18 April 2013

Gallstones - Another Little Gem From The Intelligent Designer

Opened gallbladder containing numerous gallstones
You have to hand it to the Intelligent Designer. Just look at the way it came up with the idea of gallstones. Whatever would we do without them?
A gallstone is a crystalline concretion formed within the gallbladder by accretion of bile components. These calculi are formed in the gallbladder but may distally pass into other parts of the biliary tract such as the cystic duct, common bile duct, pancreatic duct, or the ampulla of Vater. Rarely, in cases of severe inflammation, gallstones may erode through the gallbladder into adherent bowel potentially causing an obstruction termed gallstone ileus.

Presence of gallstones in the gallbladder may lead to acute cholecystitis, an inflammatory condition characterized by retention of bile in the gallbladder and often secondary infection by intestinal microorganisms, predominantly Escherichia coli and Bacteroides species. Presence of gallstones in other parts of the biliary tract can cause obstruction of the bile ducts, which can lead to serious conditions such as ascending cholangitis or pancreatitis. Either of these two conditions can be life-threatening and are therefore considered to be medical emergencies.

The archetypal sufferer from gallstones has the five 'f's:
  • Female.
  • Fertile.
  • Fair.
  • Fat.
  • Forty.
Fair referring to skin colour.

However, many exceptions are found and gallstones are not uncommon in men, postmenopausal and thin women and non-Europeans although less so than in Europeans. They are very rare in young people.

The problem starts because body fluids with a high concentration of anything and especially salts, lend themselves to the formation of stones by simple chemical processes. Unfortunately, many of these fluids are collected in temporary stores such as, in the case of gallstones, the gallbladder. Stones may also form in places like the kidneys where they can obstruct the outflow of urine, causing kidney damage or be passed down the ureter to the bladder causing excruciating pain and sometimes accumulating there to obstruct urination, or salivary glands causing the flow of saliva to be obstructed and the face and neck to swell up as saliva accumulates.

The function of the gallbladder is to store bile until food is present in the small intestine. It then contracts squirting bile down the bile duct into the small intestine where it plays a role in digestion of fats. Bile is actually a waste product produced by the liver from dead red blood cells, or rather from the haem part of haemoglobin from which most of the iron has been removed and recycled. When the bile duct is obstructed bile is retained by the liver and passes into the blood where it causes jaundice and shows up in the urine which resembles freshly brewed tea or black coffee. If not treated, this can cause renal failure.

The problem is compounded by the fact that, for no apparent good reason, the bile duct joins with the duct from the pancreas to form the hepato-pancreatic duct before it joins with the small intestine at the 'ampula of Vater', so any obstruction in the hepato-pancreatic duct also obstructs the pancreatic duct. As well as controlling blood sugar levels with insulin, the pancreas also produces enzymes for digesting proteins so any obstruction or damage to the pancreas can also cause it to begin to digest and eventually destroy itself. Infections in the bile duct can also spread to the pancreas causing acute inflammation of the pancreas or pancreatitis which is fatal in about 25% of sufferers (though not all these are caused by gallstones).

It would be a particularly nasty and vicious intelligent designer who came up with this example of bad design which, in the time before anaesthetic surgery and before modern medicine would have been a common cause of death, especially of females in midlife and still is in people without access to health care. There is no purpose to gallstones; there is no purpose to them predisposing to infection by normally benign intestinal bacteria; there is no benefit from the pancreatic duct uniting with the bile duct and so making it easy for the pancreas to become involved with gallstones and any infection they may allow. Unless, of course, the purpose was to cause illness and death.

The entire system is a kludge; an "it'll do" solution which has its origins somewhere in evolution and particularly in embryology, and so we are stuck with it.

To understand why evolution, which we would expect to eliminate these kludges and lead to perfection of 'design', has not eliminated gallstones or 're-designed' the hepato-pancreatic duct we need to look at the common predisposing factors above. The reason is the same reason we have not eliminated cancer and degenerative diseases like Alzheimer's, motor-neurone disease and Parkinsonism. There is little or no benefit to the genes from any mutations which would bring about these changes because they only present as problems after we have produced our offspring.

If there is no benefit to the genes there can be no evolution other than random genetic drift. The link to fair skin, which, in evolutionary terms provided some benefit particularly in a cloudy, relatively sunless north west Europe, suggests some linkage between changes in melanin (the dark pigment) production in the skin and gallstone formation, so they may simply be an unfortunate by-product of an otherwise beneficial mutation in the context of an environment with a lot of clouds. And that evolutionary change expresses before we produce offspring by reducing the incidence of rickets in growing children.

What benefit there might be to the genes in having mothers live long enough to be grandmothers, and so helping to raise the next generation carrying her genes is much less obvious than it would be if they affected her reproductive success directly, since her grandchildren are only one quarter her on average, but never-the-less we should expect to see some evolutionary change towards eliminating the formation of gallstones and/or reducing their potential seriousness over time even for that small advantage. But then we only evolved fair skin relatively recently so there will not have been time yet for this effect to be noticeable. Gallstones are probably part of the cost of evolving fair skin in a cloudy environment and we will still need to bear that cost for many years, possibly hundreds of thousands yet.

As an example of intelligent design and especially the design of an omni-benevolent designer, gallstones fail badly. Any designer who came up with this idea is neither intelligent nor benevolent. As an example of the mindless, undirected and amoral process of evolution, gallstones are readily understandable.

Sorry, Discovery Institute and your willing stooges who push fundamental Bible literalism disguised as science with 'Intelligent Design'. You have very many of these examples to explain. Ignoring them and relying on the ignorance of your credulous victims won't work with rational people.





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Friday 7 December 2012

Fundamentalists Should Have Sex Like Rabbits

Moment of Ovulation
Creationists really have got their knickers in a knot over sex, especially when they insist the only purpose of sex is procreation and that doing it for pleasure or as a social activity is somehow sinful, something to be ashamed of, and not what their assumed intelligent designer designed us for.

If this were so, and if we had been intelligently designed, there would be a link between ovulation (egg production) in women and intercourse, and not to an almost complete disconnect between sexual activity and ovulation. As it is, women ovulate every 28-30 days on average whether or not that have had sex. Even virgins and sexually inactive women produce a monthly egg or two. Unless they are pregnant or breast-feeding a baby, healthy women normally ovulate every month from the age of puberty until the menopause, usually between forty-five and fifty-five years of age - some thirty to forty years.

Whether or not they become pregnant will depend entirely on if and when they have sex and if a live sperm happens to come across a viable egg in the right place in her reproductive plumbing.

An intelligent designer who intended sex to be only for procreation would have designed this process so that women only had sex when they were sure to get pregnant and that every instance of intercourse resulted in pregnancy. It's not as though such a system hasn't been designed. If you believe in this intelligent designer you will believe it designed the process so I'm afraid you are hooked on your own logic here.

Ironically, one of the best examples of sexual activity being designed to ensure pregnancy, thus ensuring its purpose is exactly what religious people insist sex is for, is to be found in the very mammal frequently cited as an example of promiscuity - the rabbit.

My first job as a school-leaver many years ago was as a laboratory technician in Prof Geoffrey Harris's Neuroendocrinology Research Unit in Oxford. One of the things we were investigating was hormonal control of ovulation, using rabbits. Prof. Harris had discovered that the hormone which causes the ovary to shed its eggs is produced by the pituitary gland in response to 'releasing factors' (we were trying to find out exactly what they were) which are produced by special nerves in the stalk attaching the pituitary to the brain. These 'releasing factors' are transported to the pituitary gland in blood by a microscopic 'portal system' of small blood vessels which ensures they are concentrated and delivered to the front lobe of the pituitary where they cause the pituitary to produce 'lutenising hormone' into the blood, which, when it reaches the ovaries, causes an egg to ripen and be shed.

One drawback to using rabbits is that you have to be careful how you pick them up, otherwise you can induce them to ovulate - which is not what we wanted as we were trying to induce this with hormones.

The reason we were using rabbits is because they are spontaneous ovulators, that is, they don't have an oestrus cycle but ovulate when mated. In rabbits, there is a simple reflex system which is initiated by mating, either by direct stimulation of the vagina, or even by a male mounting and attempting to mate - and this is where we needed to be careful. If you stroke a female rabbit's back, or her hind quarters, you can simulate the act of a male mounting her and cause her to ovulate, so you need to pick them up by the scruff of the neck and keep contact to a minimum.

So, in rabbits, which have sex like rabbits - duh! sex is for procreation and the system ensures a high degree of success, where most sex acts lead to pregnancy.

So, Creationists, if your 'intelligent designer' designed this system in rabbits, why didn't it use the same system in humans where all the components are present and just need to be set up correctly to work the way you claim it intended them to work?

In fact, this system has probably been switched off in humans and in at least our close cousins, the bonobo, because sex for pleasure and for other than procreation is so beneficial in terms of pair-bonding and social interaction and where sexual activity continues well past the menopause where is can have no procreational purpose whatsoever.

Of course, Darwinian Evolution has no problem at all explaining these differences. With both humans and rabbits the respective system used produces more surviving descendants given the long, slow childhood of human children which benefits from a pair-bond between parents, compared to the short period of maturity in rabbits which are independent of their mother in a few weeks, sexually mature and in a few months and in whose nurturing fathers play no part at all.

If the religious views of Creationists were sincere, and they knew what they were talking about, they should be advocating humans behave like rabbits when it comes to sex. At least that might go some way to filling the rows of empty pews most European priests are seeing most Sundays nowadays.

This is of course just one of the problems Christians and Muslims have with trying to shoe-horn reality into the primitive superstitions of misogynistic and sex-obsessed Bronze Age tribal leaders who believed in a flat earth, magic, talking snakes and that rain is water dripping through holes in the canopy over the earth from which the sun and moon are hanging.


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Wednesday 7 March 2012

Finding Fossils In The Dark

The River Evenlode
By the age of about ten I knew every path in every wood in the square mile around the small ancient northern Oxfordshire hamlet on the edge of the Wychwood Forest I was born and grew up. The hamlet where Romans had built a villa and named the footpath Via Dessica which we still called Viziker.

I knew not just every path, but practically every tree, spring, badgers' set, rabbit burrow and briar patch. I knew where the wild gooseberries and strawberries grew, which nut trees had the best nuts, where the cleanest spring water was and which crabapple trees had the sweetest apples in autumn.
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