Computer models advancing science

Computer modeling has become a more and more important tool for science. We have seen it in Climatology for decades, as well as in a number of other fields. People who have a poor understanding of science, or who are trying to deny science, such as creationists and climate change deniers, will often claim that it isn’t really real science, but that is of course pure nonsense, as empirical evidence has demonstrated it again and again.

Now, there is a new great example of how a computer model is advancing our understanding of science. As ScienceDaily reports:

First hominin muscle reconstruction shows 3.2 million-year-old ‘Lucy’ could stand as erect as we can

A Cambridge University researcher has digitally reconstructed the missing soft tissue of an early human ancestor — or hominin — for the first time, revealing a capability to stand as erect as we do today.

Dr Ashleigh Wiseman has 3D-modelled the leg and pelvis muscles of the hominin Australopithecus afarensis using scans of ‘Lucy’: the famous fossil specimen discovered in Ethiopia in the mid-1970s.

…

Wiseman was able to use recently published open source data on the Lucy fossil to create a digital model of the 3.2 million-year-old hominin’s lower body muscle structure. The study is published in the journal Royal Society Open Science.

The research recreated 36 muscles in each leg, most of which were much larger in Lucy and occupied greater space in the legs compared to modern humans.

For example, major muscles in Lucy’s calves and thighs were over twice the size of those in modern humans, as we have a much higher fat to muscle ratio. Muscles made up 74% of the total mass in Lucy’s thigh, compared to just 50% in humans.

Paleoanthropologists agree that Lucy was bipedal, but disagree on how she walked. Some have argued that she moved in a crouching waddle, similar to chimpanzees — our common ancestor — when they walk on two legs. Others believe that her movement was closer to our own upright bipedalism.

Research in the last 20 years have seen a consensus begin to emerge for fully erect walking, and Wiseman’s work adds further weight to this. Lucy’s knee extensor muscles, and the leverage they would allow, confirm an ability to straighten the knee joints as much as a healthy person can today.

The paper can be found at the Royal Society Open Science: Three-dimensional volumetric muscle reconstruction of the Australopithecus afarensis pelvis and limb, with estimations of limb leverage

Abstract

To understand how an extinct species may have moved, we first need to reconstruct the missing soft tissues of the skeleton, which rarely preserve, with an understanding of segmental volume and muscular composition within the body. The Australopithecus afarensis specimen AL 288-1 is one of the most complete hominin skeletons. Despite 40+ years of research, the frequency and efficiency of bipedal movement in this specimen is still debated. Here, 36 muscles of the pelvis and lower limb were reconstructed using three-dimensional polygonal modelling, guided by imaging scan data and muscle scarring. Reconstructed muscle masses and configurations guided musculoskeletal modelling of the lower limb in comparison with a modern human. Results show that the moment arms of both species were comparable, hinting towards similar limb functionality. Moving forward, the polygonal muscle modelling approach has demonstrated promise for reconstructing the soft tissues of hominins and providing information on muscle configuration and space filling. This method demonstrates that volumetric reconstructions are required to know where space must be occupied by muscles and thus where lines of action might not be feasible due to interference with another muscle. This approach is effective for reconstructing muscle volumes in extinct hominins for which musculature is unknown.

The paper is an interesting read and in my opinion fairly accessible.

Lazy linking

A few interesting links.

There is no “Putin wing” of the GOP: Why almost no Republican backs Ukraine over Russia by Amanda Marcotte

Republicans may say they oppose Putin, but they keep siding with the Russian dictator over Democrats and democracy

Amanda Marcotte explains very well why the Putin Wing of the Republican Party is almost the whole party, and that the only time that most Republicans will speak out against Russia and Putin is when they are forced to by public opinion, or, more likely, when they can use it against President Biden in one way or another.

Preparing for Defeat by Francis Fukuyama

I’m writing this from Skopje, North Macedonia, where I’ve been for the last week teaching one of our Leadership Academy for Development courses. Following the Ukraine war is no different here in terms of available information, except that I’m in an adjacent time zone, and the fact that there is more support for Putin in the Balkans than in other parts of Europe. A lot of the latter is due to Serbia, and Serbia’s hosting of Sputnik.

As a general rule, don’t expect me to link to stuff by Fukuyama, but this was an interesting list of predictions by him – even if some of predictions would be better characterized as wishful thinking.

Spectacularly Colorful Fish Is First New Species Ever Described By A Scientist From The Maldives by GrrlScientist

An international team of scientists discovered a new species of mesophotic coral reef-dwelling fish in the Indian Ocean

It’s always interesting when new species are discovered, and it is great that science is getting decolonized.

Ancient DNA just became older

Most science news in recent days have been focused on the Perseverance Mars Rover and its landing on Mars. However, that is not the only major science news in recent days. We have also had the publication of the news about million years old mammoth DNA being sequenced.

The Guardian reports on this: Million-year-old mammoth genomes set record for ancient DNA

Teeth from mammoths buried in the Siberian permafrost for more than a million years have led to the world’s oldest known DNA being sequenced, according to a study that shines a genetic searchlight on the deep past.

Researchers said the three teeth specimens, one roughly 800,000 years old and two more than a million years old, provided important insights into the giant ice age mammals, including into the ancient heritage of, specifically, the woolly mammoth.

This is really exciting, and will help create a more accurate picture of the lineage of mammoths, as well as expand the possible range for future sequencing. As the Guardian states:

Dalén said new technologies could allow the sequencing of even older DNA from remains found in the permafrost, which dates back 2.6m years.

For a good look behind the science, Patrícia Pečnerová, the Postdoc involved in the research, has written a great write-up: Pushing the limits with million-year-old DNA

The write-up gives an interesting and humorous look behind the scenes, as the starting paragraph clearly shows:

I had low expectations when we went into the lab to extract DNA from samples that based on geological evidence were 600 thousand to 1.2 million years old. At that point of my PhD, I already knew better than to put faith in high-risk/high-gain projects. And attempting to extract DNA older than has ever been done before topped the list of some pretty funky projects that I have been involved in, like trying to retrieve DNA from rocks from the ocean floor. Such efforts rarely yield results and end up in the invisible section of the CV where dreams go to die. My supervisor, Love Dalén, calls it character building.

The article is unfortunately behind a paywall at Nature: Million-year-old DNA sheds light on the genomic history of mammoths

Further reading: Million-year-old DNA provides a glimpse of mammoth evolution (news write-up in Nature)

 

 

Culling the Danish mink

It is a story that has gotten some traction in international media, but which might have been overlooked by people focused on the US election.

The Danish government has ordered the culling of all mink in Danish mink farms.

Denmark is the biggest mink fur producer in the world, so this is a multi-million dollar industry that is getting wiped out.

The reason for the decision, which I am sure wasn’t taken lightly, was that the mink poses a health care risk – more precisely, they are a source of new mutations of the corona virus – some with worrying characteristics. Or as BBC explains it:

Mink kept in large numbers on mink farms have caught the virus from infected workers. And, in a small number of cases, the virus has “spilled back” from mink to humans, picking up genetic changes on the way.

Mutations in some mink-related strains are reported to involve the spike protein of the virus, which is targeted by some, but not all, vaccines being developed.

“If the mutation is on a specific protein that is being currently targeted by the vaccine developers to trigger an immune response in humans then it means that if this new virus strain comes out of the mink back into the humans, even with vaccination, the humans will start spreading it and the vaccine will not protect,” Dr Peyre told BBC News.

While the culling is going on, the region of Denmark where the strain has been observed in humans, has been shut down. People have to stay in their municipalities, avoid gatherings, and all bars, restaurants and cafés have been closed. An effort to test everyone in the region (approximately 280,000 people) has begun.

Some politicians in the Danish parliament, especially those in opposition to the government, has questioned whether the measures are necessary, but it is worth noticing that the only scientist in the Danish parliament, Stinus Lindgreen, has come out in clear support of the measures, stressing the need to react quickly to ensure this doesn’t turn into a greater problem.

Currently, there is negotiations going on about how to compensate not only the people directly affected, but also people who are indirectly affected by the culling and the shut down of the region.

 

Interesting news on the ancestry of Orangutans

An interesting bit of science news from my local University, the University of Copenhagen.

Extinct giant ape directly linked to the living orangutan

Researchers from the University of Copenhagen have succeeded in reconstructing the evolutionary relationship between a two million year old giant primate and the living orangutan. It is the first time genetic material this old has been retrieved from a fossil in a subtropical area. This allows the researchers to accurately reconstruct animal, including human, evolutionary processes way beyond the limits known today.

As the opening paragraph makes clear, this is an interesting piece of news, not only because of the results, but also because of the advancements in techniques this research has led to.

The news release from the university mostly focuses on how the expansion of the techniques are going to make broader research possible – for the actual results of the study, you’ll have to go to the article in Nature (behind a paywall)

Lazy linking

A few links to articles and blogposts that I think worth sharing

Laurie Penny has written a long-read article about not debating people: No, I Will Not Debate You

Civility will never defeat fascism, no matter what The Economist thinks.

Professor Julie Libarkin of Michigan State University has compiled a list of know harassers in academia

Rates of sexual abuse and harassment in academic science are second only to the military. It’s estimated that at least half of women faculty and staff face harassment and abuse and that 20 to 50 percent of women students in science, engineering, and medicine are abused by faculty. Those numbers are generally based on surveys, which are an important way of getting a handle on the problem and how it changes women’s career trajectories.

But when it comes to holding institutions accountable and making meaningful changes, naming perpetrators may be even more powerful.

Julie Libarkin has taken on the challenge of creating a database of harassers. She’s a professor at Michigan State University and she heads the Geocognition Research Laboratory. She’s compiled a list of some 700 cases of sexual misconduct in academia.

The human league: what separates us from other animals? by Adam Rutherford

You are an animal, but a very special one. Mostly bald, you’re an ape, descended from apes; your features and actions are carved or winnowed by natural selection. But what a special simian you are. Shakespeare crystallised this thought a good 250 years before Charles Darwin positioned us as a creature at the end of the slightest of twigs on a single, bewildering family tree that encompasses 4bn years, a lot of twists and turns, and 1 billion species.

Republicans hoped voters would forget they tried to kill Obamacare. They bet wrong. by Andy Slavitt

Andy Slavitt described his article thus on twitter:

Do you notice this phenomenon where your MOC behaves differently in odd numbered years and even numbered years? My @USATODAY column this week explains.

There’s overwhelming evidence that the criminal-justice system is racist. Here’s the proof. by Radley Balko

This is very relevant to my earlier post about the need for a reform in the US judicial system.