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.

Science Vs limiting their output

I have listened to the Science Vs podcast for a while, but had somehow missed the fact that they had become exclusive to Spotify. This is not a good situation to be in for a podcast promoting the understanding of science, and the host/producer Wendy Zukerman and the editor Blythe Terrell have taken the consequences and are now limiting their output to shows that debunk stuff released on the Spotify platform

Zukerman, the host and executive producer for “Science Vs,” and Terrell, an editor for the science podcast, plan to limit their production on new episodes because they do not believe Spotify’s rules regarding misinformation go far enough.

“Until Spotify implements stronger methods to prevent the spread of misinformation on the platform, we will no longer be making new Science Vs episodes, except those intended to counteract misinformation being spread on Spotify,” they wrote in a letter to Ek, posted on Twitter on Monday.

“Science Vs,” which is exclusive to Spotify, looks at the science behind topics including pandemics.

They have already started doing this, with their latest episode Joe Rogan: The Malone Interview, which you can listen to here.

I applaud the principled stance that they have taken. You can find their twitter feed here.

Engadget have a few more details in Spotify’s ‘Science VS’ podcast will only fact-check misinformation being spread on Spotify

NASA Webb Telescope is on its way

I am always awestruck about the feats of engineering and science that goes into space exploration, and I love when there is yet another milestone to celebrate.

 


You can follow the news on the Webb Telescope Twitter feed or the blog dedicated to the Webb Telescope over at NASA.

Words have consequences: Hospital drops anti-vaxxer as spokesperson

I don’t follow US sports, and especially not the commercial vehicle claiming to be a sport, that NFL is, so I don’t really know how big a name Kirk Cousins is, but being a quarterback on a NFL team does give you a certain reach, no matter how good you are. This is why it is rather bad that Kirk Cousins has been saying stuff that is clearly anti-vaccination. It turns out that one of his sponsors, the Holland Hospital in Michigan feels the same way.

Michigan hospital ends relationship with Kirk Cousins after anti-vaccination remarks

“While we acknowledge that each person is entitled to their own viewpoints, those who speak on our behalf must support messages that align with the hospital’s position on matters of vital importance to individual and community health,” the hospital’s statement on the matter read. “For this reason, Holland Hospital will discontinue using Kirk Cousins as our spokesperson for now. We are proud of our association with Kirk. He embodies many values we respect and share as part of our work culture. However, we must be certain that our communications about COVID vaccination are consistent and unequivocal.

“Evidence also indicates that vaccinated individuals may be less likely to carry and transmit the virus to others including children, family members and friends,” the statement said. “For these reasons, Holland Hospital has and will continue to strongly recommend the COVID vaccine to those who are eligible to receive it.”

It is a pity that they feel the need to sugarcoat the breakup, instead of just saying that having using Kirk Cousins as a spokesperson was a mistake, given his anti-science and anti-evidence stance on health care and disease prevention.

Kirk Cousins is not the only sportsperson who has made dangerous remarks about COVID-19 and vaccinations, and I hope more companies will take the lead from Holland Hospital, and distance themselves from people promoting dangerous views.

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)

 

 

The state of COVID-19 vaccine and treatment research

Yesterday I spoke with a couple of colleagues about COVID-19 vaccines, and it became clear for me that there is a lot of news about potential vaccines, but it is hard for people to get a grip of the current state.

This made me recommend the New York Times vaccine tracker to several people.

Here is the status of all the vaccines that have reached trials in humans, along with a selection of promising vaccines still being tested in cells or animals.

As the description explains, it is an overview of vaccines that has reached a stage where they are relevant to talk about.

There is a companion site to the vaccine tracker, the Coronavirus Drug and Treatment Tracker, which is described thus:

The Covid-19 pandemic is one of the greatest challenges modern medicine has ever faced. Doctors and scientists are scrambling to find treatments and drugs that can save the lives of infected people and perhaps even prevent them from getting sick in the first place.

Below is an updated list of 21 of the most-talked-about treatments for the coronavirus. While some are accumulating evidence that they’re effective, most are still at early stages of research. We also included a warning about a few that are just bunk.

Both of these sites are great resources on the current state of the research, and well worth checking up on from time to time.

More evidence of the damage from social isolation

Via Sciencedaily, I see that researchers discover a specific brain circuit damaged by social isolation during childhood

Loneliness is recognized as a serious threat to mental health. Even as our world becomes increasingly connected over digital platforms, young people in our society are feeling a growing sense of isolation. The COVID-19 pandemic, which forced many countries to implement social distancing and school closures, magnifies the need for understanding the mental health consequences of social isolation and loneliness. While research has shown that social isolation during childhood, in particular, is detrimental to adult brain function and behavior across mammalian species, the underlying neural circuit mechanisms have remained poorly understood.

The ScienceDaily article is referring the research published in the paper A prefrontal–paraventricular thalamus circuit requires juvenile social experience to regulate adult sociability in mice in Nature Neuroscience, which unfortunately is behind of a paywall.

As is clear from both the extract I posted before, this is a study using a mouse model, so we should be careful to not draw too many conclusions from it yet. Yet, it does add to the generally accepted idea that social isolation can be harmful.

I think the ScienceDaily COVID-19 angle is problematic, as most people don’t experience total social isolation, but instead  experience limited social interactions and the use of technological solutions to keep contact with other people. Rather, I think the subject is more relevant for people kept in isolation in jails or refugee detention centers around the world. Here, the article is adding more fuel to the argument that isolation is a human rights violation.

A couple of great ones are gone: Katherine Johnson and Freeman Dyson

Just under a week ago, we lost Katherine Johnson:

Katherine Johnson Dies at 101; Mathematician Broke Barriers at NASA (NY Times link)

She was one of a group of black women mathematicians at NASA and its predecessor who were celebrated in the 2016 movie “Hidden Figures.”

PZ has written more about her here.

Today, we have lost another important figure – this one more well know and celebrated through his working life.

Freeman Dyson, quantum physicist who imagined alien megastructures, has died at 96 (livescience link)

Freeman Dyson, Math Genius Turned Visionary Technologist, Dies at 96 (NY Times link)

Freeman Dyson, like so many scientists before him, did some brilliant work, and the turned towards less scientific ideas. This shouldn’t make you dismiss his importance, just make you weary of his later works.

 

I, a philosophical zombie

I have just listened to the newest episode of the Serious Inquiry Only, which is about how peoples’ brains work differently.

SIO227: Do You Have an Internal Monologue?

… because one of your beloved hosts of SIO does not! Needless to say, this was a mind blowing realization to that person. We talk about the extraordinary differences in human internal experience, and some of the current science and philosophy on the topic.

The episode mostly focused on internal monologues, but the hosts also mentioned the fact that not everyone have a mind’s eye, and even mentioned someone on twitter who had neither an internal monologues nor a mind’s eye.

In the podcast, one of the hosts, Thomas Smith, said that people with neither an internal monologue nor a mind’s eye must be philosophical zombies.

As I understand the podcast, having an internal monologue means that there is an auditory aspect to peoples’ thought process, where they hear their thoughts as voices, either their own or someone else’s.

You might have guessed it from my description and the post’s headline, but I don’t have an internal monologue. Nor do I have a mind’s eye (I just learned that not haven’t a mind’s eye is called aphantasia,I have just always said that I’m not visual).

This means that, for me:

  • An earworm is just a song that I instantly recognize
  • I don’t visualize characters in books
  • I don’t read dialogue in the voice of the characters/people
  • For me, picture this/visualize this is just a metaphor for thinking about some

It also means for me that most memorizing techniques doesn’t work for me, since they often require the ability to visualize things.

What it doesn’t mean:

  • I am unable to make figures and diagrams that are useful

Quite contrary, I often make quite clear and useful diagrams/figures, since I have to think about how to communicate through them than people who make them “on the fly”.

  • I don’t enjoy reading

I have always read a lot, and I enjoy well written books. Unlike what some might think, I can also be affected emotionally by books.

  • I can’t improvise speeches and writing

On the rare occasions where I am giving a speech, I usually note a couple of subjects that I need to cover, and then improvise from there. When writing for my blog, I only have a faint outline of what I want to cover, before starting to read the blogpost.

Having listening to the podcast, I did realize that there probably is a connection between my lack of inner monologue, and why I don’t particular sing along songs. I much prefer to listen to the artists doing the singing, and I don’t have a inner monologue pushing me to open my own voice.

Feel free to ask questions about how my thinking process work, but do remember that I don’t have a shared experience with most of you, so I can’t describe the differences, just how I experience it.

 

 

 

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)