Showing posts with label biology. Show all posts
Showing posts with label biology. Show all posts

Sunday, 11 October 2026

flightosome

Many years ago, a colleague in Biology introduced me to the paper "Can a biologist fix a radio?—Or, what I learned while studying apoptosis".  It is a funny and educational look at the different approaches to understanding in biological sciences and electronic engineering, including such gems as:

How would we begin? First, we would secure funds to obtain a large supply of identical functioning radios in order to dissect and compare them to the one that is broken. We would eventually find how to open the radios and will find objects of various shape, color, and size (Figure 2). We would describe and classify them into families according to their appearance. We would describe a family of square metal objects, a family of round brightly colored objects with two legs, round-shaped objects with three legs and so on. Because the objects would vary in color, we would investigate whether changing the colors affects the radio's performance. Although changing the colors would have only attenuating effects (the music is still playing but a trained ear of some can discern some distortion) this approach will produce many publications and result in a lively debate.

And so on. 

So when I came agross the blog post "The Flightosome" with the wonderful sketch showing a biologist's model of air travel:

(I particularly like the inhibitory links)

I had to send him the link immediately.  His response: "it’s hilarious (and tragic)"

It's just that biology is so complex, and complicated, and messy, and variable.  And endlessly fascinating.






Tuesday, 7 October 2025

ALife 2025 day 2

Tuesday, and the full conference gets going.  

We started with a great keynote from Hector Zenil, on using Kolmogorov Complexity measures.  Just because it is uncomputable doesn't mean it is useless.  Most of mathematics is undecidable, but that doesn't stop us using maths!  We shouldn't just give up and use simple lossless compression algorithms. We can do better, and getter better bounds, better approximations, by trying harder and harder (running the search algorithm for longer), which means we can be better at filtering out randomness from things that superficially look random, but that have algorithmic patterns.  It was a fascinating talk.  I've had Hector's book on Algorithmic Information Dynamics on my to-read pile for a while now -- I need to bump it up nearer to the top.

Then on to the contributed papers.  During one of these, on Synthetic Ecosystems, I became one of today's "Lucky 10,000", when I discovered that until relatively recently, Ascension Island was an essentially lifeless desert.  Darwin stopped there on his way home, and decided it needed "greening".  Today, after a lot of work, it has a lush, totally artificial, ecosystem!

The poster session has lots of interesting work on display, including a contribution by my student.  There were also some beautiful "Analogue Atomic Automata": large, carefully grown bismuth crystals, by Solvi Arnold:


In the evening we had a fascinating online keynote from Michael Levin, on biological embodiment, agential material, and bioengineering.  It might have been 8pm for us, but it was 7am for him!  (We live on a sphere.)



Tuesday, 26 August 2025

sequestering carbon, several books at a time CLIV

The latest batch:


Some of these are due to recommendations at the Belfast Eastercon; some from the Seattle Worldcon (which we attended virtually).

Wednesday, 16 April 2025

sequestering carbon, several books at a time CL

The latest batch:


 

The company who I have been with for over 40 years for insuring house contents is no longer insuring house contents.  So we are looking for a new insurer.  

We have a lot of books (no!)  This causes issues: everyone who is quoting wants to insure them as "antiques", in danger of being stolen.  No, there are a lot of individually not very valuable books (some are indeed old, but not that old, and not rare).  No-one is going to steal these: it would take forever, and they have very little resale value.  We can't be the only ones in this situation, surely?


Monday, 6 January 2025

Raman SOM

Daniel West, Susan Stepney, Y. Hancock.  Unsupervised self-organising map classification of Raman spectra from prostate cell lines uncovers substratified prostate cancer disease states.  Scientific Reports, 15:773, 2025. doi:10.1038/s41598-024-83708-6

This started out as a feasibility study, to see if Kohonen Self-Organising Maps (SOMs) could be used to cluster minimally preprocessed Raman spectroscopy data taken from individual cells.  SOM an unsupervised learning approach, and can cluster high dimensional data (here, over 1000D) down into a 2D visual representation.  We had Raman spectra of prostate cells, some cancerous, some not.  Could a SOM distinguish these two classes?

We blinded the data, so that the system did not know which spectrum was in which class, to ensure this was truly an unsupervised exercise.  After some fiddling about to understand what values several parameters should be, we fed the data in, and looked at the resulting map.  We could see three clusters.

Had it worked?  We unblinded the data, and yes, one of the clusters was the non-cancerous cells, and the other two clusters were cancerous cells.  Why two clusters?  Well, it turns out the mapping process had managed to discover two distinct classes of cancerous cells.  Further research is underway to investigate these differences.

So yes, it works, and better than we had hoped!



Monday, 23 December 2024

sequestering carbon, several books at a time CXLVII

The latest batch before the Christmas presents drop (which means I'm up-to-date on databasing, for a day or so at least!):



Friday, 13 December 2024

sequestering carbon, several books at a time CXLVI

If you follow my book reviews over on my website, you may have noticed several reviews for Great Courses lecture series.  Each course is 12-48 lectures, on DVD, accompanied by a coursebook.  These make great watching while, say, eating lunch.  We wait until interesting courses are on special offer, and have watched many of these, from science and economics to literature and history.

Recently, Great Courses decided to discontinue several of their DVDs, leaving only streaming options.  We dislike this, so have bought up a load of cheap courses while they are still available.  These should last us a while!






Sunday, 8 December 2024

sequestering carbon, several books at a time CXLV

I am beginning to catch up with my book databasing backlog.  Here's the batch from the end of October.


Saturday, 30 November 2024

sequestering carbon, several books at a time CXLIV

These are some books we bought in York on the way home from our Scottish holiday in August, some undatabased books I discovered when I packed up my office in October, plus a few maths books related to a potential retirement project I'm thinking about.








Saturday, 3 August 2024

Tuesday, 27 February 2024

view from a hotel window

I arrived in Dublin yesterday evening, ready for a two-day research project meeting.  The hotel room has an ... interesting ... layout.

Which way round are you supposed to sleep?

The bed takes up the entire end of the room.  The "wardrobe" is three coat hangers on the wall.  There is a perfectly normal en suite next to where I'm standing to take the photo.  The two wall switches by the bed raise and lower the blinds on the window.

I slept across the bed, so I didn't have to scramble across it (except to grab a pillow), and could have my phone (aka alarm clock) by my head.  It was perfectly comfortable.

What's outside the window?  In the morning light, I could see out (after scrambling across the bed again):

a view into an office block

Now off to hear about progress on our interdisciplinary computational synthetic biology project.



Saturday, 9 December 2023

sequestering carbon, several books at a time CXXXV

 The latest, pre-Christmas, batch:


A third Checquy book!  I didn't know there was another one. Yay!