Evolution on Michael’s Domain

Do fish have difficulty breathing?

Fri, 28 Jun 2024 00:00:00 +0000

Fish are breathing with their gills, but this is literally, for many of them, only half of the story. The difficulty of extracting oxygen from water is the single most defining force that shapes fish evolution. Land animals are mostly exposed to the same oxygen concentration, but fish need to operate in waters of vastly different and rapidly changing oxygen content. Moreover, water contains much less oxygen than air, and the diffusion of oxygen in water is magnitudes slower than the diffusion of oxygen in air. Therefore, fish evolution was forced to come up with creative ways to

It’s difficult to grade student’s assignments

Sat, 16 Dec 2023 00:00:00 +0000

I have been reading hundreds of student assignments this autumn. In many of these assignments, the students are expected to answer questions. Grading these assignments means deciding whether the answer is “right” or “wrong”. This is sometimes difficult. Most answers are somewhere between “right” and “wrong”. Therefore, the need for grading exposes a deeper problem: Before I can decide where on the spectrum from “right” to “wrong” the students’ answers fall, there needs to be an objective “right” and “wrong”. Otherwise, objective grades are an illusion to begin with (not even considering the problem of how to determine them reliably).However, all our scientific knowledge is preliminary. It is subject to modification or even reversal when new, better data becomes available. So, how can one grade any assignment with any certainty? Luckily, not all of our knowledge is equal. One important hallmark of a scientific statement is falsifiability , a concept that was perhaps first popularised by the science philosopher Karl Popper in his book The Logic of Scientific Discovery . What are examples of scientifically falsifiable theories?

OMG: T. rex did not have VEGF-B!

Wed, 05 Apr 2023 00:00:00 +0000

Our work on the evolutionary origin of the PDGF and VEGF growth factors has just been published in Angiogenesis: https://doi.org/10.1007/s10456-023-09874-9 . We analyzed both PDGFs and VEGFs, but our focus was naturally on the VEGF side of things. It’s just a coincidence that the PDGFs happened to be a subgroup of the VEGFs and not vice versa, but that’s of course just our biased point of view :-)Since we do lymphatic research, we can proudly announce that the phylogenetic oldest VEGF likely resembled VEGF-C and featured the enigmatic silk homology domain. It makes intuitive sense (and had been proposed before by Jörg Wilting), because the most simple vascular systems that we know of are the so-called hemolymph systems (e.g., in insects), which share many features with the lymphatic system.With this publication, we did not do something exceptional that only a few can do. We did something everybody could do but nobody had done so far: looking systematically at which animals have which PDGFs and VEGFs. Actually, we did something new: we developed a crowdsourcing method for classifying PDGFs and VEGFs. Instead of asking people, we asked databases. There are many PDGF-like and VEGF-like sequences in databases, which are only recognizable as such by the homology of their amino acid sequence. In order to know whether we are dealing, e.g., with a VEGF-C or a VEGF-D, we are running many (PSI)BLAST searches, and then we tally up the majority opinion (as determined by the top hits).Many surprises waited for us after the bioinformatics script had finished its job after two weeks of finding and comparing PDGF- and VEGF-like sequences:

The evolution of PDGF/VEGF growth factors

Thu, 22 Sep 2022 00:00:00 +0000

We have uploaded a preprint of our most recent manuscript about the evolution of PDGF/VEGF growth factors to bioRxiv. We comprehensively analyzed the PDGF/VEGF part of the proteome in all animal species for which data is available. We have had some of this data already for a while, but now we enhance it with a detailed look at fishes. The vascular biology of fishes has become even more facinating after the publication of Das et al. earlier this year ( read more about this exceptional piece of work ).The remarkable heterogeneity of vascular systems in fishes seems to be supported by a similar extensive heterogeneity at the molecular level. Often, but not always can this genetic heterogeneity be traced back to whole genome duplications. Fishes tolerate full genome duplications better than mammals. At least there have been quite a few such duplications in various branches of the fish phylogenetic tree resulting in polyploid or even tetraploid species. That has resulted in some fish species featuring 4 times as many PDGF/VEGF genes compared to humans, and much more opportunities to diversify the functions of these molecules.The very first PDGF/VEGF-like molecule appeared likely more than 800 Million years ago during the Precambrian period when marine organisms started to show signs of tissue organization. If we set out to reconstruct this molecule, it would look remarkably similar to a modern VEGF-C. Specifically the C-terminal “silk homology domain” seems to have been invented early on in evolution. In fact, a large number of extant morphologically simple organisms feature such VEGF-C-like molecules still today (e.g. the nematode C. elegans). Beyond these insights into the evolution of PDGFs and VEGFs, there are some useful take-home messages for vascular biologists: For example, we did not find any functional VEGF-B genes in birds. Similarly, there seem to be no PlGFs in amphibians. Then, on the other hand, the VEGF-Fs - identified from snake venoms - appear to exist more broadly also in non-venomous lizards. This poses some limitations on some animal models (Xenopus, CAM assay), but it would be nice to know what VEGF-F is doing in geckos…Have a look at the manuscript and please comment or criticize, if you have any thoughts! The idea is to make this manuscript still a bit better before submitting it to a journal for the traditional peer-review.

E-mail: migrating from kmail to Evolution

Tue, 17 Jul 2007 00:00:00 +0000

I recently switched from kde to gnome and at the same time from kmail to Evolution. There is no easy way to transfer you mail if you have organized it in several mailboxes in kmail. You need to select all messages in a folder and then right-click and save them in mbox format. This step you need to repeat for every folder. Then you can use the import function of Evolution (import from single file). If you can accept that all files end up in the same folder, you can concatenate your .mbox files to save you the trouble of importing multiple files:cat *.mbox > allmail.mbox