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User Journal

Journal Journal: Denisovan find in Laos

Since I'm rewriting this as a journal, I'll add a few more links.

According to the scientific journal Nature: "A fossilized tooth unearthed in a cave in northern Laos might have belonged to a young Denisovan girl that died between 164,000 and 131,000 years ago. If confirmed, it would be the first fossil evidence that Denisovans â" an extinct hominin species that co-existed with Neanderthals and modern humans â" lived in southeast Asia."

Whilst not strictly surprising, as Denisovan genes had previously been found in Tibetan people, there had been no archaeological evidence of Denisovans outside of Siberia, the genes might have arrived later. This new find makes it likely that the Denisovans were there at the time.

There has been work on East-Asia-specific Denisovan markers

In Bajau, the genetic markers that allow Sherpas and other peoples to live at high altitudes also allow islanders to freedive for longer than other humans, which raises some interesting questions over who inhabited what areas in ancient times.

This new find would imply that the Denisovans lived in these areas with humans moving in later on, with the two coexisting for a while, rather than having crossbreeds move in from somewhere else.

User Journal

Journal Journal: Flawed spam detector 2

https://slashdot.org/submission/15967006/denisovan-find-in-laos

This was marked as spam. How and why? It's not a gratuitous quote from the article and is followed by what it implies.

User Journal

Journal Journal: Conspiracy theories 9

If we look at a lot of the modern conspiracy theories (antivax, covid being fake, gun crime against schools being a hoax, global warming being a hoax, etc), they all seem to be things that people feel powerless about.

The four I listed are things individuals can't do much about. And modern society is all about the cult of the individual. It would require large scale collective action to deal with them, and if you reject outright the concept of collective action then the easiest way to cope is to pretend the issues don't exist.

Having vaccine anxiety is distinct here. There, some power does indeed rest with the individual. You can test for hyperactive immune systems and allergies, so can know if a given type of vaccine is safe. And yet people who are anxious aren't obviously getting tested.

Now, some who are aren't getting listened to by doctors, and that's a legitimate complaint. Some of that is because doctors are overworked, and that too is a perfectly legitimate complaint. And there has been (and still is) a lot of sexism and racism in the medical profession, leading to poorer outcomes and unnecessary injury/death.

These issues are verifiable, very real, urgently need to be fixed and should not be accepted by anyone. But that is precisely what makes them different from conspiracy theories. They're trivially verifiable. There are no aliens or crime syndicates hiding this information.

There are other conspiracy theories, such as the tendencies of politicians and the powerful, whether Lord Lucan is alive, a new world order, and so on.

These also look like a feeling of being powerless, and a way to "explain" why the person is powerless. After all, if politicians are alien lizards or part of an organized crime syndicate, then the public would obviously be powerless. That would be a natural conclusion.

The last category, what might be called traditional conspiracy theories, would be the flat Earth movement, the fake moon landings belief, and so on.

The idea here seems to be, again, powerlessness., this time based on the notion that the public isn't being told everything, that scientists are keeping secrets.

I can understand that to some extent. Governments are loathe to let scientists talk freely, it's natural to be suspicious about things you're not told and the paranoia over secrecy extends to things that the public already know.

(Strong encryption exports were only legalised in the US after one person had the RSA algorithm tattooed onto him.)

Extrapolating from this paranoia to the idea that the moon is a hologram is a stretch, but it's understandable that some people will react badly to this feeling of powerlessness and helplessness, and unelected scientists are easy, soft, targets.

All of the above also involve this idea of having secret inside knowlegde about "the truth" (which is also about control, since now you get to be the one who controls it).

Since the underlying issues revolve around the worship of the individual over all else (and thus making personal power sacrosanct and all that denies such power a heresy), maybe one step would be to have schools teach a more balanced approach rather than reinforcing this absolute ideal.

Extremes (be it a communal extreme, an individualist extreme, a hedonistic extreme or an ascetic extreme) are toxic but modern discourse doesn't leave any room for the middle ground any more.

And when that middle ground is claimed, it needs to be claimed by all sides. The extreme position, I suspect, is a reflex reaction of all the other extremes.

The second part is about control issues. Everyone wants to be the leader, nobody likes following, and in a world that respects status and glamour rather than people, there's an obvious reason for that. Control is also a mental health issue and in the whole strong, self-sufficient ideology, mental health issues are something only other people have.

Banish the extremes and the glorification of indvidualism and power. Science isn't the problem, nature is never a problem, and even politicians don't have to be a problem if they don't want to be.

Then we can finally start seeing rational debates and actual solutions to problems.

User Journal

Journal Journal: Slashdot issues 1

For many years now, the side bar on the front page has been linked to DustyM's account but to my account on all of the secondary pages. This has been annoying and I've given feedback on it a few times with no response.

Does anyone know of a way to fix that damn sidebar? If not, I have been using the workaround for a long time now, but it is exceedingly irritating.

User Journal

Journal Journal: Transcribing WW1 biography 5

My great great grandmother wrote a biography of her three brothers killed in WW1. I'm typing it all into a LaTeX editor and will be adding a family tree along with a sketched outline of their lives and newspaper clippings.

A best-seller it ain't, but it may interest a few here as these guys show autistic traits and are geeks from just over a century ago.

User Journal

Journal Journal: Review: Bird of Prey 4

TL;DR version: 80s dystopian techno-horror geekfest with relatively accurate portrayal of cryptography and hacking.

Long version: Pretty much the same as above. It's a low budget BBC production that scores highly on accuracy of methods, exploits and technology of the era, insofar as TV ever gets.

The premise: a low-rank civil servant, tracking down bank fraud, discovers a trail of blackmail, corruption by intelligence services, deliberate weaknesses in security and criminal gangs operating with impunity.

By season 2, he's keeping himself alive the same way the Wikileaks journalists did, his wife has what we would call severe PTSD and the body count isn't slowing down.

Given trauma was barely understood in the 80s, the portrayal there and the bouts of temporary insanity are extremely close to what happens, again allowing for this being TV drama and not a psychological documentary.

The storyline deals with cryptography, surveillance society, backdoors and institutional corruption. All hot button issues of today. It even covers the inevitable issues of DIY security.

The conspiracy aspect is a trifle OTT bit, again, it's TV. It has to be to have a program.

It's geared to nerds, geeks and dystopia lovers, though, rather than the mainstream. I saw more reviews in computer journals than in TV guides.

It's the sort of show that would really need updating to be watchable by modern audiences, but fans of older shows would likely enjoy it.

It wasn't unusual for the time, which is the great thing

The 80s were a time for really bleak geek television - Codename Icarus (for the younger viewers), Edge of Darkness, Terry Nation's Survivors, Threads - all productions in this decade.

(Even late 70s had some dark stuff, Blake's 7, The Omega Factor, Day of the Triffids, and ABC/Central's Sapphire & Steel were not light watching. You have to go back to the start of the decade and Doomwatch to see a plausible contemporary dystopia.)

The stuff of a thousand bad dreams, these shows.

User Journal

Journal Journal: Teaching history via RPGs 3

There's a new RPG pack under development, called Carved In Stone. Well, it's called an RPG pack, but basically it's a fairly comprehensive history lesson about the Picts that can be used in roleplaying games. This is quite a neat idea and it got me wondering.

There were, at one point, quite a few historical wargames (Britannia, Decline and Fall, etc) but they were mostly about large-scale strategy rather than the history itself (which was mostly an excuse for blowing up other people's counters). History lessons via roleplaying games sounds quite an interesting approach and could be used to cover all kinds of events.

The expansion pack isn't out yet (it's still in kickstart) but there's enough information about it to get a good feel for how much depth there is in there. If it's done well, it could be very effective in the same way "...and then the Huns came and beat the sh*t out of the Romans before leaving again" isn't. Unless you're a Hun.

I'd like to get people's views on the use of roleplaying games and which system would be best for such gaming. Rolemaster? Call of Cthulhu? The ever-present Dungeons and Dragons? ("My 20th level mage casts a fireball at the fleeing Scots" sounds ahistorical.)

User Journal

Journal Journal: Consumer Genetics, the current state of play

Ok, so let's start be defining a few terms, as it is obvious from Facebook genetic genealogy groups that people are truly ignorant on the subject. (Not that I believe this is common on Slashdot, where we're all much more knowledgeable.)

First off, most genetic testing is NOT carried out by sequencing all of your DNA, a widespread belief that resulted in outrage on one Facebook group when I pointed that out.

The vast majority of consumer testing is done by SNP genotyping. They look at very specific genetic markers and see if those markers have changed from one base pair to another. That's the only type of mutation looked for and they typically look at only a few.

So we've our first way to group companies: sequencing vs genotyping.

SNPs (single nucleotide polymorphisms) are, as mentioned above, one type of mutation. Another is called STR (short tandem repeat), where a block of DNA is duplicated.

FamilyTreeDNA does both STR and SNP testing, STRs mostly for the Y chromosome. Both can be used for family history.

Most labs, though, use only SNP tests. It's quicker and cheaper than counting repeats but with many of the more interesting ones covered by patents or kept private by other means, there's a lot more secrecy involved.

(Note: This has doubtless led to a lot of unnecessary deaths, as genetic markers indicating a high probability of getting certain forms of cancer are being milked by private companies for profit. Few people get more than one test, so most people won't know if they carry such markers and can't take action in advance.)

So the second piece of jargon is SNP vs STR.

Finally, we come to the different areas of DNA. There are regions that are especially good for ancestrial reserch (mostly non-coding DNA), then there's the exome (which is where most of the protein coding takes place), you've telomeres (suicidal buffers between chromosomes, which have a function in longevity), and so on. I won't list them all.

The Y chromosome is particularly good for ancestry, but only has 9 coding genes left in it. It's possible it will vanish in time, but it seems to be fairly stable for right now.

Most companies test only DNA that is good for ancestral research in the autosomal regions (aDNA, the regions outside the sex chromosomes). This allows you to identify anyone who is genetically connected, but because you (on average) get just under 50% (remember, there's mutations in each generation and that DNA comes from neither parent) of your DNA from each parent, the distance you can track depends on how many markers are tested (very few). Reliability falls off sharply.

YDNA (Y chromosome DNA) tests only test for paternal ancestry, but if two people have a common paternal-line ancestor, it's a lot more precise once you're past about second cousins. It's popular with anthropologists as it's very good for tracking how men have migrated.

mtDNA (mitochondrial DNA) is only inherited through the maternal line. Again, it's very popular, this time for tracking how women have migrated. There are certain forms of mtDNA that are linked to health benefits and others to genetic diseases, so this one tends to be the most controversial of the ancestral DNA tests. It also changes very slowly, so you don't get high resolution on population movements.

These two (YDNA and mtDNA) tests can tell you a lot about whether societies are open or closed, and whether it was men who travelled to find partners, women, or both. So we can know something of the culture of even long-extinct societies.

The data I have been able to find is for 2019. It shows: Myheritage tests for 702,442 autosomal SNPS, AncestryDNA for 637,639, FTDNA for 612,272 and 23andme for 630,132. This is out of a total of 3 billion base pairs. So the best test that year looked at 0.0023% of the genome.

ISOGG produced a chart as well, but it's far older. Their chart is dated around 2013.

Since you inherit a random 50% from each parent, the assumption that this is statistically meaningful for such a small fraction of the DNA is questionable. It seems to work adequately, but I'm not sure what the error bars are.

FTDNA also tests up to 111 STRs on regular tests and 600+ STRs for their "BigY" (it depends on the quality of the genetic sample).

Companies that do sequencing sometimes offer partial kits (in the order of tens of millions of SNPs) or full sequencing (which is what the same suggests). These are rarer and more expensive.

Most DNA companies allow you to access the raw data, some only allow it if you pay vast sums of money, and some don't allow you to at all. Always check in advance.

When you download your own data, you can use public databases to search for matches (either for relatives or genetic conditions). The quality of public databases is less controlled, both in terms of privacy and quality of data. However, corporate databases will usually be smaller for both types of data and will also usually not contain data from rivals. If you want broad data sets, public databases are the way to go.

I've only tested with 23&Me, FamilyTreeDNA, CRI Genetics and Nebula Genomics, so can't tell you anything much about the quality of the other companies.

(Ok, I also tested with uBiome, a microbiome testing company in the US, but they had their computers seized some time back due to fraud. I have no idea what happened to my data on there, or whether there's a way to access it.)

The quality seems to be reasonable for all four.

FTDNA is the most expensive for a lot of things, but has less of a sticker shock than Nebula and gets more data than 23&Me. It looks like there are a few companies that are better for ancestry but it's one of the best and the one the Genomics Project used. They're the only ancestral company that gives you STRs AFAIK and they give you a much more detailed evaluation of haplogroups than anyone else I've tested with.

Nebula does up to medical grade (100x oversampling) DNA testing, so if you want results a hospital will trust, that's where you part with a vast amount of money.

23&Me is good for a lot of medical stuff and if you want to help with research is probably the best.

CRI Genetics produces a lot of data with much higher reliability than most of the others, but you can't access the raw data and their databases won't be as extensive. However, because you can't access the raw data, you have to test with them to compare against their database.

User Journal

Journal Journal: Tea 7

I have now passed the total of 30 different black teas. Not fruit, not spice, not herbal, not even green, white or red tea. Just black teas. No, blends like PG Tips and Yorkshire Gold don't count either.

Why so many? Aside from being my current monomania, it's because I'm fascinated by how different they are.

I couldn't tell you the chemistry that makes that difference, nor could I tell you what difference it makes in terms of the various compounds affecting alertness or sedation. (It contains both), in terms of health benefits or even in the simplest term of how water is retained in the body.

But I'm determined to find out at least some of this. It'll have to be on my own, as essentially no research is being done on the subject, and I've no idea of what that'll require beyond a very good gas spectrometer (I'm going to have to count molecules, not atoms).

But I think it would be fun to find out, and definitely worth doing as long as I can figure out how to (a) control the parameters, and (b) afford said piece of gear.

User Journal

Journal Journal: Installing Kali Linux Under Pureboot/Heads 2

Using a Librem 13v3 with Pureboot, Heads for BIOS, and a Librem Key normally works without a hitch. However, I was wanting to install Kali on the 2nd internal drive and dual-boot. This presented a pain-in-the-ass challenge.

Kali Live works fine on the laptop. However the installer crashes the display. It seems there is a kexec parameter of vga=788 that the laptop chokes on. Updating the grub config on the Kali ISO, then repackaging it is the long, hard way to deal with this. The simple way would be to install direct from the running Live instance. Unfortunately the Kali gods have decided to remove that feature. Idiots.

Here's the fix. From running Live open a shell and "sudo apt install debian-installer-launcher". Then "sudo debian-installer-launcher" and follow the prompts. Works like a charm.

I'm posting this here because it took way too long to search for a working answer, not knowing exactly what to look for.

User Journal

Journal Journal: Forced Perspective 2

Forced perspective is a technique which employs optical illusion to make an object appear farther away, closer, larger or smaller than it actually is. It manipulates human visual perception through the use of scaled objects and the correlation between them and the vantage point of the spectator or camera.

Squid can range in length anywhere from 1 inch up to 80 feet. The Colossal Squid is the largest known variety, and thought to be the inspiration behind legendary monsters such as The Kraken of Greek mythology.

Calimari is the term for he culinary specimens of squid, and typically measure less than 12 inches. Squid lends itself to hot and fast cooking methods such as grilling, broiling, sauteing, and deep-frying. Or, by irritated judges when hack lawyers try and pass off itty-bitty lawsuits as "the Kraken" when they're really just suitable for calimari.

User Journal

Journal Journal: Hello All: OPNSense 2

Note sure who from the old group is left here. I haven't posted in over a decade and I'm here with a question. :) If anyone is using OPNSense or PFSense, you might be able to weigh in. Story time... I started using OPNSense (based on PFSense) as my internet gateway at home in January of this year because I had a need for speed. My WRT54G with ddwrt wasn't up to the task of my new gigabit internet connection since it only has 100 Mb/s ports. I had an old PC lying around and an extra gigabit PCIe card, so I did what any Slashdotter worth his salt would do: I built a gateway. (Heheh, actually about as prefab as ddwrt).

I chose OPNSense over PFSense since PFSense wouldn't boot on that machine (an old 64-bit AMD CPU) no matter what I tried, and I tried a LOT. Things were fine until something in early September. One morning I woke up to no internet access. I checked a bunch of other things first because I had literally built a new DHCP/DNS/NTP server a day and a half earlier. Eventually I realized there really was no internet access and when I checked out the PC, it was off.

This happened one more time two days later, and with what appear to be missing syslog entries (I just don't know enough about BSD and OPNSense to know if that is OK or not), I started wondering if the box was compromised somehow. I doubted that since FreeBSD is supposed to be about as safe as you can get for a internet facing machine and I've NEVER had a Linux box get compromised out in the wild in the 25+ years I've been using it. As a result I'm really leaning towards the idea that this is a hardware bug or potentially failing hardware. The PC is at least ten years old. Given that PFSense wouldn't boot on it at all (it would lock up from the boot DVD once it attempted to load the kernel), it's likely there is something about my PC that just doesn't work well with FreeBSD.

Given that, since I still had a slight suspicion that someone might have been messing with the machine, I connected to it from another machine using a GNU screen multiplexer session so that if I got disconnected, I'd have a logged, searchable history even if the syslog got wiped. I was watching the syslog with 'clog'. It sat there for 13 days without shutting down and nary a new syslog entry in sight. I didn't check it daily and given that it had been up for over a week I stopped checking the screen session. Yesterday, I connected to the screen session to take a peek, and there was a disconnect message just after the syslog which still had no new entries in it. What's interesting to me is that this time it wasn't off, it was a reboot while I was at work. Since I'm working from home and use a different part of the network for work, I didn't notice the outage. Neither did my wife and kid since they were both not using the internet connection at 9:20 in the morning that day.

So I connected to see what the logs showed. This time the log picked up from where it was before the reboot, It just showed standard boot stuff starting at 9:20 AM, a redundant disk rebuild and that's it. It's been like that since last Tuesday. I've run the updates and audits on it, and there is only one vulnerability in an XML library that's been in FreeBSD since January and is not fixed yet.

I'm still leaning pretty hard on hardware failure or a CPU bug that didn't cause issues with booting the OPNSense installer DVD like PFSense, but those are both just guesses. I don't know if a normal syslog would show shutdown info on FreeBSD, but I assume it would. If that's true, then it's possible a hard crash would explain the missing shutdown info in the logs. Otherwise, I'm still in the dark.

As a side note, I've also confirmed that there were no power blips at any of these times. My Linux laptops showed no change to battery during the days these shutdowns and the reboot occurred. The only other item that I noticed that seemed odd was that after I powered on after the first shutdown, a few hours later there were some messages on the console from a service (can't remember the name) that slows down the restart of a process if it continually segfaults. This is supposed to discourage attackers. I think the process that was segfaulting repeatedly was flowd (for netflow).

So anyone here familiar with this and have any recommendations? Agree that this is likely a hardware issue since it should theoretically be harder to compromise a internet facing BSD box than a Linux box? Or have I been h4x0r3d by a 1337 d00d and should I kill this system with fire and get a new fanless PC to start over with?

NASA

Journal Journal: PULSE - A Pendant to Warn You When You Touch Your Face 1

PULSE, developed by a small team at NASA's Jet Propulsion Lab (JPL), is a 3D-printed wearable device that pulses, or vibrates, when a person's hand is nearing their face. The haptic feedback from a vibration motor simulates a nudge, reminding the wearer to avoid touching these entryways in order to reduce potential infection.

The project is open source, with all the information from parts list to assembly instructions freely available online.

User Journal

Journal Journal: Pi Audio 1

My wife picked up a Google Home unit so she could listen to music without constant obnoxious advertisements. I've been wanting to replace it because I don't want a spy device in my house. As I'd been fiddling with a Raspberry Pi audio player for some time, this finally prompted me to finish it.

So the Google Home will do more than play music, but that is 99% of what she used it for, so that's all I tried to replicate. I normally rip all media I buy, and have a fairly extensive music collection that was almost exclusively purchased as used CDs from second hand stores, like Goodwill. For $1 to $4 I can pick up anything that catches my attention. I also have quite a few comedy albums, a few audio books purchased on CD, and several radio plays from either the BBC or HPLHS.

All of the music is ripped to Ogg-FLAC format, with a .oga extension. All of the spoken word stuff is just plain Ogg-Vorbis, with the traditional .ogg extension. For those who don't know, .oga files are FLAC lossless audio in an Ogg container. The native FLAC container is fairly barebones, whereas the Ogg container has better support for extensive tagging and the bits needed to properly stream and seek. It makes for better streaming of audio whereas FLAC has a tendency to just download the entire file before playing.

Streaming audio with MPD doesn't take a lot of horsepower, and can easily be done with 1 Gb of RAM on even the minimalist RPi Zero. For my house I use RPi 3B+ board with HiFi Berry DAC+ add-on if I want to support analog speakers. That was my original plan, but have since switched to the Bose SoundTouch 10 wireless speaker for convenience. It can be used as a plain Jane BlueTooth speaker and doesn't need their app or anything other than "pair and go". It is Bose's "dumb" speaker, with no built-in Alexa or Google and can be had for under $100. If you want two, they will pair wirelessly for a stereo pair, but as I was replacing those little pod-style speakers, I went with just one.

That being said, if you're an audio snob, the HiFi Berry like of DACs will give you audiophile quality sound to your favorite pair of overpriced sound reproducing boxes.

There are several full-blown FOSS projects designed to turn an RPi into an audio jukebox, and I went thru three of the more popular before settling on my eventual choice. I tried Rune Audio and Volumio before settling on Moode Audio.

There are plenty of online reviews and comparisons of all three, so I won't repeat any of that here. If you're interested in doing this sort of project I suggest to check all three out. They support plugins for handing things like Apple's Air Play, Spotify, UPnP, DLNA, SMB, local touchscreens for the Pi, whole-house synchronized audio, and web interfaces. What clinched it for me was Moode is the only one to support BlueTooth as an output option. For me, fewer wires is a plus.

This brings me to the real point of my writing this journal entry -- documenting a few quirks to maybe help out some poor soul, or maybe my future self after I forget it all.

The big one is that the Pi's BCM43438 wireless LAN and Bluetooth Low Energy (BLE) chip REALLY doesn't like running both WiFi and BT at the same time. Streaming audio from a remote source thru WiFi and then playing on a BT speaker is just crap. Either by themselves is fine, but the chip interferes with itself even if you're doing WiFi in the 5 GHz spectrum, so it isn't a signal interference thing. Save yourself the headaches and disable on-board BlueTooth and just add one of those mini dongles. I use a ZEXMTE USB dongle, which costs around $10 and works out of the box with Linux, no custom drivers needed.

Now that I think of it, that was really the only major problem, but it was a doosey. Depending on how the on-board chip initializes it can either start and give you fits where things randomly freeze, or leave things in an odd state where systemd won't recognize the BT part.

I haven't had a chance to test on the Pi 4, which has an upgraded CYW43455 chip (now owned by Cypress Semi) that support 802.11ac and BT 4.2.

The only other quirk is that these programs rely on your IDv2 tags and honestly the most time I spent on the project -- other than debugging WiFi/BT issues -- was on ensuring my files were tagged correctly and consistently.

eol

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I tell them to turn to the study of mathematics, for it is only there that they might escape the lusts of the flesh. -- Thomas Mann, "The Magic Mountain"

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