#i thought archaea was a domain

[absurdumsid]

one of u are lying but i dont know who

[thatfandomslut]

Kiss Me Harder

Regina George x Reader

Word Count: 2.3k

Trigger Warnings: SMUT, 18+!!! Power Bottom Regina, Soft Top Reader, fingering (Regina receiving), oral (Regina receiving), thigh riding (reader receiving). There is a plot, and it is almost a slowburn to it.

Request:

can i request a regina george x reader smut with bottom regina ?

Mean Girls (2024) requests are open.

(Y/n) would consider herself lucky to be paired up with Regina George for the dorms at Harvard University. Not only that, but they shared several freshman courses, and were able to work on homework and study together. (Y/n) admired the way Regina seemed to know exactly what she wanted. She was ambitious and beautiful. (Y/n) could also appreciate how cutthroat Regina could be. Similarly, Regina appreciated how spontaneous and carefree that (Y/n) was. Unlike her cutthroat attitude, (Y/n) seemed to follow the vibes of the people around them. Which was why they worked so well together.

Their first kiss was during a long night of studying for their Biology 101 class. They had thrown pillows and blankets on the fuzzy rug they picked out together in the center of their room. Regina had lit up some candles, hoping to ensure that there was a calming aroma around them. They began to exchange candy as a point system for every right question, but it wasn't long before they seemed to run out of candy. "What if, for every right answer, you kiss me." (Y/n) teased, a smirk dancing on her lips as she looked over to Regina. They often flirted shamelessly with each other. However, something was different about the atmosphere in the air.

Regina could only lick her lips briefly before looking back over to (Y/n), mirroring the smirk. How could she refuse an offer like that? "Deal," Regina confirmed. (Y/n) still didn't expect her to go through with it. They were always exchanging flirty quips such as those. "Name three domains of species for me." Regina let her cool blue eyes flicker across (Y/n) face. There was recognition to the question, and she realized how easy this question was. Regina seemed to be going easy on her.

(Y/n) leaned in slightly, watching Regina's eyes continue to glide along her face to her lips before meeting (Y/n)'s eyes. With a cheeky smile, (Y/n) allowed her lips to ghost Regina's, and their breaths mingled. "Bacteria, archaea, and eurkarya," she answered in a whisper. She was about to pull away, but Regina beat her to the action, kissing her deeply. (Y/n)'s eyes widened, but it only took her seconds to melt into Regina's lips easily. That led to several dates, make-out sessions on their twin-sized dorm beds, and the official label of 'girlfriends.'

As final exams were getting closer, (Y/n) and Regina could conclude that they weren't ready. They were ready for the exams, studying became fun due to their new point system. The problem was those three weeks spent apart. The two had almost become inseparable over their semester romance. Eventually, Regina realized she could just invite (Y/n) to stay over the holidays. The question came after pushing their beds together the night before, the two lay together sleepily, having been up studying for a couple of hours prior. "What if you just spent some of your breaks with me? I could convince my dad to fly you out to North Shore after Christmas." Regina offered, her head resting calmly on (Y/n)'s chest.

(Y/n) smiled at the thought, playing with Regina's hair. "Okay, but I don't think I could ask you to pay for my ticket. I will probably have to talk to my parents about it, too, but I can call them tomorrow. I don't think they'd be opposed to it." (Y/n) spoke softly, finding herself having to make sure to stay awake during their conversation. She was drifting off just moments ago before Regina brought her idea up.

Regina lifted her chin, moving to a spot where she could kiss (Y/n) on the nose softly. "Baby, I insist. It would be no problem whatsoever. Consider it as part of your Christmas gift if you have to." Regina stated simply, knowing she wasn't going to let (Y/n) spend a dime. She was someone who enjoyed spoiling her significant other, though (Y/n) would make sure to slip some money in Regina's book bag or make sure to get the bill first. She always felt a bit guilty, even if she knew Regina was a lot more well-off than her. Nodding sleepily, (Y/n) knew she wouldn't win this. Regina grinned before cuddling back into her girlfriend as the two fell asleep.

Finals week flew by in a breeze of late nights and several coffee orders. At the end of finals, (Y/n) and Regina dreaded leaving their dorms. With their bags packed, they were forced to separate. Fortunately, this was only for a week. Despite this, they were sending messages back and forth, expressing how much they had already missed each other. Some might judge and describe their relationship as clingy, but neither of them really cared what anyone else thought. They were happy, and that was what mattered.

After Christmas came around, (Y/n) found herself anxiously awaiting the twenty-seventh. The best Christmas gift she could receive was to already be flying to see Regina. She was excited because Regina said she was going to introduce her to her friends, Gretchen, Karen, and Cady. All of whom (Y/n) has heard a lot about. Not only that, but her parents were going on a trip, so they were going to have the entire place to themselves for a couple of days. This excited (Y/n) because they would finally be able to spend alone time without college work somehow having to be done at some point in the night. Now, they could be together without any academic distractions between them. Especially because in their last few study sessions, their point system kept becoming more heated before realizing they had to get back to the task at hand. In fact, they had to go back to the candy system in order to remain on track.

When the time finally came for their reuniting, (Y/n) felt excitement fill her the whole way to the airport and the whole plane ride. Regina was waiting for her at the bottom of an escalator in white light pink turtle neck and a tan trench coat kept her warm. (Y/n) couldn't help but admire her as the escalator descended. "Hey, beautiful," (Y/n) greeted with a bright smile as she finally was able to make her way to the blonde. Regina flipped some of her blonde hair over her shoulder with a smile, planting a kiss on (Y/n)'s lips. "Looks like someone missed me." (Y/n) teased as they pulled apart.

Regina shook her head as she rolled her eyes playfully. "Shut up, loser," she joked before taking (Y/n)'s hand and leading them to her jeep. (Y/n) followed Regina, and admired her Jeep as they drove. "I can't wait to give you your Christmas gift. I think you're going to love it." Regina expressed as she parked in front of a large home. (Y/n) felt slightly insecure when she realized how wealthy Regina's family must be in order to afford this in the current economy. Choosing not to speak about it, she followed Regina into her home and to her room. She did remember the discussion of convincing her parents to give her the biggest bedroom in the house, but she wasn't expecting it to be as big as it was. Looking around as Regina put (Y/n)'s bag in her closet, (Y/n) looked over at all the photos on the wall with a smile.

"The girl with ginger hair is Cady, the girl with honey-blonde hair is Gretchen, and then the dark brown-haired girl is Karen." She pointed to each person, having walked up behind (Y/n) as she looked. (Y/n) listened intently as Regina told her some things about the group. (Y/n) could appreciate a tight-knit group from high school having hung out with some of her high school friends over the last week. "I think you're going to love them."

Regina fell back on her bed, grinning over to (Y/n). "I'm sure I will," (Y/n) agreed before slipping out of her shoes and joining Regina happily. "I missed you," (Y/n) whispered as she moved close to Regina. Regina grinned at this before kissing the girl happily. It was one of the best kisses they ever shared. This was probably because they weren't forced to return to studying afterward. It might also be because they were allowing each other's hands to roam each other's bodies as they deepened the kiss. (Y/n)'s breath hitched slightly as Regina's hands found her breasts over her shirt. She was surprised, but she was waiting for this moment. There was a lot of built-up tension still from their finals week.

"Is this okay?" Regina inquired, not wanting to do anything without consent. (Y/n) got out a shaky yes. This was something she wanted more than anything. Regina smiled softly before kissing (Y/n) deeply. (Y/n) moaned softly in the kiss, allowing herself to move so she could straddle Regina's hips. A position they had found themselves in several times in the past. (Y/n)'s hips ground gently against Regina's as she gasped in pleasure. "(Y/n), I want to keep going. I want to make love to you."

(Y/n) smiled softly, kissing her softly. "I want that, too." She was happy that Regina communicated this, because she was ready, too. Pulling at Regina's top, she pulled it off. Regina doing the same for (Y/n) quickly. It wasn't long before their clothes made a small pile on the floor and (Y/n) was kissing Regina as her hands massaged her breasts. "Kiss me harder, you don't have to be so soft with me," Regina whispered on her lips. (Y/n) was happy to oblige, kissing Regina deeper as their tongues fought for dominance. (Y/n) kissed down Regina's body, momentarily asking if Regina was sure once more. Once Regina answered with a quick yes, (Y/n) let her lips latch onto Regina's breasts, sucking at the nipple between her teeth.

Regina's moan filled the room as one of (Y/n)'s hands made its way down, massaging Regina's clit. Regina cursed loudly as her hands found their way into (Y/n)'s hair. "Fuck, (Y/n), don't stop." She told her. (Y/n) tried not to smirk, but failed that mission as she inserted a finger, rubbing at Regina's G-spot in a way that caused the blonde's back to arch. "Faster, baby," Regina moaned out to the best of her ability as (Y/n) sped up to Regina's liking. "Just like that, you're fucking perfect." Regina could already feel herself close to her climax as (Y/n) made love to her. This was unlike any sex she had ever experienced before. She felt her leg shaking as (Y/n) drew her closer. Announcing her climax, she felt herself cum over (Y/n)'s fingers. Her hand gripped the arm that kept (Y/n) upright as she cried out in pleasure as (Y/n) continued to help her ride out her high.

Regina counted herself lucky as (Y/n) felt like this wasn't enough. She needed to make Regina cum again. Kissing down the rest of Regina's body, she found her face between the girl's thighs. Regina's head fell back as (Y/n) sucked her clit. She was already sensitive, so she knew it wasn't going to take (Y/n) long to make her cum again. "Fuck, you're doing great, please don't stop." Regina wasn't someone to say 'please' unless she wanted something. And that something was for (Y/n) to continue to fuck her until she saw stars. Which, she was very close to as she felt herself grow closer once more. "I'm going to cum, baby." She got out, and (Y/n) continued. As Regina came, (Y/n) made sure to clean her all up. Which, to Regina, was the hottest thing that had ever happened to her. Which said a lot about (Y/n)'s skills, in the long run.

"Come ride my thigh, baby. I want to help you cum, too." Regina had remembered from a discussion they had during one of their late-night deep dives that (Y/n) was someone who enjoyed thigh riding. (Y/n) kissed her, Regina receiving a taste of herself as (Y/n) straddled Regina's hips. "Perfect, baby, just like that. Mommy will help you."

(Y/n) smiled down at Regina as her hands took hold of (Y/n)'s breasts, pinching and twisting at the nipples delicately. (Y/n) moaned at Regina's actions, her hips moving back and forward. "You feel so good, Regina." She said, pleasure warming up her entire body. She moaned as Regina instructed her to continue. She listened to whatever Regina told her to do as she felt herself getting closer to her orgasm. "I'm going to cum, Mommy." She said in between moans. Regina smirked at this, her hands falling to (Y/n)'s hips gently.

"Cum for me," Regina's tone in her voice brought (Y/n) to her orgasm as she rocked on Regina's thigh to ride it out. "That's it, baby. Keep going for as long as you need. You did so good."

(Y/n) finished before laying next to Regina, both girls in a moment of bliss. They were seeing stars as their fingers found each other, intertwining under the sheets that (Y/n) pulled over them after a chill made its way through the air. The two found themselves there for a long moment before pulling each other close and holding each other's clammy bodies together. Neither minded as they smiled to themselves, Regina's head tucked under (Y/n)'s chin. Their cuddles became their version of aftercare. The two didn't mean to, but they ended up falling asleep like that, not caring about their clothes still piled on the floor.

[braveclementine]

Chapter 20

Warnings: 18+readers only, pet names

Copyright: I do not own any Marvel characters or locations. However, I do own my OCs: Elizabeth Silvertongue and Clementine Greenleaf. I also own Clementines' brother Donavan. The following OCs are owned by other Wattpad writers as this is a collaboration project. Their OCs are on the face claim page. I do not condone any copying of this.

"Elizabeth!" 

"Go away." I called over my shoulder, striding towards my Biology class. 

"No, c'mon, Elizabeth!" Donavan dodged through students, trying to get to my side. "I just want to talk-" 

I turned down a hallway to hopefully lose him as the students streamed past us. But Donavan managed to catch a break in the flow, quickly catching up to my side. 

"Leave me alone Donavan." I grouched. 

"Elizabeth, please, it's not about me." Donavan said, sounding desperate. He reached for my arm and I jerked away, before coming to a stop. He paused, looking thankful. 

"What?" I asked harshly. 

"My mom wants to know if you are joining Clem on coming home for Thanksgiving." He said in a rushed breath. 

It took me a second to digest his words and then asked, "Clementine is going home for Thanksgiving break?" 

"Yes." Donavan answered, seeming pleased that we were having a civil conversation. "I thought she would talk to you about it, but then mom called and said that she hadn't heard if you were coming and asked me to ask you or Clem if you were coming. I haven't seen Clem all day so when I saw you-" 

"I don't think so. I had only planned on coming home for Christmas." I answered. 

"Miss Silvertongue?" Professor Banner's voice said. I turned to see the biology Professor standing there, holding a textbook under his arm. "You're going to be late for class if you don't hurry up." 

"Of course, Professor." I said quickly, looking at Donavan once more. "No, I'm not. Tell your mom I said sorry." 

I turned and walked away, heading into the classroom to sit down. I was fuming with Clementine. Why would she keep putting herself in such a position to get hurt? Why go back home for Thanksgiving- without telling me- where she would just be around her brother more? 

I hesitated before pulling out my phone. 

: Can we talk? 

Clementine texted back fairly quickly. 

: When? Sort've busy

I stared at the text message. Clementine had never been to busy to talk to me. I felt my stomach turn uncomfortably just as Professor Banner came into the room. He glanced at me, but didn't say or do anything. I wondered if he had texted Bucky or Steve to let them know Donavan was around or if he had minded his own business. 

I didn't answer Clementine, putting my phone away as we started on chapter twelve: Diversity of Life. 

Dr. Banner pulled up a picture of a bee on a flower and started to speak, "This bee and the Echinacea flower could no look more different, yet they are related, as are all living organisms on Earth and the planets beyond. All life on Earth evolved from a common ancestor. Other planets, while we don't have the exact specifics, are most likely the same, though we may learn differently in time." 

He went onto the next slide, which showed a diagram of some sort with three main categories: Bacteria, Archaea, and Eukarya in different colours. Words and lines connected the three of them together in many different ways. 

"Notice that from a single point, the three domains of Archaea, Bacteria, and Eukarya diverge and then branch repeatedly." He pointed along the diagram. "The small branch that plants and animals occupy in this diagram shows how recently these groups had their origin compared with other groups." 

I felt my phone buzz in my pocket, reminding me of how I hadn't turned my phone off before class. Dr. Banner had continued onto the next slide so I pulled my phone out, seeing that it was from an unknown number. 

: When is it bad luck to see a black cat? 

I turned the phone off, figuring it was a wrong number, looking up at the screen. Goosebumps broke out on my arms for no apparent reason, other than at the moment, a black cat was on the slideshow. But, as Dr. Banner went onto the next slide, I assumed it to be a coincidence. 

"There are several kingdoms, six to be exact. Anyone tell me what some of them are?" 

I raised my hand. "Class, Order, Family, and Species." 

"Nicely done. And the last two anyone?" 

"Phylum and genus!" One of the girls at the front called out. 

"Great." Dr. Banner smiled shyly as he always did. "Now, for example, we take a look at this chart." 

It was looked like a step pyramid, with each new step adding another animal. 

"So we start with the subspecies, the Canis lupus familiaris also known as the common, domestic dog." Dr. Banner said, pointing to the top of the pyramid. "And at the next level we have the Species: Canus lupus which can add the wolf in. At each sublevel in the taxonomic classification system, organisms become more similar. Dogs and wolves are the same species because they can breed and produce viable offspring, but they are different enough to be classified as different subspecies." 

He pointed to the last level. "As we can see, dogs and plants don't have anything in common until the Domain: Eukarya." 

He then proceeded to put on a PBS video about taxonomy on, which I sort've glazed through, my mind occupied with the strange text I had gotten. It wasn't until the lights were coming back on that I snapped back to reality to hear Dr. Banner already discussing the homework. 

"Using the textbook, you will be creating your own phylogenetic tree diagram. You can start with any species, plant or animal, though obviously you may not use the one from the example, nor can you use any of the animals from the example. It must be original. Also, you need to finish reading Chapter twelve since we didn't get through the entire chapter. I will see all of you after Thanksgiving break." 

Students left with many 'Happy Thanksgivings'. I was planning on being one of them until Dr. Banner said, "I reckon I'll see you on Thanksgiving, Miss Silvertongue." 

"Oh?" I questioned, feeling startled. "Why?" 

"Well, perhaps I'm being presumptuous." He was immediately flustered, cheeks red. "My apologies." 

I left, feeling more startled than before, turning my phone back on. I got two buzzes. I checked on Clementines' first, despite my interest in the second, anonymous text. 

: Where u want 2 meet? 

To which I quickly texted back 

: I mean, we have the same class in thirty minutes or so. . . vending machines? 

: Ight, I'll b there in 10

I started making my way towards the Psychology classroom, while also opening the other text. 

: When you're a mouse

Another text popped up immediately after opening the first. 

: Run, prey, run

The adrenaline that spiked through my was incredible. I checked my surroundings for familiar faces first. Finding none, I scanned for unsettling or people that gave me a bad feeling. Finding none, I hurried towards the vending machines. 

Hurrying turned into running before I even realized I was moving that quickly. I raced down the hallway, weaving in and out of students without care, hearing them mutter darkly behind me. 

Clementine was not at the vending machines, but I hadn't quite expected her to, knowing that it hadn't even been two minutes since we said we were going to meet. 

I called her right then and there, looking around as the phone dial droned in my ear. 

"Yeah?" Clementine's voice said in my ear. 

"Clem, don't come to the vending machines." I rushed out, looking down one of the hallways. Students flowed through it like cockroaches, which was good if I needed a crowd to escape into. "Get to Sam. Don't let anyone stop you until you get to Sam, do you understand me?" 

"What happened? What's wrong?" 

I saw them. "Go." was all I whispered before hanging up on her, dialing Bucky without thinking, before turning tail and running away from them. 

They looked like students, but too casual. The kind of students that were students in a movie, not real life. The kind of students that were the main characters so they were wearing smart sweaters and downturned collars and dress pants. Like they were portraying a college scene without ever having stepped foot on a college campus. 

Bucky's phone wasn't answered- not a surprise; he was in class and rarely checked his phone during this time. Steve was next, who also did not pick up. I alternated between calling the two of them as I ran, feeling more and more desperate each time they didn't pick up. 

The hallway was empty now. Most of the classes had started, except for a few that started in fifteen minutes- like my Psychology class. I wondered if I could survive long enough to make it to my next class and learn about conformity and obedience. 

"Hey!" A voice called out. It was light, accented, friendly sounding. I looked long enough to see an extremely tall, very handsome and thin man standing there, holding papers. He was wearing a black button up shirt, sleeves rolled up to his elbows. His tie was green, though slightly loose, the shirt tucked into black jeans. His hair was gelled back and he had brilliant blue eyes. If I wasn't so in love with Steve and Bucky, I might have given him a second look. 

Instead, not knowing who he was- though at a guess he might've been a teacher- I wheeled away from him, darting down the next hallway. I called Bucky again. 

I heard feet pounding behind me, making me sprint faster, but clearly not fast enough, for even as I turned the corner, strong arms wrapped around me, pulling me into a small, dark room. 

"Elizabeth?" Bucky's voice finally answered the phone, worry evident in in his voice. A hand clamped down on mine, which I struggled against as the other hand plucked the phone out of mine. 

"She's with me Barnes." The voice was now Lokis', and I turned my head to see the God of Mischief there. He lowered his hand from my mouth, putting a finger to his lips to tell me to stay quiet. 

"Why?" Bucky demanded. 

"Because she was sprinting through the school like a mad woman and I figured if she was in trouble, I might as well intervene." Loki hissed back. 

We both stiffened suddenly as we heard voices outside of the door, "Go that way, she can't have gone far. Start checking the rooms!" 

Loki immediately let out a green mist which highlighted the back of the door. It shuddered in its frame as someone tried the handle, but held. 

"Someone is looking for her." Loki whispered. "Do you want me to get her to Sams'?" 

"What do you mean someone is looking for her? Where? Who?" Bucky demanded angrily. 

"This door won't give way!" One of the men shouted. 

"In the school." Loki hissed through his teeth. "They are outside this door right now so I need to know if you want me to fight through or get her to Sams'." 

"Get her to Sams, now." Bucky ordered. 

Loki didn't even bother saying anything else, hanging up on Buck, and wrapping both arms around me. I closed my eyes as the banging increased, Loki doing what I thought could accurately be described as a 'poofing' motion, and suddenly we were standing in the kitchen of Sams' house. 

We apparently were not the only ones there, for Dr. Banner and Professor Stark were in the kitchen. Neither of them had noticed us, probably because they were lip locked over the counter. 

Loki cleared his throat, making the men jump, jerking away from each other. 

"What mischief?" Tony asked, exasperated, while Dr. Banner quickly turned to the stove where the grilled cheese was cooking. 

"Oh just bad guys in the school, nothing more." Loki rolled his eyes. He teleported away in a puff of green. I wondered  slightly how Dr. Banner had gotten here so quickly when the house was so far from the school. 

I felt my phone ding and hesitated before pulling it out. 

: You got lucky this time. Watch your back little mouse, the cat is always out to play 

The door slammed open and I jumped. Tony and Bruce whirled around, the Iron man suit coming out around Tony while Dr. Banner surprisingly grabbed the knife he'd been cutting the bread with. 

But it was just Bucky, who made a beeline straight for me, pulling me into his arms without even looking at the others. "Stephen portaled me here. Are you alright? Are you hurt? Did you-" 

"I'm fine." I said softly. Despite my previous panic, it was obvious that he was even more panicked, the fear painfully obvious in his eyes. "Are you? Where's Steve?" 

"He's hunting them down in the school with Nat and Clint." Bucky responded. "Loki will probably help them out." 

He led me over to the couch and soon after, a cup of hot chocolate was put in my hands by Dr. Banner. 

It took them an hour, before Steve came through the door. He wasn't wearing his Captain America uniform, although he had a circular shaped bag that had his shield in it, which he put down by the side of the couch as he came over. 

"Are you alright?" He asked, cupping my face, tilting my head up. He had that same worried, panicked look Bucky had had at first, when he'd come through the door. 

"Yes, I'm fine." I whispered, touching his hand gently. "I'm alright Steve, I promise." 

"Who were they?" He immediately turned on Tony, looking at the man like he should have all of the answers. 

"I don't know Rogers. Bruce and I flew up here immediately after the bell rang." Tony sighed. "F.R.I.D.A.Y. didn't tell me there were any intruders either." 

"Well what good is an AI if it can't keep the students safe from danger?" Bucky snarled. 

"Watch it tinman." Tony glared right back at him, an angry edge in his voice. 

"Okay, whoa, hold on." I quickly stood up, putting a hand against Bucky's chest, which was heaving up and down heavily. He was furious, but I didn't think it was fair to be angry with Tony. "First off, I am fine. Okay? F-I-N-E fine. Secondly, it is not Tonys' fault if the AI couldn't pick up these bad guys. AI is not perfect, even one created by Tony Stark. And, thirdly, can we not get angry at each other? You guys are like family, right?" 

The room was silent for a second, with Steve conceding first as he sat back down on the couch with a heavy sigh, muttering a 'sorry' to the room. Bucky on the other hand, continued his staring contest with Tony until I pushed against his chest a little, giving him a warning look. Bucky sat down with a huff and nothing more. 

"Right." I said, looking at the rest of them. "So what do we do now?" 

"You, are staying here." Bucky answered immediately, straightening up, his hand on my leg. 

"Is that alright with Sam?" I asked with a slight frown. 

"It's fine." Sam said, walking through the door. Clementine was with him thankfully, along with another tall black man that I had never seen before. He had braces around each of his legs, with small red glowy lights on them. "Although Heimdall is supposed to be coming home tonight." 

"Good, maybe he'll have some insight." Bucky said stressfully. 

Loki materialized back in the living room, his head tilted to the side, "Heimdall's coming?" 

"Only with us." Sam said with a smirk which made Loki frown. 

"How uncouth." Loki retorted. 

Steve sighed, pulling me into his lap to hug me, startling me as I had been observing the rest of the Professors behavior. "You okay Princess? I'm sure you had a scare." 

"It was." I admitted quietly as the others started to chat quite loudly. Whoever this Heimdall person was, he seemed to be quite popular amongst the others. "I didn't know what to do. If it was safe to call you or where to run. I didn't know if our house was safe or if I should try to just drive or something. . . what?" I asked as I saw his eyes brighten. 

"Sorry." Steve cleared his throat. "It's just. . . you called it 'our' house." 

I stared at him for a second before turning pink. "Oh, I'm sorry-" 

"No!" Steve said quickly. "No I. . . I liked hearing you say that." He murmured the last part so softly I strained to hear it. 

I blushed, saying nothing more, simply snuggling into him. Bucky just smiled and looked out the window. 

Suddenly, there was a flash of brilliant light that made me flinch, shielding my face with my hands. Steve's hands were tight on my body and comforting as the light finally died away. 

"He's here!" The man who I hadn't been introduced to yet said, his chocolate brown eyes lighting up. 

"No shit Rhodes." Tony rolled his eyes. "I think I just went blind." 

Rhodes- as Tony called him- flipped Tony the bird. 

Another African American man stepped inside the house, smiling gently at Sam and 'Rhodes'. The first thing I noticed was that his eyes were amber gold, and that they were glowing. They were. . . actually sort of beautiful. I then took in his rugged appearance, his unattended dreadlocks and beard. He also looked like he was wearing old traveling garments. He also, had a large sword strapped to his back. 

Heimdall smiled at the others, but turned to face me instead, or well, more Steve. "Change in plans I see. Miss Silvertongue will have to move into the Avengers tower." 

"Whoa hold on-" Tony started. 

"It is not up for discussion." Heimdall said gravely. "It is a matter, of life, or death."

[bongo-clash]

Ectobiology: Ectoplasmic Anatomy of Ghosts & Halfas!!!

Okay, I mentioned in my post about ghost taxonomy a couple things about ectoplasm that helped with the different category sections, and I thought it’d be nice to go over that stuff plus some other ideas in more detail!!! Please don’t mind too much if the science is a little wonky, because I love this kind of thing but I am not a STEM guy, and my only resource is questionable websites and my own brain!!! Anyway, let’s get into some of it!!!!

(Everything under cut!!! :D) 

Before I start, I want to make a point of saying that I’m only talking about Ghost Ectoplasm™ specifically and not ectoplasm as a whole (i.e., atmospheric/ambient ectoplasm), and while I might mention it in a section or two in terms of how it interacts with Ghost Ectoplasm™, I won’t go into too many details on the stuff itself (Might do a smaller thing for that though too, if I ever get in the mood for ectochemistry I guess!!!)!! (I also mentioned mediums in my taxonomy post, but we’re ignoring them for now because this stuff doesn’t really apply to them!!! This is exclusively ghost and halfa stuff!!!)

But, now that that’s out of the way, here we go!!!!

-

Section 1: Ectoplasm’s Prokaryoticism

I’ll start with one of the things that came up in my taxonomy post- specifically to do with why ghosts that were alive at some point are classified as post-eukarya, which definitely raises questions to what they’re like now. Let’s talk about that!!

Post-eukaryotic kind of implies they’re now prokaryotic, meaning they lack a nucleus/membrane bound organelles. In the Domain category of taxonomy (the normal not-ghost one lmao!!), there are two other sections other than eukarya, which are bacteria and archaea. I bring these up because they kind of serve as a base to understand ectoplasm with!!! Post-eukarya ghosts’ ectoplasmic structure more closely resembles organisms labelled bacteria, whereas natural ghosts’ more closely resembles archaea. I wanted to make this distinction because it makes sense given their different niches:

(From the three-domain system wikipedia page)

‘Bacteria tend to be the most prolific reproducers, at least in moderate environments. Archaeans tend to adapt quickly to extreme environments, such as high temperatures, high acids, high sulfur, etc. This includes adapting to use a wide variety of food sources. Eukaryotes are the most flexible with regard to forming cooperative colonies, such as in multi-cellular organisms, including humans.’

An archaean-like structure makes a lot of sense for natural ghosts because of its ability to thrive in extreme conditions, since the Ghost Zone definitely counts as an extreme environment (for non-ectoplasmic entities at least). Bacteria-like qualities, on the other hand, make more sense for post-eukarya ghosts due to them being more likely go into the human world, and thus needing to be much more prolific cell-reproducers and restorers, having to be more ‘self-sufficient’ in that sense as a result of there being a lesser supply of ectoplasm to draw from. 

So I feel like I should mention now that I’m not thinking of ghosts as single-celled organisms here, even though that’s how prokaryotic organisms usually are because!!! They’re not always!!! It’s been a least a little bit evidenced that certain bacterial species can aggregate together, which is what multicellular organisms do, and even though there’s a big debate about whether or not we can really call them multicellular, I’ve made the elective decision that we can for ectoplasm!!!! Because they have at least some adhesion even if they’re pretty easily and harmlessly separated (which we can see in most ghost fights), and because the cells can clearly communicate seeing as they all move as part of a body!!!!

Anyway, back to more structure stuff, I’m gonna focus on post-eukarya ghosts just because (though a lot of this could be applied vaguely to natural ghosts too) we’re gonna look into a more specific part of it now to do with the subsistence category- which if you didn’t read the taxonomy post, is basically how ghosts ‘get’ their energy- either by naturally absorbing the ambient ectoplasm in the atmosphere or by having to actively consume energy through any one of various methods. 

I mentioned before that post-eukaryotic ghosts are more ‘bacteria-like’. But there’s also a further distinction in the ectoplasmic structure of ambient and active ghosts!!!! There’s a type of bacteria called cyanobacteria (also known as blue-green algae) which can perform photosynthesis thanks to them containing internal membranes unlike heterotrophic prokaryotes (that can’t produce their own ‘food’), as well as photosynthetic pigments. Ambient ghosts function in a similar way to this, able to absorb the energy from atmospheric ectoplasm rather than having to actively consume anything- also why most post-eukaryotic ghosts are ambient!!! It’s advantageous when taking into consideration the lesser ectoplasm supply in the human world; if they’re constantly, automatically ‘recharging’, then it’s easier to quickly recover from damage (though we’ll get onto the specifics of that later)!!!

However!!! Active post-eukaryotic ghosts also exist (like Spectra!!), so their structure is a little different!!! Their structure can vary more wildly than an ambient’s can, but the more common structural resemblance is to the bacteria Actinomycetota, which can have a kind of symbiotic relationship with their surroundings. 

I think it’d be good to have an example for this, so Spectra’s ability is probably an easier way to look at it!!! Some kinds of Actinomycetota help out in ecosystems by converting nitrogen in the air into ammonia for plants, and in ‘return’ gain access to some of those plants’ saccharides. Spectra’s ability works in a similar way, even though the symbiotic nature isn’t mutually beneficial. She induces mood alteration (of the negative kind), and uses that to kind of ‘gain access’ to a target’s energy!!!! But not all active ghosts function this way- some can be beneficial like the kind of Actinomycetota mentioned before, and some are less symbiotic and just stay in the zone to ‘feed’ off its natural supply!!!!

Okay I’m gonna be honest my eyes are blurring looking at all this stuff about prokaryoticism so we’re gonna move on to a new section now for the sake of my brain staying not-melted!!!!!

-

Section 2: Anaerobic Classifications

Just to make sure I’ve got a definition down before we get into it, aerobic and anaerobic respiration basically refers to whether or not an organism respires with oxygen/uses oxygen for growth or not- aerobic is when it uses oxygen, anaerobic is when it doesn’t!!!

Ghosts are anaerobic!!!! The GZ doesn’t naturally contain breathable/sufficient levels of oxygen (although it can be found in higher contents in areas with a higher population of post-eukaryotic ghosts and portals!!), so it makes sense that they don’t actually have a need for it, however!! There are actually different classifications of anaerobe, and a ghost can fall into almost any one of those categories!!!! There is a little bit of debate about the accuracy of these categories as classifications, but rn we’re just going to ignore that because they work well enough for ghosts!!! 

Anyway- there are three categories of anaerobes!!! They’re pretty easy to understand, so I’m just gonna put down what the Wikipedia page says!!! :

Obligate anaerobes, which are harmed by the presence of oxygen. Two examples of obligate anaerobes are Clostridium botulinum and the bacteria which live near hydrothermal vents on the deep-sea ocean floor.

Aerotolerant organisms, which cannot use oxygen for growth, but tolerate its presence.

Facultative anaerobes, which can grow without oxygen but use oxygen if it is present.

So, which ghosts fit what definition?? Well, no ghosts are actually facultative except halfas in their human form!!! Or, well, on the whole they’re kind of a weird mix of a microaerophile (which is fully aerobic but higher concentrations of oxygen are poisonous) but also maybe slightly facultative, which I know sounds weird but halfas are just super weird either way [and we’ll get into some of that weirdness more in the fourth section lmao]!! Mediums are full microaerophiles but I haven’t talked about them properly yet so we’ll leave them for another day!!!!

Moving on, the majority of natural ghosts are actually fully obligate with a couple of noteworthy exceptions like Clockwork, Undergrowth, Nocturn, and some others!!!! I know you might be thinking if you read the taxonomy post- ‘why is this not a section in the taxonomic classification system??’ And my answer to this is!!! Because if a ghost isn’t fully obligate, it can get pretty complicated. I say fully obligate because, in reality, all ghosts are obligate in a weird way, but some- namely, post-eukaryotic ghosts- have adaptations to help with this!!!!

I’m going to say the adaptation is kind of like. A protective layer of sorts??? They have a kind of ‘outermost layer’ of aerotolerant ectoplasm to protect everything underneath from coming into contact with oxygen, and it also works as a filter system for ambient ghosts so that the ectoplasm absorbed from the atmosphere is pure and any oxygen it might have reacted with is separated and left behind!!! It’s pretty quick to cover over again when a ghost is hit unless the damage is serious- I guess you could compare it to potassium metal!!! If you’ve ever seen a video of someone messing around with potassium metal, it’s got this kind of dirty-looking layer over it, and if you cut it the inside’ll go bright at first but it tarnishes super quickly, and it’ll soon look the same as the other uncut parts of the outer layer!!! 

Speaking of which, this is a pretty good way to bring in how ecto-weapons work and why they hurt ghosts beyond just the force of the shot!!! Like I mentioned before (and Might get into more sometime in another post), atmospheric ectoplasm will react with oxygen!!!! This is important because that’s the stuff that ecto-weapons use; it’s not pure ectoplasm because you can’t find that naturally outside the GZ!!!

So, if the stuff is shot at a ghost through something like an ecto-gun, because it’s obviously forceful and makes contact at a high-speed, it can damage and even break through that aerotolerant layer and get oxygen into their system, which really isn’t good!!!! If the damage is just surface-layer/superficial, it can be recovered from pretty quickly (thinking back to the potassium analogy!!), but if the damage is more serious and that oxygen- even reacted with ectoplasm- manages to really get into a ghost’s anatomy, preventative measures need to be taken in order to ensure that it doesn’t reach the ghost’s core/the rest of their body, and this is where the next section comes into play!!!!

-

(TW: There's some pretty bad injury/medical talk in these next sections (Section 4 especially), so please be mindful!!!!)

-

Section 3: Programmed Cell Death

Okay when I said I was done talking about prokaryoticism I actually meant I was done talking about cyanobacteria and actinomycetota similarities. Prokaryotic organisms like bacteria don’t really have ‘immune systems’ in the same way most eukaryotic organisms do, so they sometimes can’t fight off things like infection if the infection isn’t manageable from the get-go. Instead, they initiate a form of ‘programmed cell death’ in order to prevent the pathogen from reproducing!!! And now here’s how that’s relevant to ghost injury!!!!

So!!! Long story short, if a ghost gets oxygen into their ‘inner system’ thanks to something like an ecto-gun, the area the injury originates at literally just dies off, and separates from the body before it can spread to other parts. For example, if a ghost was hit in the arm badly, that arm can literally just fall off and grow back like a lizard tail!!! This can be done with pretty much any part of a ghost’s body- the only aspect of a ghost that’s actually genuinely problematic to injure is the core, because most ghosts- provided they’re not already low-energy- can just regrow everything else, though they may need to head back to the GZ for the higher ectoplasm quantity if the loss is severe enough!!!!

Really short section, I know, however!!! There is a complication to this stuff, and this is where we get into the difficult bit!!!!

-

Section 4: Halfas

The problem with halfas is that they’re not totally ghosts or totally humans no matter which form they’re in, and this can cause a lot of complications when it comes to stuff like injuries- but first, we’re going to go into integration. 

Ghosts are prokaryotic. Humans are eukaryotic. Halfas are…???????? Kind of both kind of neither????? There’s this one thing called a Parakaryon that we can’t classify as either eukaryotic or prokaryotic because it’s so weird, and it’s kind of like that, in that their cells have aspects unique to both types. This is probably a result of all their ghost stuff and all their human stuff trying to combine/integrate into one thing, and ending up as something almost entirely different in the process. This also means that their structures in both ghost and human form are weird, because halfas at least somewhat need organs, which ghosts don’t (other than a core if you count that as an organ), and they also need ectoplasm, which humans don’t. 

Because of all this weirdness, there can be a lot of potential issues with a halfa getting injured, because humans can’t and don’t defend against harm in the same way ghosts do, and vice versa. While ghosts can just get rid of something and grow it back, that’s not a natural option at all for humans, and while humans can fight against infection in an injury thanks to their white blood cells, ghosts don’t have that in the same way. So what does that mean for a halfa?????

What I’m thinking is that, for most non-lethal but slightly beyond superficial injuries (slashes, broken bones, burns, etc.), they’re able to defend against them in a human way, since they still have a human-immune system. So, for injuries like that, especially if it’s caused by an ecto-weapon, it’s weirdly enough best to deal with those in human form, since they can be pretty easily recovered from and it’d really suck for your finger to just. Fall off because you hurt it pretty bad and stayed in ghost-form for too long so your ghost-recovery-system kicked in before your human one did. I’m almost completely sure it’d grow back, but that’d still cause a lot of problems, since you wouldn’t have a finger. 

However, major injuries are a bit more… difficult. Because at this point your ghost-recovery-system would be kicking in regardless of what form you’re in. It’d want to activate programmed cell death and separate from the body, but human bodies just don’t do it the way ghosts do, and it’d be fighting to keep all your everything attached because separating could make it a lot worse. So major injuries aren’t just problematic because they’re major, but also because they present a whole new issue: necrosis. 

Basically, the ghost stuff wants the whole injured section totally separate from the body, so when the human stuff doesn’t let that happen, it does what it thinks the next best thing is: having the cells sort of ‘spew their guts’ as like, a really weird and warped form of ‘separation’. The cell membrane ruptures and releases the contents of the cell, but because it’s such an uncontrolled release into a space outside the cells, it causes an inflammatory response in the surrounding tissue. This then gets the attention of the human white blood cells to get rid of the dead cells, which is all well and good, except that some kinds of white blood cells (leukocytes) release a microbial-damaging substance that ends up causing more damage in that inflamed surrounding tissue. That all ends up inhibiting the healing process, so the decomposing surrounding tissue and the dead cells can just build up around and cause even more issues (Like, gangrene in particularly nasty cases, which. Ah. Eugh.). 

If it doesn’t heal on its own and does just build up, the only real way of getting anything better is to surgically remove the necrotic tissue. Thankfully, despite all the horrific stuff I’ve just said about halfas’ injury-response systems, they do actually have an accelerated healing factor thanks to the extra energy source (ectoplasm), so it doesn’t tend to get to this point in the first place. This is just what happens if that rapid-response system decides that the only way to solve the problem is to try and totally get rid of the problem, which I guess is just one of the downfalls of being someone made up of a combination of things that shouldn’t really exist together. A double-edged sword of sorts!!!

-

Maybe not the lightest note to end on, but either way, that’s all I’ve really got the energy to give you right now!!! This ended up even longer than my taxonomy post, but if you have any questions, feel free to ask because I love talking to people!!! I might add onto this at some point with another post- mainly because there’s some very brief stuff about atmospheric/ambient ectoplasm that I kind of want to cover (which, like I said at the beginning is more ectochemistry anyway, and I might do a separate post for that too)- but for now, that’s it!!!!! Hope you’re all having a good day!!! :D

[fatehbaz]

It is spring in Houston, which means that each day the temperature rises and so does the humidity. The dampness has darkened the flower bed, and from the black mulch has emerged what looks like a pile of snotty scrambled eggs [...]. I recognize this curious specimen as the aethalial state of Fuligo septica, more commonly known as “dog vomit slime mold.” Despite its name, it’s not actually a mold -- not any type of fungus at all -- but rather a myxomycete (pronounced MIX-oh-my-seat), a small, understudied class of creatures that occasionally appear in yards and gardens as strange, Technicolor blobs. Like fungi, myxomycetes begin their lives as spores, but when a myxomycete spore germinates and cracks open, a microscopic amoeba slithers out. [...] When the amoeba encounters another amoeba with whom it is genetically compatible, the two fuse, joining chromosomes and nuclei [...], growing ever larger, until at the end of its life, it transforms into an aethalia, a “fruiting body” that might be spongelike in some species, or like a hardened calcium deposit in others, or, as with Stemonitis axifera, grows into hundreds of delicate rust-colored stalks. [...]

These creatures exist on every continent and almost everywhere people have looked for them: from Antarctica, where Calomyxa metallica forms iridescent beads, to the Sonoran Desert, where Didymium eremophilum clings to the skeletons of decaying saguaro cacti [...]. Throughout their lives, myxomycetes only ever exist as a single cell, inside which the cytoplasm always flows -- out to its extremities, back to the center. When it encounters something it likes, such as oatmeal, the cytoplasm pulsates more quickly. If it finds something it dislikes, like salt, quinine, bright light, cold, or caffeine, it pulsates more slowly [...]. It can solve mazes in pursuit of a single oat flake, and later, can recall the path it took to reach it. [...]

How do you classify a creature such as this?

In the ninth century, Chinese scholar Twang Ching-Shih referred to a pale yellow substance that grows in damp, shady conditions as kwei hi, literally “demon droppings.” In European folklore, slime mold is depicted as the work of witches, trolls, and demons -- a curse sent from a neighbor to spoil the butter and milk. In Carl Linnaeus’s Species Plantarum -- a book that aspires to list every species of plant known at the time (nearly seven thousand by the 1753 edition) -- he names only seven species of slime molds. Among those seven we recognize Fuligo in the species he calls Mucor septicus (“rotting mucus”), which he classifies, incorrectly, as a type of fungus. [...]

These “ladders” or “scales of ascent,” in turn, inspired the “Great Chain of Being” -- the [...] worldview central to European thought from the end of the Roman Empire through the Middle Ages, that ordered all of creation from lowest to highest [...]. Over time, Linnaeus revised his classifications of Homo sapiens, naming “varieties” that at first corresponded to what he saw as the four geographic corners of the planet, but which became hierarchical, assigned different intellectual and moral value based on phenotypes and physical attributes. The idea that humans could and should be ordered -- that some were superior to others, that this superiority had a physical as well as social component -- was deeply embedded in many previous schema. But Linnaeus’s taxonomy, unlike the systems that came before, gave these prejudices the appearance of objectivity, of being backed by scientific proof. When Darwin’s On the Origin of Species was published in 1859, it was on the foundation of this “science,” which had taught white Europeans to reject the idea of evolution unless it crowned them in glory.

But the history of taxonomic classification has always been about establishing hierarchy [...].

I did not learn until college about a taxonomic category that superseded kingdom, proposed in the 1970s by biologists Carl Woese and George Fox and based on genetic sequencing, that divided life into three domains: Bacteria, Eukarya, and Archaea, a recently discovered single-celled organism that has survived in geysers and swamps and hydrothermal vents at the bottom of the ocean for billions of years. 

Perhaps a limit of our so-called intelligence is that we cannot fathom ourselves in the context of time at this scale, and that so many of us fail, so consistently, to marvel at any lives but our own. [...]

A few years ago, near a rural village in Myanmar, miners came across a piece of amber containing a fossilized Stemonitis slime mold dating from the mid-Cretaceous period. Scientists were thrilled by the discovery, because few slime mold fossils exist, and noted that the 100-million-year-old Stemonitis looks indistinguishable from the one oozing around forests today. [...]

One special ability of slime molds that supports this possibility is their capacity for cryptobiosis: the process of exchanging all the water in one’s body for sugars, allowing a creature to enter a kind of stasis for weeks, months, years, centuries, perhaps even for millennia. [...] The only other species who have this ability are the so-called “living fossils” such as tardigrades and Notostraca (commonly known as water bears and tadpole shrimp, respectively). [...]

In laboratory environments, researchers have cut Physarum polycephalum into pieces and found that it can fuse back together within two minutes. Or, each piece can go off and live separate lives, learn new things, and return later to fuse together, and in the fusing, each individual can teach the other what it knows, and can learn from it in return.

Though, in truth, “individual” is not the right word to use here, because “individuality” [...] doesn’t apply to the slime mold worldview. A single cell might look to us like a coherent whole, but that cell can divide itself into countless spores, creating countless possible cycles of amoeba to plasmodium to aethalia, which in turn will divide and repeat the cycle again. It can choose to “fruit” or not, to reproduce sexually or asexually or not at all, challenging every traditional concept of “species,” the most basic and fundamental unit of our flawed and imprecise understanding of the biological world. As a consequence, we have no way of knowing whether slime molds, as a broad class of beings, are stable or whether climate change threatens their survival, as it does our own. Without a way to count their population as a species, we can’t measure whether they are endangered or thriving. Should individuals that produce similar fruiting bodies be considered a species? What if two separate slime molds do not mate but share genetic material?

The very idea of separateness seems antithetical to slime mold existence. It has so much to teach us.

-------

Headline and all text published by: Lacy M. Johnson. “What Slime Knows.” Orion Magazine. August 2021. Photos by Alison Pollack and published alongside article.

[puppypunkrock]

i have this guy in a game i’m playing, self proclaimed “only did 7th grade science”, “never leaves his appartment”, telling me about all his awesome thoughts about science. Telling me that the 3 domains are prokaryotes, archaea and eukaryotes, and that the kingdoms came from archaea. Oh cool, but you’re wrong, let me explain it properly since we’ve already established i study this.

He’s talking about magnetic fields, i havent said anything for 5 minutes and he just keeps going.

[vagabondretired]

Boy, thought I was old....... Researchers at UCLA and the University of Wisconsin-Madison have confirmed that microscopic fossils discovered in a nearly 3.5 billion-year-old piece of rock in Western Australia are the oldest fossils ever found and indeed the earliest direct evidence of life on Earth. The study, published today in the Proceedings of the National Academy of Sciences, was led by J. William Schopf, professor of paleobiology at UCLA, and John W. Valley, professor of geoscience at the University of Wisconsin-Madison. The research relied on new technology and scientific expertise developed by researchers in the UW-Madison WiscSIMS Laboratory. The study describes 11 microbial specimens from five separate taxa, linking their morphologies to chemical signatures that are characteristic of life. Some represent now-extinct bacteria and microbes from a domain of life called Archaea, while others are similar to microbial species still found today. The findings also suggest how each may have survived on an oxygen-free planet. The microfossils—so called because they are not evident to the naked eye—were first described in the journal Science in 1993 by Schopf and his team, which identified them based largely on the fossils' unique, cylindrical and filamentous shapes. Schopf, director of UCLA's Center for the Study of Evolution and the Origin of Life, published further supporting evidence of their biological identities in 2002.

[warninggraphiccontent]

13 December 2019

The morning after...

...the fright before, in Labour's case, with their worst general election performance since 1935. I think this is the current composition of the Commons:

Expect more #dataviz from my team and me throughout the day - and weekend, and whenever a reshuffle happens...

In brief:

Last week's Inside Briefing sonification - literally, actually singing the polls - will be difficult to top. We also did this one on general election results. Helpfully, all our sonifications will be collected in this thread for as long as I remember to update it.

A reminder of last week's data reading list and list of UK government reports on data - please do add to them. And thanks to Alex for flagging this.

It's important to vote, despite widespread public apathy. A lesson Alice and I learnt this week as we tried to bring some jollity to people's Twitter timelines with the news/politics #ThemeTuneWorldCup. Catch up on what happened here - final couple of rounds here. Some of you have very strange tastes (On The Record getting knocked out that early, seriously?!). I think I only lost five followers.

Escape the election in favour of festive fun and come to the New Tottenham Singers Christmas concert tomorrow evening.

Until next week

Gavin

Today's links:

Graphic content

#GE2019: aftermath

Composition of the Commons (me for IfG)

Results (BBC News)

Britain’s 2019 general election* (The Economist)

Britain votes resoundingly for Boris Johnson* (The Economist)

Live forecasting (The Economist)

Live results: UK general election 2019* (FT)

UK election results live: Boris Johnson returned as PM after Tory majority confirmed (The Guardian)

VOTE 2019: Results Centre (Sky News)

Some Sky News visualisations (Will Jennings)

Results (Flourish)

Britain Elects/New Statesman

Share of seats: exit poll (me for IfG)

State of the parties: exit poll (Marcus for IfG)

Exit poll vs polls (Lewis for IfG)

Welcome to the Electoral Reform Society’s 2019 general election results hub. (Electoral Reform Society, via Akash)

#GE2019: The calm before the storm

Thread (me for IfG)

Singing the polls in four part harmony (Katie, Jess, Lewis and me for IfG)

Vote share since 1945 (me for IfG)

Britain’s exit poll has an exceptional record* (The Economist)

GB seats (Chris Cook)

Lies, fake news, “alternative facts” (Tortoise)

Constituency estimates (YouGov)

Final 2019 general election MRP model: small Conservative majority likely (YouGov)

Tories still set for majority but lead narrows, latest poll shows* (FT)

Media appearances by frontbenchers (Matt Chorley)

Brexit positions (Haydon and Melissa for IfG)

This chart from @TheEconomist is outstanding, so I thought I'd have a go at replicating it for every election in my lifetime (Colin Angus, via Tim)

Election results mapped: 63 seats that always back the winner* (The Times, via Sukh)

Election turnout: Britain’s most politically engaged seats revealed (The Times)

Jo Swinson has a Facebook problem (Sky News - somehow missed this)

Constituency profiles (David Kane)

British Political Atlas (Ipsos MORI)

Coalition government at Westminster (IfG)

How have gender policies landed with the electorate? (YouGov)

Facebook under fire as political ads vanish from archive* (FT)

U.K. Election Winners Will Find Reviving Economy No Easy Task* (Bloomberg)

General Election 2019: The Final Week (Deltapoll)

A #dataviz review of the UK Election Poll trackers (Andy Cotgreave)

USA

How the New Primary Calendar Changes the Contest for Democrats* (New York Times)

A SECRET HISTORY OF THE WAR* (Washington Post)

#dataviz

The Pudding Cup: The best visual and data-driven stories of 2019 (The Pudding)

10 think tanks nailing data visualisation (Cast from Clay, via Melissa. Old but interesting, even if there's an obvious omission... static viz still has its place, you know)

Everything else

The Ipsos MORI Almanac 2019

What unites us: 10 reasons why we're not a divided nation (BBC News)

MPs think personal principles should influence decision making, but the public aren’t so sure (Ipsos MORI)

Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea (Nature, via Marcus)

Mistrust and the Hunt for Spies Among Chinese Americans* (Bloomberg)

How big are the fires burning on the east coast of Australia? Interactive map (The Guardian)

Meta data

#GE2019

Exit polling explained (Department of Statistics, Warwick)

The digital election (Rowland Manthorpe)

Political ads on Facebook disappeared ahead of UK election (Politico)

General election 2019: Do social media ads work, are they fair? (BBC News)

Political parties spend more on leaflets than Facebook ads. Why? (Wired)

How to police political advertising* (The Economist)

Researchers fear 'catastrophe' as political ads 'disappear' from Facebook library (Sky News)

Wrexham Roulette (The Critic)

Why are polls from different pollsters so different? (Elections Etc)

By ignoring the digital world, the party manifestos ignore the future (Giles for IfG)

Where is the vision for our digital future? (King's Policy Institute)

#GE2019: fact checking

Online fact-checkers warn of misinformation on unprecedented scale in 2019 election (Computer Weekly)

'Do not believe a stranger on social media who disappears into the night' - An open letter from our editor to you (Yorkshire Post)

The rise of fake news as a political strategy should terrify us all (New Statesman)

The Toxins We Carry (CJR)

Why the BBC needs a social media overhaul* (New Statesman)

AI etc

The first effort to regulate AI was a spectacular failure (Fast Company)

The Second Wave of Algorithmic Accountability (Frank Pasquale, via Lewis)

AI-driven Personalization in Digital Media: Political and Societal Implications (Chatham House)

Health data

Amazon ready to cash in on free access to NHS data* (Sunday Times)

FoI and analysis (Privacy International)

The story about @amazon and the NHS is so overblown (Daniel Korski)

Patient data from GP surgeries sold to US companies (The Observer)

What happens to patient data in practice (Understanding Patient Data)

NHS data is a goldmine. It must be saved from big tech (James Meadway for The Guardian)

Health data

Inside Ring’s Quest to Become Law Enforcement’s Best Friend (Motherboard)

France Plans a Revolution to Rein in the Kings of Big Tech* (Wired)

How to take back control from the Big Tech barons* (Rana Foroohar, FT)

This Man May Be Big Tech’s Biggest Threat* (New York Times)

Openness

The Politics of Open Government Data: Understanding Organizational Responses to Pressure for More Transparency (The American Review of Public Administration, via Andrew)

Let’s ‘think different’ about procurement* (Apolitical)

Open data is needed for collaborative climate action (Open Data Charter)

Everything else

Collective Intelligence Design Playbook (beta) (Nesta)

A Manifesto for Better Government (CPI)

How to gamify government* (Apolitical)

On India's new Data Protection Bill (via Jeni)

History as a giant data set: how analysing the past could help save the future (The Guardian)

#FoI on ICO priorities (Tim Turner)

Opportunities

JOBS: Election/graphics (New York Times)

Contracts Finder - Measuring Tender and Award Publication (Cabinet Office)

Apply to our stimulus fund: Using data to improve safety in the engineering sector (ODI)

And finally...

May the force, etc

Adieu to a galaxy far, far away (The Times)

Star Wars, In One Chart (FiveThirtyEight)

Every Color Of Every Lightsaber In ‘Star Wars,’ In One Chart (FiveThirtyEight - more here)

The five best lightsaber battles in Star Wars history* (Washington Post)

Everything else

Here’s everything we learned from this election-themed tube map we just made (CityMetric, via Haydon)

Salmon... (Per Axbom, via Nick)

A Dessert Table Tutorial: Charts Named After Food (Viz Zen Data)

State-backed crypto is a contradiction* (FT Alphaville)

[sbgridconsortium]

Data Whisperer

Karolin Luger University of Colorado Boulder

Like others in her sporty college town, Karolin Luger heeds the call of the mountains she can see from her laboratory at University of Colorado Boulder. Trail running and a daily 20-mile round-trip bike commute at altitude have kept her fit, but she would like to put to rest the rumors that she runs her research collaborators ragged on strenuous hikes. “All these crazy stories,” Luger says. “I only did that once.” And lately, she says, she’s the one who has a hard time keeping up on group outings.

Her collaborators can relax, but Luger wants to see more dynamic motion in the chromosome structures she studies. After all, they have to move to do what they do. Luger’s research addresses a fundamental question: How does the human genome store information and then access that information at the appropriate time? Part of the answer, she and her collaborators have learned, goes back billions of years.

In animals, a full genome must be squeezed into the nucleus of each cell. In humans, that means six feet of DNA must fit into something less than one-fifth the size of what the human eye can see. This can happen thanks to the compact packaging of DNA into an assembly called chromatin. Chromatin consists of a long strand of tightly twisted DNA wrapped twice around repeating flat spools of histone proteins, like a string of beads. The protein-DNA spools, or nucleosomes, are the basic repeating unit of chromatin. They are further folded and arranged into a higher order structure that Luger’s lab also studies.

“Imagine a super-long sewing thread and wrap it around a million tiny hockey pucks,” Luger says. “It’s actually really a miracle that there are not knots and tangles.”

Chromatin controls access to genes in ways Luger and her colleagues are still learning. The tightly packed hockey pucks, or nucleosomes, must unspool to activate certain working genes, to duplicate DNA during cell division, or to repair damaged DNA, and then rewrap. “We’re still far away from figuring out how that works,” she says.

Complicating matters, genes can be independently activated or silenced by small chemicals that tag the histone spools or the DNA itself. Luger’s lab is trying to figure out how those small epigenetic tags affect the packaging of the hockey pucks, especially during development, as the same genetic blueprint produces such different cells—brain, heart, muscle, liver and skin, blood, bone.

Luger grew up Austria in a landscape dominated by mountains and science. Her father was an engineer, and her brothers were interested in electronics and physics. Luger was first drawn to botany and zoology. She studied microbiology at University of Innsbruck. Bleak job prospects and a rewarding undergraduate experience in a biochemistry lab inspired her to pursue a PhD in protein engineering at University of Basel, Switzerland.

Given a free hand by her mentor, she wanted to learn if a protein could fold normally if it came out of the protein-translating ribosome backwards, somewhat like a breech birth. (The answer is yes, it can.) She developed a new technique to test the idea, joining two ends of a gene together and cutting it open in a different place. The results were published in Science in 1989. Her studies with such proteins ended with her doctorate, but others have used the information in evolutionary studies to detect genes that make proteins of similar structure and function, but whose gene sequence might be permuted in this manner.

Her PhD program had required her to take classes in structural biology. To satisfy a new craving to learn crystallography, she joined the lab of Timothy Richmond at Swiss Federal Institute of Technology as a postdoctoral fellow. Her project resulted in the long-sought high-resolution structure of a nucleosome at 2.8 angstrom, published in Nature in 1997.

“I had no idea what a super-gnarly problem it was,” she says. “I learned the hard way, but it was a good learning experience.” She also learned that she had a visual brain highly suited to structural biology and developed the methodology (now used in many labs world wide) to make nucleosomes for crystallization and for biochemical and biophysical studies.

She joined the Colorado State University (CSU) faculty in 1999 and became a Howard Hughes Medical Institute investigator six years later. In 2015, she moved her lab to the University of Colorado, Boulder. Luger continues to collaborate with CSU faculty at the Institute for Genome Architecture and Function, a research consortium she and two fellow CSU women faculty members founded in 2015.

Her lab’s work has broadened from solving crystal structures to using cryo-EM, and also to asking scientific questions using structural biology as one of many tools, including live cell experiments. Luger likes to find new ways to see something that wasn’t previously observable. “I almost like the process of doing science more than the actual results,” she says. “I love the process of discovery, to figure out mechanisms and trick the system to tell me its secrets.”

She has also become more action-oriented. “We can stare endlessly at structures,” says Luger, who admits she still is blown away by the transformative power of hydrogen bonds and amino acid packing. “But we need to think about function even more. Most of the structures we study are machines and have to move. We are more and more interested in catching these machines in the act of going about their business. It’s immeasurably harder than looking at the static structure, which is already hard enough.”

Luger describes the narrative arc of her lab’s research path as a “directed random walk.” She adds, “My feelers are open all the time to see what I can learn from others. I just love collaborating with people and integrating ideas out of left field into my research program. It drives people in my lab crazy sometimes, because they are the ones that have to do the hard work.”

In one collaboration reported in Science in 2006, Luger and her colleagues examined a crucial binding point between a protein on the virus that causes Kaposi’s sarcoma and a pair of histone proteins in the nucleosome. “This was the first time it was shown how nucleosomes can serve as docking stations for other proteins,” Luger says. “As far as the virus goes, this gives its genome a nifty way to hitchhike on the host’s chromosomes to escape its defense mechanisms.”

Two years later, Luger and her collaborators used new techniques to mimic the chemical marks on tightly wound DNA-protein complexes that silence gene expression. They reported that repressive epigenetic marks on histone proteins cause nucleosome arrays to become more compacted, while activating methylation did little to the chromatin. The findings were published in Nature Structural & Molecular Biology.

Scientists have wondered about the origins of nucleosomes. Luger and her collaborators looked for answers in archaea, an extended family of ubiquitous single cell organisms thought to be the ancient precursors of eukarya. In this study, they determined the structure of nucleosomes of a species thought to be endemic to Icelandic hot springs.

“One surprising thing we have learned from our studies of archaeal chromatin is that the way DNA is bent into shape by histones is older than eukaryotes,” Luger says. “This principle is being used by an ancient domain of life, the archaea. But unlike in eukaryotes, were we have defined particles, archaea have kind of 'continuous nucleosomes' that look like a slinky. What really surprised me was how similar the organizing principle is between these two domains of life that are separated by billions of years.” The findings were reported in Science in 2017.

Above: In archaea, the histone-DNA complex can vary in the length of wrapped DNA, as shown here, while eukaryotic nucleosomes have about 2 DNA wraps each. (Images courtesy of K.Luger and CU Boulder)

Other projects include looking at how a dividing cell makes and assembles new nucleosomes for the newly replicated genome. The Luger lab is also interested in DNA repair proteins targeted by promising new anticancer drugs, seeking to learn how proteins know the DNA is damaged and then how the proteins help repair the damage. One project aims to develop an “outlandish tool” to target nucleosomes for gene editing. “It’s always fun to have at least one ‘crazy’ project,” she says. When taking on new lab members, Luger looks for new perspectives, such as enzymologists, “hard core physicists,” or cell biologists, who look at things differently. It’s one way of fighting what she considers the most dangerous threat to science in any lab: Confirmation bias, or the innate human tendency to interpret results in a way that confirms one's hypotheses, especially when results contradict each other are unexpectedly confusing. “I find myself all the time saying let’s assume the whole premise is wrong and let’s rearrange our assumptions,” Luger says. “I don’t believe results lie. It’s literally like a puzzle. A couple of pieces kind of look like they should fit but they don’t, and we have to start over again.” “That’s my mantra,” Luger says. “Problems are three-dimensional. You have to walk around and look at them from another viewpoint. You have to constantly check your premise. Even if nothing fits, people (including me) are reluctant to let it go. I keep telling my coworkers: Your results are telling you something. You have to listen. If they are confusing, it’s not the results’ fault. I really do believe the systems we’re studying are trying to communicate with us: ‘I’m right here. This is what I’m doing.’ I feel their desperation, which is mutual. Most people in lab are quite sick of hearing me say this, I am quite certain.” -Carol Cruzan Morton

[weblistposting-blog]

New Post has been published on Weblistposting

New Post has been published on https://weblistposting.com/massive-virus-discovery-sparks-debate-over-tree-of-lifestyles/

Massive virus discovery sparks debate over tree of lifestyles

Evolutionary biologists have by no means recognized what to make of viruses, arguing over their origins for many years. However, a newly found group of Giant viruses, referred to as Klosneuviruses, can be a ‘missing link’ that helps to settle the controversy — or initiate even greater discord.

In 2003, researchers suggested that they’d determined Large viruses, which they named Mimiviruses, with genes that counseled their ancestors should stay outside of a number cell1. The discovery breaks up researchers into camps. One group thinks viruses started out-outself-sufficient organisms that became trapped inner other cells, subsequently turning into parasitic and jettisoning genes they no longer needed. Any other organization views viruses as particles that snatched genetic material from host organisms overloads of hundreds of thousands of years.

A study2 published on 6 April in Technological know-how offers proof for the latter idea, that viruses are made of a patchwork of stolen parts. However, it has already sparked controversy and is not going to settle the raucous debate.

After the Mimivirus discovery, a few researchers developed an idea that put viruses close to the foundation of the evolutionary tree. They proposed that viruses comprised a ‘fourth domain’ along microorganism, eukaryotes — organisms whose cells comprise inner systems together with nuclei — and bacteria-sized organisms known as archaea.

Mimiviruses, which at 400 nanometres throughout are about half the width of an E. Coli cell and can be visible under a microscope, were particular in that they contain DNA encoding the molecules that translate RNA messages into proteins. Normal viruses make their host cells produce proteins for them.

The crew that located Mimiviruses thought the virus’ capability to make their own proteins counseled that those viral giants descended from ancient free-living cell kind that could now not exist2. “They reinitiated the controversy about the living nature of viruses, and in their courting with the ‘mobile’ international,” says evolutionary biologist Jean-Michel Claverie of Aix-Marseille University in France, a co-author of the original Mimivirus paper.

Filling the gaps The question could be resolved by means of evaluating genome sequences from viruses with the ones of their eukaryotic hosts. Mimiviruses contain too few eukaryotic-like genes to perform a statistical evaluation that could determine their evolutionary relationships. The difficulty is compounded by means of the reality that viral genomes mutate right away.

Klosneuviruses might also fill this gap. Their genomes comprise code for dozens of enzymes and different molecular equipment used in making proteins. A number of these elements have in no way been visible earlier than in any virus, including Mimiviruses. “They’re sort of this lacking link we haven’t had before,” says take a look at co-writer Tanja Woyke, a microbiologist at the Joint Genome Institute in Walnut Creek, California.

Woyke and her colleagues found the Klosneuviruses by way of twist of fate while reading how microorganism break down sewage at a remedy plant in Austria. They sequenced the genomes in their samples to perceive the organisms gift and discovered four genomes just like those of Mimiviruses.

Using state-of-the-art software to trace the evolutionary history of their thriller genomes, the researchers observed that the translation genes appeared to were picked up one at a time over hundreds of tens of millions of years. This evidence supports the concept that viruses stole elements of their genomes, they are saying. It is viable, however, that Mimiviruses and Klosneuviruses originated in distinct ways, making each thoughts on viral origins possible, says Frederik Schulz, a bioinformatician on the Joint Genome Institute and a co-author on the brand new study.

Debating domain names It’s unclear which eukaryotic organisms donated their genes to the Klassevirus organization. And because they have not recognized the host, the researchers cannot develop the virus but. The viruses do now not appear to infect the same sort of ameba as Mimivirus and other regarded Large viruses.

Claverie factors out that the majority of the Klosneuviruses’ translation machinery does no longer match that of some other known organism. And the concerns that the computational version used to deduce the viruses’ ancestry could choose up leftover pieces of DNA within the sample, probably contaminating the data. “I’m waiting to peer a real virus isolated with its host in a tube, before I would believe any of their evolutionary interpretations,” he says.

David Moreira, an evolutionary biologist at the University of Paris-South, doesn’t suppose that’s important. He says that lots of evolutionary paintings can be completed on a genome alone, and he is happy to peer more papers coming to the belief that viruses aren’t the fourth domain of life.

Mimivirus co-discover Didier Raoult, a microbiologist at Aix-Marseille College, says this trendy discovery received settle the debate, But it’s a nice locate despite the fact that. “We’re locating part of the arena that has been absolutely neglected and wants to be patient.”

The Tree of life Tapestry Artwork Captures Our Hearts Deep thoughts and the splendor of interpretation comes with the numerous meanings of The Tree of existence. To look upon the various artist’s masterpieces of their paintings that symbolize the Tree of existence it’s far charming and fun. As a result, we will have a look at the Tree of life Tapestry Art and the way it captures our hearts.

Best recognized is possibly William Morris’s model of the Tree of existence with its medieval fashion. It turned into William Morris that let his creativeness layout the paintings of Artwork that changed into at the beginning woven right into a tapestry rather than a portray.

Maximum tapestries are woven from a layout this is taken from a portray by way of Every other artist. William Morris created his layout and woven them and is a mythical guy who pushed the best-woven items into the arena as we understand them nowadays.

The Tree of lifestyles is symbolic in many cultures and is studied in Technology, faith, philosophy, mythology, and different faculties of the notion. The fundamental notion for Maximum is the Tree of life is symbolic of growth, immortality, resurrection and the promise of continuous lifestyles. The tree is the link to heaven and earth and the underworld. It is pretty magical when you think about all it represents.

The branches and leaves reach to the heavens where the truck stands strongly on earth and It’s rooted dive deep into the underworld. The Tree of lifestyles Tapestry Art appears to capture the existence and beauty surrounding our mind.

From Klimt’s Artwork Deco patterns to William Morris’s medieval stylish designs to fashionable and fanciful versions through Natasha Wescoat we discover that beauty is in the eye of the beholder. It’s fun to have a diffusion of choices and styles within the inventive interpretation for this culturally wealthy symbolic tree.

The Tree of Knowledge, The Cosmic Tree, The Acacia Tree of Saosis (Egyptian), Celtic Tree of life, and other names from different cultures all tied to the Tree of existence. They may be versions or taking a barely special slant on the which means and symbolism of this tree. This is shown inside the Tree of life Tapestry is woven from the form of artists artwork.

Color, composition, style and design all take an element in the look that seems please the owner of those inspiring and exquisite Tree of existence Tapestry wall hangings. It is best to have so many choices in relation to such a notion upsetting work-of-Artwork.

The Tree of life Tapestry is a great concept frightening piece proven in lots of unique styles. You will discover the Celtic Tapestry designed for the Tree of existence has a totally distinct appearance with its Celtic knots and colorful colorations.

[repwinpril9y0a1]

Eugene Koonin: "The New Evolutionary Biology"

Eugene Viktorovich Koonin "They should have invited Eugene Koonin," Canadian biochemist Larry Moran told me in the hallway during a break at the November Royal Society "new trends" in evolution conference in London -- somewhat exasperated by the proceedings. And I agreed. But Eugene Koonin doesn't quite see it that way, as he revealed during our recent conversation. Eugene Koonin is a consummate scientist, Leader of the Evolutionary Genomics Group at the National Center for Biotechnology Information, NIH, who sees science scandals and controversy as unproductive. He prefers the lab to the battlefield and is regarded as one of the most qualitative and prolific thinkers in science today (H-index 177; author of more than 600 scientific papers). But his numbers as a road runner are not bad either, per his Chevy Chase Turkey Chase stats. Eugene Koonin: #660 (photo by Antonio Estrada) In our interview that follows, Koonin sorts out any confusion over his recent statements about the importance of population genetics -- part of the Modern Synthesis -- and his 2009 statement: "Not to mince words the Modern Synthesis is gone." He agrees with Richard Lewontin that the term natural selection is metaphorical and goes further noting, "No one in the mainstream community now takes selection literally." And he also agrees with the Woese-Goldenfeld perspective about biology as "the new condensed matter physics," although Koonin thinks biology is still en route there. Eugene Koonin is the author of several books, among them The Logic of Chance: The Nature and Origin of Biological Evolution; and Sequence -- Evolution --Function: Computational Approaches in Comparative Genomics (with Michael Galperin). He is also founder and editor-in-chief of the journal Biology Direct. In 2002, Koonin and NCBI colleague Kira Makarova identified the genetic region now known as CRISPR-Cas. I spoke by phone with Eugene Koonin at his lab in Bethesda, Maryland. Suzan Mazur: Do you have any thoughts about the recent Royal Society meeting on new trends in evolutionary biology? Eugene Koonin: Yes. Perhaps there is a need to make some comment. I was quite unhappy reading at and around this public evolutionary meeting at the Royal Society. Frankly, I think that the less sensationalism, the less controversy brought into these discussions the better. It's really important that we try at all costs to do normal science rather than some sort of scandalous activity. I was happy about one thing, though -- that I was not there and was not directly involved. Suzan Mazur: Why is it so difficult to pull together the most compelling ideas in evolutionary biology and come up with an approximate understanding of how it all works? Michael Lynch once told me it was because reaching out to other fields is a "daunting task." But if scientists across the board won't come together to give us a coherent understanding of how it all works -- however approximate -- the public will lose confidence in the science establishment's ability to deliver. This is already beginning to happen. Would you comment? Eugene Koonin: First of all, I think the public may not have much to lose in terms of confidence in the scientific establishment in this case because the public is already extremely skeptical about the value and the scientific nature of evolutionary biology. It's not quite that way about science in general but I think largely so when it comes to the study of evolution. Much of the public is poorly informed about it, poorly understands it and is highly skeptical for various reasons. So I would frame the discussion a little differently, in the sense that evolutionary science may not be doing the best possible job to convince the public of the true importance of evolutionary biology. That said, I do believe that a coherent understanding of "how it works" is slowly but steadily emerging in evolutionary biology. However, one has to face the facts: first, it is a slow process, and we are still far from the goal; second, the emerging picture is highly complex and, furthermore, makes little sense without mathematical theory. Thus, communicating modern evolutionary biology (as opposed to deceptively simple antiquated ideas) is indeed a daunting task. Suzan Mazur: If you were organizing a public evolution summit, what discoveries in biology would you showcase? Eugene Koonin: I would try to focus on two aspects. One is genomics, and in particular, comparative genomics and metagenomics discoveries -- all this comes under the wide umbrella of genomics. That's one. The other is the existence of solid theory in evolutionary biology. I'll elaborate on both aspects. The first aspect, genomics, has in roughly the last 25 years completely transformed the ability to investigate, assess and measure evolutionary processes. All our conclusions on the course of evolution until the advent of genomics had been indirect. It's remarkable how many of these conclusions and findings remain relevant, but the fact is that all our ways to peer into the evolutionary process and evolutionary past had previously been indirect. Genomics now provides us windows into the evolutionary past by which we can compare directly the DNA and protein sequences from a rapidly widening range of organisms and thereby make solid conclusions about evolution. Suzan Mazur: Are you saying this is the top discovery in evolutionary biology in the last 50 years? Eugene Koonin: The word "discovery" may not apply quite directly here. It's a transformation of the whole science, which is based on a variety of discoveries. The very approach to evolutionary studies has changed completely. Not only the fact of evolution itself but the existence of deep evolutionary connections between different domains of life -- to be concrete -- evolutionary connections between, let us say, mammals, such as humans, and prokaryotes, bacteria and archaea, have become indisputable. These findings make questioning not only the reality of evolution but the evolutionary unity of all life on earth completely ridiculous and outside of the field of rational discourse. Then to be more specific, I would probably showcase the advances of metagenomics -- you know, the genomic revolution continues in the sense that now through metagenomics scientists are able to obtain a less and less biased picture of the diversity and evolution of life on Earth. It's becoming not so unrealistic to think about something approaching a complete picture of the evolutionary history of life. And then I would showcase something very specific. That is the latest discovery of the particular group of archaea that was the direct ancestor of eukaryotes. And in this case, "discovery" is the right word. There is a necessity to bring to the broader audience of biologists and lay public Mike Lynch's reformulation of the principles of genomics in terms of population genetics. Paraphrasing the famous pronouncement of Theodosius Dobzhansky, one of the Founding Fathers of the Modern Synthesis ["Nothing in biology makes sense except in the light of evolution."], Lynch wrote in one of his papers: "Nothing in evolution makes sense except in the sense of population genetics." That is absolutely true. The details of population genetic theory are difficult to explain even to biologists who are not specially trained, yet we have to communicate these ideas to a broader audience, including the lay public, and in qualitative terms. Suzan Mazur: How much of the research in your lab is bench experiments and how much is computer modeling? Eugene Koonin: That's easy, 100% of the research in my lab is computational, not necessarily modeling, but 100% is done by computer and 0% is done experimentally. Of course, we constantly collaborate with experimental laboratories. Suzan Mazur: In a 2009 paper of yours commenting on the 150th anniversary of the Origin of Species you make the following statement: "So, not to mince words, the Modern Synthesis is gone." Yet in your recent BioMed Central paper you write that it's time for biologists to start paying attention to population genetics because of advances in functional genomes. But population biology IS part of the Modern Synthesis. So your current position has some in the science community confused. Would you talk about the evolution of your thinking about evolution and begin by how you define "gene" and "genome"? Eugene Koonin: Such confusion makes one wish, at least for a moment, they never made such general statements aimed at a mass audience, yet I think such generalizations are necessary. There isn't really much change in my thinking. There isn't any dramatic change let alone a turn-around in my thinking. Population genetics is a mathematical framework that is essential for building evolutionary theory but it is not the theory itself. The Modern Synthesis does employ that framework and is a correct theory but only for a narrow range of evolutionary processes in certain groups of organisms. It is quite a typical situation in science, actually. Suzan Mazur: There's also a lot of confusion in the evolutionary biology community about what a gene is. For instance, Jim Shapiro says he doesn't think in terms of genes as entities. He thinks in terms of systems all the way down. Eugene Koonin: This is a completely different level of discussion. Let's try to separate it, whatever. I know exactly what Jim Shapiro said and a lot of people say. It's just a translation into a different language, from a somewhat different viewpoint. I do not disagree, genomes are dynamic systems evolving in space and time not static collections of genes. But it is also OK to view them as entities, information storage devices. These viewpoints are complementary. Coming back to the evolution of my thinking from 2009 to 2016, which really hasn't been much. Quite frankly, if I were writing what I wrote back in 2009, I would have been even more cautious and non-combative than I was then. I don't think I was ever really bombastic. But I would have been even less demonstrative and maybe I would not have written that the Modern Synthesis is gone. Suzan Mazur: I think your paper in 2009 does sort of leave the door open for the paper that you just published in BioMed Central. Eugene Koonin: Absolutely, all the doors were open. I would not say that it's [Modern Synthesis] gone just like that. It has to be understood in context. I think now any actively working scientist in evolutionary biology probably realizes that the Modern Synthesis or neo-Darwinism, or whatever the name is, is insufficient in the post-genomic era. This is a set of concepts that is insufficient for understanding the entirety of evolution. It doesn't mean it's wrong. It's only becoming wrong if someone claims that they need nothing past the concepts in the Modern Synthesis. Suzan Mazur: Again, there are complaints in the evolution science community that nothing ever seems to get solved. You've commented in the BMC paper that there continues to be a parade of just-so narratives and that "if biology is to evolve into a "hard" science with a solid theoretical core, it must be based on null models, no other path is known." You note further that null models are standard in physics but not in biology. Would you say more, beginning with your definition of "null model." Eugene Koonin: Sure. In any field, null model is the simplest explanation of the available data that does not violate physical laws. Good and sensible scientific practice in physics but also in other sciences. Scientists first come up with the simplest rational explanation of the available data and then see if anything in the data refutes that explanation and requires a more complex model. And so on and so forth. Suzan Mazur: Nigel Goldenfeld in recent years referred to biology as the "new condensed matter physics." Eugene Koonin: Yes. He wrote a paper with the late Carl Woese where they expressed this, and I agree. Maybe with a caveat. I would rather say biology has to become the new condensed matter physics. Suzan Mazur: At the November Royal Society public evolution meeting mentioned above, Sir Pat Bateson cautioned about the overuse of the metaphor of natural selection. And Richard Lewontin has famously said in the New York Review of Books that Darwin never meant the metaphorical term to be taken literally by generations of scientists. You keep natural selection in your most recent BMC paper and identify a family of selection terms: "weak selection," "purifying selection," "positive selection," "local selection," and "global selection." Aren't these all metaphorical as well and contrary to your interest in seeing biology "evolve into a 'hard' science"? Eugene Koonin: Well. Yes, these are metaphorical. From Darwin to this day. I also agree with Lewontin, Darwin did not mean natural selection to be taken literally. But we have to be, I guess, a little more specific about what it means to take natural selection or any kind of selection literally. It means, one would assume, the existence of a selecting agent. Perhaps making all these parallels between natural selection and artificial selection, the way Darwin does in his book, could be somewhat dangerous because in artificial selection there is someone who is selecting, even if unconsciously. In that respect, the evolutionary process is very different in nature where nothing is there to actually select. Darwin certainly realized this and wrote more precisely of "survival of the fittest." In modern evolutionary biology, it is sometimes "random survival" but the key point remains the same: organisms survive and leave progeny differentially. I think it is quite alright to denote some forms of differential survival selection, metaphorically. And there is no confusion here, within mainstream thinking. No one in the mainstream scientific community now takes selection literally. Suzan Mazur: You also say in the BMC paper: "Counterintuitive as this might seem, evolutionary reconstruction in my laboratory clearly indicates that the ancestral state in most major groups of eukaryotes and apparently the last common eukaryotic ancestor had an intron density close to that in extant animals." You note that introns persist in eukaryotes because introns invaded their genomes as mobile elements early on and that selection was too weak to get rid of them. You also say "the substantial majority" of introns harbor no detectable gene. What is the significance of this observation? And would you define, in this case, what you mean by intron because you cite two groups of introns in your October table of defined virus terms. Thank you for that paper, by the way -- it's very useful -- the paper in Studies in History and Philosophy of Science Part C. Eugene Koonin: Thank you. I appreciate that. What was said there in the virus paper? Suzan Mazur: You provide an extensive table of defined virus terms, and you identify two groups of introns: Group I and Group II. Eugene Koonin: We are going into technicalities here, so just very briefly. Prokaryotes also have genetic elements that are called introns but they're very, very different from eukaryotic introns. Prokaryotic introns are more like mobile elements, self-splicing introns, unlike the eukaryotic introns that just sit there and wait to be excised by the spliceosome. Prokaryotic introns are active. They have the machinery to excise themselves and even to move to a different location. There are two classes of such self-splicing introns, Group I and Group II, but the distinctions between these groups are important only for those who study these things. The point for the general reader is that the eukaryotic introns evolved from the Group II self-splicing introns, which invaded the genomes of early eukaryotes and then lost their mobility. Suzan Mazur: Would you touch on the possible importance of stem-loop RNA in origin and evolution of life? Eugene Koonin: It's a bit of an unexpected turn. All RNAs contain stems and loops, all RNAs that exist in life forms, in organisms are stem and loop structures. Suzan Mazur: Luis Villarreal is very keen on this idea. Eugene Koonin: I cannot right now comment on the specific statements of Luis. I simply don't remember them. Sounds very generic as long as one believes in the primordial RNA world, in some form. Yes, within the RNA world model, stem and loop structures are essential. But random stems and loops do not form the right structure, they cannot have ribozyme activity let alone complex ribozyme activity. So they are only starting material for pre-biological evolution, they do not solve any problems by themselves Suzan Mazur: In a presentation last year in Tokyo at ELSI (Earth-Life Science Institute) on the emergence of the biosphere, Uppsala University scientist Ajith Harish pointed out that "advances in our understanding of protein evolution indicate that tertiary structures of proteins are the molecular fossils of evolution while coding sequences are transients." Harish also says the Universal Common Ancestor of the contemporary Tree of Life (TOL) "is distinct from any specific modern descendant, that the Universal Common Ancestor was not the first cell lineage and that the modern TOL is the crown of a "recently" rerooted tree, that "bottlenecked survivors of an environmental collapse, which preceded the flourishing of the modern crown, seeded the current phylogenetic tree." Harish concludes that the "new data raises questions about traditional hypotheses based on sequence-based gene trees as well as divergence time estimates based on limited information in gene sequences," noting further that "there are so far no identifiable 'universal' viral genes that are common to viruses such as the ubiquitous cellular genes." Would you like to comment on this? Eugene Koonin: The short answer is no, I do not want to comment on that, because it's impossible to make any responsible comment on a long and complex quote like this unless I've heard the lecture (or much better yet, read the paper). There are a variety of things on which I would agree (for example, that protein structures are more conserved than sequences which is common knowledge) and a variety of things on which I cannot immediately agree. But the bottom line is I did not hear the lecture. Suzan Mazur: At the same ELSI meeting, Hiromi Saito from Osaka University questioned whether the common ancestor of bacteria had a cell wall noting, "many bacteria can transform themselves to a cell-wall-deficient state" called an "L-form." Do you have any thoughts about that? Eugene Koonin: I know very well what L-forms are, in particular with respect to their simple cell division mechanism. And this is an interesting possibility when we think about early evolution of cells. The modern L-forms obviously are derived, and comparative genomics tells us that the last common ancestor of bacteria probably did have a cell wall. Wall-less forms might have been important in evolution of cells but at an even earlier stage. Suzan Mazur: Would you like to make a final point? Eugene Koonin: Yes. I would like to come back to this issue of the Modern Synthesis, population genetics theory and the like because it is true that population genetics theory is part of the Modern Synthesis. And that is great. That is part of the power of the concept and why it remains quite relevant in explanations of microevolution but also an important part of the new evolutionary biology. That's what I wanted to convey in the BMC paper, that population genetics theory (in its modernized form because it too has not remained static over 50 years) has to be systematically applied in evolutionary genomics, which is the new mainstream of evolutionary biology. Indeed, it's changed dramatically over the last 25 years, and as previously mentioned, has completely transformed the ability to investigate, assess and measure evolutionary processes. The modern version of population genetics theory (it too has not remained static over 50 years) has to be actively, constantly and systematically applied to our understanding of genome evolution. That is too often not the case. The whole of Mike Lynch's work on this, his talks, papers and books are of paramount importance, even if I sometimes disagree with Mike on specific issues. The foundation Mike Lynch laid for modern evolutionary.. from DIYS http://ift.tt/2jIbFq9

[repwincoml4a0a5]

Eugene Koonin: "The New Evolutionary Biology"

Eugene Viktorovich Koonin "They should have invited Eugene Koonin," Canadian biochemist Larry Moran told me in the hallway during a break at the November Royal Society "new trends" in evolution conference in London -- somewhat exasperated by the proceedings. And I agreed. But Eugene Koonin doesn't quite see it that way, as he revealed during our recent conversation. Eugene Koonin is a consummate scientist, Leader of the Evolutionary Genomics Group at the National Center for Biotechnology Information, NIH, who sees science scandals and controversy as unproductive. He prefers the lab to the battlefield and is regarded as one of the most qualitative and prolific thinkers in science today (H-index 177; author of more than 600 scientific papers). But his numbers as a road runner are not bad either, per his Chevy Chase Turkey Chase stats. Eugene Koonin: #660 (photo by Antonio Estrada) In our interview that follows, Koonin sorts out any confusion over his recent statements about the importance of population genetics -- part of the Modern Synthesis -- and his 2009 statement: "Not to mince words the Modern Synthesis is gone." He agrees with Richard Lewontin that the term natural selection is metaphorical and goes further noting, "No one in the mainstream community now takes selection literally." And he also agrees with the Woese-Goldenfeld perspective about biology as "the new condensed matter physics," although Koonin thinks biology is still en route there. Eugene Koonin is the author of several books, among them The Logic of Chance: The Nature and Origin of Biological Evolution; and Sequence -- Evolution --Function: Computational Approaches in Comparative Genomics (with Michael Galperin). He is also founder and editor-in-chief of the journal Biology Direct. In 2002, Koonin and NCBI colleague Kira Makarova identified the genetic region now known as CRISPR-Cas. I spoke by phone with Eugene Koonin at his lab in Bethesda, Maryland. Suzan Mazur: Do you have any thoughts about the recent Royal Society meeting on new trends in evolutionary biology? Eugene Koonin: Yes. Perhaps there is a need to make some comment. I was quite unhappy reading at and around this public evolutionary meeting at the Royal Society. Frankly, I think that the less sensationalism, the less controversy brought into these discussions the better. It's really important that we try at all costs to do normal science rather than some sort of scandalous activity. I was happy about one thing, though -- that I was not there and was not directly involved. Suzan Mazur: Why is it so difficult to pull together the most compelling ideas in evolutionary biology and come up with an approximate understanding of how it all works? Michael Lynch once told me it was because reaching out to other fields is a "daunting task." But if scientists across the board won't come together to give us a coherent understanding of how it all works -- however approximate -- the public will lose confidence in the science establishment's ability to deliver. This is already beginning to happen. Would you comment? Eugene Koonin: First of all, I think the public may not have much to lose in terms of confidence in the scientific establishment in this case because the public is already extremely skeptical about the value and the scientific nature of evolutionary biology. It's not quite that way about science in general but I think largely so when it comes to the study of evolution. Much of the public is poorly informed about it, poorly understands it and is highly skeptical for various reasons. So I would frame the discussion a little differently, in the sense that evolutionary science may not be doing the best possible job to convince the public of the true importance of evolutionary biology. That said, I do believe that a coherent understanding of "how it works" is slowly but steadily emerging in evolutionary biology. However, one has to face the facts: first, it is a slow process, and we are still far from the goal; second, the emerging picture is highly complex and, furthermore, makes little sense without mathematical theory. Thus, communicating modern evolutionary biology (as opposed to deceptively simple antiquated ideas) is indeed a daunting task. Suzan Mazur: If you were organizing a public evolution summit, what discoveries in biology would you showcase? Eugene Koonin: I would try to focus on two aspects. One is genomics, and in particular, comparative genomics and metagenomics discoveries -- all this comes under the wide umbrella of genomics. That's one. The other is the existence of solid theory in evolutionary biology. I'll elaborate on both aspects. The first aspect, genomics, has in roughly the last 25 years completely transformed the ability to investigate, assess and measure evolutionary processes. All our conclusions on the course of evolution until the advent of genomics had been indirect. It's remarkable how many of these conclusions and findings remain relevant, but the fact is that all our ways to peer into the evolutionary process and evolutionary past had previously been indirect. Genomics now provides us windows into the evolutionary past by which we can compare directly the DNA and protein sequences from a rapidly widening range of organisms and thereby make solid conclusions about evolution. Suzan Mazur: Are you saying this is the top discovery in evolutionary biology in the last 50 years? Eugene Koonin: The word "discovery" may not apply quite directly here. It's a transformation of the whole science, which is based on a variety of discoveries. The very approach to evolutionary studies has changed completely. Not only the fact of evolution itself but the existence of deep evolutionary connections between different domains of life -- to be concrete -- evolutionary connections between, let us say, mammals, such as humans, and prokaryotes, bacteria and archaea, have become indisputable. These findings make questioning not only the reality of evolution but the evolutionary unity of all life on earth completely ridiculous and outside of the field of rational discourse. Then to be more specific, I would probably showcase the advances of metagenomics -- you know, the genomic revolution continues in the sense that now through metagenomics scientists are able to obtain a less and less biased picture of the diversity and evolution of life on Earth. It's becoming not so unrealistic to think about something approaching a complete picture of the evolutionary history of life. And then I would showcase something very specific. That is the latest discovery of the particular group of archaea that was the direct ancestor of eukaryotes. And in this case, "discovery" is the right word. There is a necessity to bring to the broader audience of biologists and lay public Mike Lynch's reformulation of the principles of genomics in terms of population genetics. Paraphrasing the famous pronouncement of Theodosius Dobzhansky, one of the Founding Fathers of the Modern Synthesis ["Nothing in biology makes sense except in the light of evolution."], Lynch wrote in one of his papers: "Nothing in evolution makes sense except in the sense of population genetics." That is absolutely true. The details of population genetic theory are difficult to explain even to biologists who are not specially trained, yet we have to communicate these ideas to a broader audience, including the lay public, and in qualitative terms. Suzan Mazur: How much of the research in your lab is bench experiments and how much is computer modeling? Eugene Koonin: That's easy, 100% of the research in my lab is computational, not necessarily modeling, but 100% is done by computer and 0% is done experimentally. Of course, we constantly collaborate with experimental laboratories. Suzan Mazur: In a 2009 paper of yours commenting on the 150th anniversary of the Origin of Species you make the following statement: "So, not to mince words, the Modern Synthesis is gone." Yet in your recent BioMed Central paper you write that it's time for biologists to start paying attention to population genetics because of advances in functional genomes. But population biology IS part of the Modern Synthesis. So your current position has some in the science community confused. Would you talk about the evolution of your thinking about evolution and begin by how you define "gene" and "genome"? Eugene Koonin: Such confusion makes one wish, at least for a moment, they never made such general statements aimed at a mass audience, yet I think such generalizations are necessary. There isn't really much change in my thinking. There isn't any dramatic change let alone a turn-around in my thinking. Population genetics is a mathematical framework that is essential for building evolutionary theory but it is not the theory itself. The Modern Synthesis does employ that framework and is a correct theory but only for a narrow range of evolutionary processes in certain groups of organisms. It is quite a typical situation in science, actually. Suzan Mazur: There's also a lot of confusion in the evolutionary biology community about what a gene is. For instance, Jim Shapiro says he doesn't think in terms of genes as entities. He thinks in terms of systems all the way down. Eugene Koonin: This is a completely different level of discussion. Let's try to separate it, whatever. I know exactly what Jim Shapiro said and a lot of people say. It's just a translation into a different language, from a somewhat different viewpoint. I do not disagree, genomes are dynamic systems evolving in space and time not static collections of genes. But it is also OK to view them as entities, information storage devices. These viewpoints are complementary. Coming back to the evolution of my thinking from 2009 to 2016, which really hasn't been much. Quite frankly, if I were writing what I wrote back in 2009, I would have been even more cautious and non-combative than I was then. I don't think I was ever really bombastic. But I would have been even less demonstrative and maybe I would not have written that the Modern Synthesis is gone. Suzan Mazur: I think your paper in 2009 does sort of leave the door open for the paper that you just published in BioMed Central. Eugene Koonin: Absolutely, all the doors were open. I would not say that it's [Modern Synthesis] gone just like that. It has to be understood in context. I think now any actively working scientist in evolutionary biology probably realizes that the Modern Synthesis or neo-Darwinism, or whatever the name is, is insufficient in the post-genomic era. This is a set of concepts that is insufficient for understanding the entirety of evolution. It doesn't mean it's wrong. It's only becoming wrong if someone claims that they need nothing past the concepts in the Modern Synthesis. Suzan Mazur: Again, there are complaints in the evolution science community that nothing ever seems to get solved. You've commented in the BMC paper that there continues to be a parade of just-so narratives and that "if biology is to evolve into a "hard" science with a solid theoretical core, it must be based on null models, no other path is known." You note further that null models are standard in physics but not in biology. Would you say more, beginning with your definition of "null model." Eugene Koonin: Sure. In any field, null model is the simplest explanation of the available data that does not violate physical laws. Good and sensible scientific practice in physics but also in other sciences. Scientists first come up with the simplest rational explanation of the available data and then see if anything in the data refutes that explanation and requires a more complex model. And so on and so forth. Suzan Mazur: Nigel Goldenfeld in recent years referred to biology as the "new condensed matter physics." Eugene Koonin: Yes. He wrote a paper with the late Carl Woese where they expressed this, and I agree. Maybe with a caveat. I would rather say biology has to become the new condensed matter physics. Suzan Mazur: At the November Royal Society public evolution meeting mentioned above, Sir Pat Bateson cautioned about the overuse of the metaphor of natural selection. And Richard Lewontin has famously said in the New York Review of Books that Darwin never meant the metaphorical term to be taken literally by generations of scientists. You keep natural selection in your most recent BMC paper and identify a family of selection terms: "weak selection," "purifying selection," "positive selection," "local selection," and "global selection." Aren't these all metaphorical as well and contrary to your interest in seeing biology "evolve into a 'hard' science"? Eugene Koonin: Well. Yes, these are metaphorical. From Darwin to this day. I also agree with Lewontin, Darwin did not mean natural selection to be taken literally. But we have to be, I guess, a little more specific about what it means to take natural selection or any kind of selection literally. It means, one would assume, the existence of a selecting agent. Perhaps making all these parallels between natural selection and artificial selection, the way Darwin does in his book, could be somewhat dangerous because in artificial selection there is someone who is selecting, even if unconsciously. In that respect, the evolutionary process is very different in nature where nothing is there to actually select. Darwin certainly realized this and wrote more precisely of "survival of the fittest." In modern evolutionary biology, it is sometimes "random survival" but the key point remains the same: organisms survive and leave progeny differentially. I think it is quite alright to denote some forms of differential survival selection, metaphorically. And there is no confusion here, within mainstream thinking. No one in the mainstream scientific community now takes selection literally. Suzan Mazur: You also say in the BMC paper: "Counterintuitive as this might seem, evolutionary reconstruction in my laboratory clearly indicates that the ancestral state in most major groups of eukaryotes and apparently the last common eukaryotic ancestor had an intron density close to that in extant animals." You note that introns persist in eukaryotes because introns invaded their genomes as mobile elements early on and that selection was too weak to get rid of them. You also say "the substantial majority" of introns harbor no detectable gene. What is the significance of this observation? And would you define, in this case, what you mean by intron because you cite two groups of introns in your October table of defined virus terms. Thank you for that paper, by the way -- it's very useful -- the paper in Studies in History and Philosophy of Science Part C. Eugene Koonin: Thank you. I appreciate that. What was said there in the virus paper? Suzan Mazur: You provide an extensive table of defined virus terms, and you identify two groups of introns: Group I and Group II. Eugene Koonin: We are going into technicalities here, so just very briefly. Prokaryotes also have genetic elements that are called introns but they're very, very different from eukaryotic introns. Prokaryotic introns are more like mobile elements, self-splicing introns, unlike the eukaryotic introns that just sit there and wait to be excised by the spliceosome. Prokaryotic introns are active. They have the machinery to excise themselves and even to move to a different location. There are two classes of such self-splicing introns, Group I and Group II, but the distinctions between these groups are important only for those who study these things. The point for the general reader is that the eukaryotic introns evolved from the Group II self-splicing introns, which invaded the genomes of early eukaryotes and then lost their mobility. Suzan Mazur: Would you touch on the possible importance of stem-loop RNA in origin and evolution of life? Eugene Koonin: It's a bit of an unexpected turn. All RNAs contain stems and loops, all RNAs that exist in life forms, in organisms are stem and loop structures. Suzan Mazur: Luis Villarreal is very keen on this idea. Eugene Koonin: I cannot right now comment on the specific statements of Luis. I simply don't remember them. Sounds very generic as long as one believes in the primordial RNA world, in some form. Yes, within the RNA world model, stem and loop structures are essential. But random stems and loops do not form the right structure, they cannot have ribozyme activity let alone complex ribozyme activity. So they are only starting material for pre-biological evolution, they do not solve any problems by themselves Suzan Mazur: In a presentation last year in Tokyo at ELSI (Earth-Life Science Institute) on the emergence of the biosphere, Uppsala University scientist Ajith Harish pointed out that "advances in our understanding of protein evolution indicate that tertiary structures of proteins are the molecular fossils of evolution while coding sequences are transients." Harish also says the Universal Common Ancestor of the contemporary Tree of Life (TOL) "is distinct from any specific modern descendant, that the Universal Common Ancestor was not the first cell lineage and that the modern TOL is the crown of a "recently" rerooted tree, that "bottlenecked survivors of an environmental collapse, which preceded the flourishing of the modern crown, seeded the current phylogenetic tree." Harish concludes that the "new data raises questions about traditional hypotheses based on sequence-based gene trees as well as divergence time estimates based on limited information in gene sequences," noting further that "there are so far no identifiable 'universal' viral genes that are common to viruses such as the ubiquitous cellular genes." Would you like to comment on this? Eugene Koonin: The short answer is no, I do not want to comment on that, because it's impossible to make any responsible comment on a long and complex quote like this unless I've heard the lecture (or much better yet, read the paper). There are a variety of things on which I would agree (for example, that protein structures are more conserved than sequences which is common knowledge) and a variety of things on which I cannot immediately agree. But the bottom line is I did not hear the lecture. Suzan Mazur: At the same ELSI meeting, Hiromi Saito from Osaka University questioned whether the common ancestor of bacteria had a cell wall noting, "many bacteria can transform themselves to a cell-wall-deficient state" called an "L-form." Do you have any thoughts about that? Eugene Koonin: I know very well what L-forms are, in particular with respect to their simple cell division mechanism. And this is an interesting possibility when we think about early evolution of cells. The modern L-forms obviously are derived, and comparative genomics tells us that the last common ancestor of bacteria probably did have a cell wall. Wall-less forms might have been important in evolution of cells but at an even earlier stage. Suzan Mazur: Would you like to make a final point? Eugene Koonin: Yes. I would like to come back to this issue of the Modern Synthesis, population genetics theory and the like because it is true that population genetics theory is part of the Modern Synthesis. And that is great. That is part of the power of the concept and why it remains quite relevant in explanations of microevolution but also an important part of the new evolutionary biology. That's what I wanted to convey in the BMC paper, that population genetics theory (in its modernized form because it too has not remained static over 50 years) has to be systematically applied in evolutionary genomics, which is the new mainstream of evolutionary biology. Indeed, it's changed dramatically over the last 25 years, and as previously mentioned, has completely transformed the ability to investigate, assess and measure evolutionary processes. The modern version of population genetics theory (it too has not remained static over 50 years) has to be actively, constantly and systematically applied to our understanding of genome evolution. That is too often not the case. The whole of Mike Lynch's work on this, his talks, papers and books are of paramount importance, even if I sometimes disagree with Mike on specific issues. The foundation Mike Lynch laid for modern evolutionary.. from DIYS http://ift.tt/2jIbFq9

[exfrenchdorsl4p0a1]

Eugene Koonin: "The New Evolutionary Biology"

Eugene Viktorovich Koonin "They should have invited Eugene Koonin," Canadian biochemist Larry Moran told me in the hallway during a break at the November Royal Society "new trends" in evolution conference in London -- somewhat exasperated by the proceedings. And I agreed. But Eugene Koonin doesn't quite see it that way, as he revealed during our recent conversation. Eugene Koonin is a consummate scientist, Leader of the Evolutionary Genomics Group at the National Center for Biotechnology Information, NIH, who sees science scandals and controversy as unproductive. He prefers the lab to the battlefield and is regarded as one of the most qualitative and prolific thinkers in science today (H-index 177; author of more than 600 scientific papers). But his numbers as a road runner are not bad either, per his Chevy Chase Turkey Chase stats. Eugene Koonin: #660 (photo by Antonio Estrada) In our interview that follows, Koonin sorts out any confusion over his recent statements about the importance of population genetics -- part of the Modern Synthesis -- and his 2009 statement: "Not to mince words the Modern Synthesis is gone." He agrees with Richard Lewontin that the term natural selection is metaphorical and goes further noting, "No one in the mainstream community now takes selection literally." And he also agrees with the Woese-Goldenfeld perspective about biology as "the new condensed matter physics," although Koonin thinks biology is still en route there. Eugene Koonin is the author of several books, among them The Logic of Chance: The Nature and Origin of Biological Evolution; and Sequence -- Evolution --Function: Computational Approaches in Comparative Genomics (with Michael Galperin). He is also founder and editor-in-chief of the journal Biology Direct. In 2002, Koonin and NCBI colleague Kira Makarova identified the genetic region now known as CRISPR-Cas. I spoke by phone with Eugene Koonin at his lab in Bethesda, Maryland. Suzan Mazur: Do you have any thoughts about the recent Royal Society meeting on new trends in evolutionary biology? Eugene Koonin: Yes. Perhaps there is a need to make some comment. I was quite unhappy reading at and around this public evolutionary meeting at the Royal Society. Frankly, I think that the less sensationalism, the less controversy brought into these discussions the better. It's really important that we try at all costs to do normal science rather than some sort of scandalous activity. I was happy about one thing, though -- that I was not there and was not directly involved. Suzan Mazur: Why is it so difficult to pull together the most compelling ideas in evolutionary biology and come up with an approximate understanding of how it all works? Michael Lynch once told me it was because reaching out to other fields is a "daunting task." But if scientists across the board won't come together to give us a coherent understanding of how it all works -- however approximate -- the public will lose confidence in the science establishment's ability to deliver. This is already beginning to happen. Would you comment? Eugene Koonin: First of all, I think the public may not have much to lose in terms of confidence in the scientific establishment in this case because the public is already extremely skeptical about the value and the scientific nature of evolutionary biology. It's not quite that way about science in general but I think largely so when it comes to the study of evolution. Much of the public is poorly informed about it, poorly understands it and is highly skeptical for various reasons. So I would frame the discussion a little differently, in the sense that evolutionary science may not be doing the best possible job to convince the public of the true importance of evolutionary biology. That said, I do believe that a coherent understanding of "how it works" is slowly but steadily emerging in evolutionary biology. However, one has to face the facts: first, it is a slow process, and we are still far from the goal; second, the emerging picture is highly complex and, furthermore, makes little sense without mathematical theory. Thus, communicating modern evolutionary biology (as opposed to deceptively simple antiquated ideas) is indeed a daunting task. Suzan Mazur: If you were organizing a public evolution summit, what discoveries in biology would you showcase? Eugene Koonin: I would try to focus on two aspects. One is genomics, and in particular, comparative genomics and metagenomics discoveries -- all this comes under the wide umbrella of genomics. That's one. The other is the existence of solid theory in evolutionary biology. I'll elaborate on both aspects. The first aspect, genomics, has in roughly the last 25 years completely transformed the ability to investigate, assess and measure evolutionary processes. All our conclusions on the course of evolution until the advent of genomics had been indirect. It's remarkable how many of these conclusions and findings remain relevant, but the fact is that all our ways to peer into the evolutionary process and evolutionary past had previously been indirect. Genomics now provides us windows into the evolutionary past by which we can compare directly the DNA and protein sequences from a rapidly widening range of organisms and thereby make solid conclusions about evolution. Suzan Mazur: Are you saying this is the top discovery in evolutionary biology in the last 50 years? Eugene Koonin: The word "discovery" may not apply quite directly here. It's a transformation of the whole science, which is based on a variety of discoveries. The very approach to evolutionary studies has changed completely. Not only the fact of evolution itself but the existence of deep evolutionary connections between different domains of life -- to be concrete -- evolutionary connections between, let us say, mammals, such as humans, and prokaryotes, bacteria and archaea, have become indisputable. These findings make questioning not only the reality of evolution but the evolutionary unity of all life on earth completely ridiculous and outside of the field of rational discourse. Then to be more specific, I would probably showcase the advances of metagenomics -- you know, the genomic revolution continues in the sense that now through metagenomics scientists are able to obtain a less and less biased picture of the diversity and evolution of life on Earth. It's becoming not so unrealistic to think about something approaching a complete picture of the evolutionary history of life. And then I would showcase something very specific. That is the latest discovery of the particular group of archaea that was the direct ancestor of eukaryotes. And in this case, "discovery" is the right word. There is a necessity to bring to the broader audience of biologists and lay public Mike Lynch's reformulation of the principles of genomics in terms of population genetics. Paraphrasing the famous pronouncement of Theodosius Dobzhansky, one of the Founding Fathers of the Modern Synthesis ["Nothing in biology makes sense except in the light of evolution."], Lynch wrote in one of his papers: "Nothing in evolution makes sense except in the sense of population genetics." That is absolutely true. The details of population genetic theory are difficult to explain even to biologists who are not specially trained, yet we have to communicate these ideas to a broader audience, including the lay public, and in qualitative terms. Suzan Mazur: How much of the research in your lab is bench experiments and how much is computer modeling? Eugene Koonin: That's easy, 100% of the research in my lab is computational, not necessarily modeling, but 100% is done by computer and 0% is done experimentally. Of course, we constantly collaborate with experimental laboratories. Suzan Mazur: In a 2009 paper of yours commenting on the 150th anniversary of the Origin of Species you make the following statement: "So, not to mince words, the Modern Synthesis is gone." Yet in your recent BioMed Central paper you write that it's time for biologists to start paying attention to population genetics because of advances in functional genomes. But population biology IS part of the Modern Synthesis. So your current position has some in the science community confused. Would you talk about the evolution of your thinking about evolution and begin by how you define "gene" and "genome"? Eugene Koonin: Such confusion makes one wish, at least for a moment, they never made such general statements aimed at a mass audience, yet I think such generalizations are necessary. There isn't really much change in my thinking. There isn't any dramatic change let alone a turn-around in my thinking. Population genetics is a mathematical framework that is essential for building evolutionary theory but it is not the theory itself. The Modern Synthesis does employ that framework and is a correct theory but only for a narrow range of evolutionary processes in certain groups of organisms. It is quite a typical situation in science, actually. Suzan Mazur: There's also a lot of confusion in the evolutionary biology community about what a gene is. For instance, Jim Shapiro says he doesn't think in terms of genes as entities. He thinks in terms of systems all the way down. Eugene Koonin: This is a completely different level of discussion. Let's try to separate it, whatever. I know exactly what Jim Shapiro said and a lot of people say. It's just a translation into a different language, from a somewhat different viewpoint. I do not disagree, genomes are dynamic systems evolving in space and time not static collections of genes. But it is also OK to view them as entities, information storage devices. These viewpoints are complementary. Coming back to the evolution of my thinking from 2009 to 2016, which really hasn't been much. Quite frankly, if I were writing what I wrote back in 2009, I would have been even more cautious and non-combative than I was then. I don't think I was ever really bombastic. But I would have been even less demonstrative and maybe I would not have written that the Modern Synthesis is gone. Suzan Mazur: I think your paper in 2009 does sort of leave the door open for the paper that you just published in BioMed Central. Eugene Koonin: Absolutely, all the doors were open. I would not say that it's [Modern Synthesis] gone just like that. It has to be understood in context. I think now any actively working scientist in evolutionary biology probably realizes that the Modern Synthesis or neo-Darwinism, or whatever the name is, is insufficient in the post-genomic era. This is a set of concepts that is insufficient for understanding the entirety of evolution. It doesn't mean it's wrong. It's only becoming wrong if someone claims that they need nothing past the concepts in the Modern Synthesis. Suzan Mazur: Again, there are complaints in the evolution science community that nothing ever seems to get solved. You've commented in the BMC paper that there continues to be a parade of just-so narratives and that "if biology is to evolve into a "hard" science with a solid theoretical core, it must be based on null models, no other path is known." You note further that null models are standard in physics but not in biology. Would you say more, beginning with your definition of "null model." Eugene Koonin: Sure. In any field, null model is the simplest explanation of the available data that does not violate physical laws. Good and sensible scientific practice in physics but also in other sciences. Scientists first come up with the simplest rational explanation of the available data and then see if anything in the data refutes that explanation and requires a more complex model. And so on and so forth. Suzan Mazur: Nigel Goldenfeld in recent years referred to biology as the "new condensed matter physics." Eugene Koonin: Yes. He wrote a paper with the late Carl Woese where they expressed this, and I agree. Maybe with a caveat. I would rather say biology has to become the new condensed matter physics. Suzan Mazur: At the November Royal Society public evolution meeting mentioned above, Sir Pat Bateson cautioned about the overuse of the metaphor of natural selection. And Richard Lewontin has famously said in the New York Review of Books that Darwin never meant the metaphorical term to be taken literally by generations of scientists. You keep natural selection in your most recent BMC paper and identify a family of selection terms: "weak selection," "purifying selection," "positive selection," "local selection," and "global selection." Aren't these all metaphorical as well and contrary to your interest in seeing biology "evolve into a 'hard' science"? Eugene Koonin: Well. Yes, these are metaphorical. From Darwin to this day. I also agree with Lewontin, Darwin did not mean natural selection to be taken literally. But we have to be, I guess, a little more specific about what it means to take natural selection or any kind of selection literally. It means, one would assume, the existence of a selecting agent. Perhaps making all these parallels between natural selection and artificial selection, the way Darwin does in his book, could be somewhat dangerous because in artificial selection there is someone who is selecting, even if unconsciously. In that respect, the evolutionary process is very different in nature where nothing is there to actually select. Darwin certainly realized this and wrote more precisely of "survival of the fittest." In modern evolutionary biology, it is sometimes "random survival" but the key point remains the same: organisms survive and leave progeny differentially. I think it is quite alright to denote some forms of differential survival selection, metaphorically. And there is no confusion here, within mainstream thinking. No one in the mainstream scientific community now takes selection literally. Suzan Mazur: You also say in the BMC paper: "Counterintuitive as this might seem, evolutionary reconstruction in my laboratory clearly indicates that the ancestral state in most major groups of eukaryotes and apparently the last common eukaryotic ancestor had an intron density close to that in extant animals." You note that introns persist in eukaryotes because introns invaded their genomes as mobile elements early on and that selection was too weak to get rid of them. You also say "the substantial majority" of introns harbor no detectable gene. What is the significance of this observation? And would you define, in this case, what you mean by intron because you cite two groups of introns in your October table of defined virus terms. Thank you for that paper, by the way -- it's very useful -- the paper in Studies in History and Philosophy of Science Part C. Eugene Koonin: Thank you. I appreciate that. What was said there in the virus paper? Suzan Mazur: You provide an extensive table of defined virus terms, and you identify two groups of introns: Group I and Group II. Eugene Koonin: We are going into technicalities here, so just very briefly. Prokaryotes also have genetic elements that are called introns but they're very, very different from eukaryotic introns. Prokaryotic introns are more like mobile elements, self-splicing introns, unlike the eukaryotic introns that just sit there and wait to be excised by the spliceosome. Prokaryotic introns are active. They have the machinery to excise themselves and even to move to a different location. There are two classes of such self-splicing introns, Group I and Group II, but the distinctions between these groups are important only for those who study these things. The point for the general reader is that the eukaryotic introns evolved from the Group II self-splicing introns, which invaded the genomes of early eukaryotes and then lost their mobility. Suzan Mazur: Would you touch on the possible importance of stem-loop RNA in origin and evolution of life? Eugene Koonin: It's a bit of an unexpected turn. All RNAs contain stems and loops, all RNAs that exist in life forms, in organisms are stem and loop structures. Suzan Mazur: Luis Villarreal is very keen on this idea. Eugene Koonin: I cannot right now comment on the specific statements of Luis. I simply don't remember them. Sounds very generic as long as one believes in the primordial RNA world, in some form. Yes, within the RNA world model, stem and loop structures are essential. But random stems and loops do not form the right structure, they cannot have ribozyme activity let alone complex ribozyme activity. So they are only starting material for pre-biological evolution, they do not solve any problems by themselves Suzan Mazur: In a presentation last year in Tokyo at ELSI (Earth-Life Science Institute) on the emergence of the biosphere, Uppsala University scientist Ajith Harish pointed out that "advances in our understanding of protein evolution indicate that tertiary structures of proteins are the molecular fossils of evolution while coding sequences are transients." Harish also says the Universal Common Ancestor of the contemporary Tree of Life (TOL) "is distinct from any specific modern descendant, that the Universal Common Ancestor was not the first cell lineage and that the modern TOL is the crown of a "recently" rerooted tree, that "bottlenecked survivors of an environmental collapse, which preceded the flourishing of the modern crown, seeded the current phylogenetic tree." Harish concludes that the "new data raises questions about traditional hypotheses based on sequence-based gene trees as well as divergence time estimates based on limited information in gene sequences," noting further that "there are so far no identifiable 'universal' viral genes that are common to viruses such as the ubiquitous cellular genes." Would you like to comment on this? Eugene Koonin: The short answer is no, I do not want to comment on that, because it's impossible to make any responsible comment on a long and complex quote like this unless I've heard the lecture (or much better yet, read the paper). There are a variety of things on which I would agree (for example, that protein structures are more conserved than sequences which is common knowledge) and a variety of things on which I cannot immediately agree. But the bottom line is I did not hear the lecture. Suzan Mazur: At the same ELSI meeting, Hiromi Saito from Osaka University questioned whether the common ancestor of bacteria had a cell wall noting, "many bacteria can transform themselves to a cell-wall-deficient state" called an "L-form." Do you have any thoughts about that? Eugene Koonin: I know very well what L-forms are, in particular with respect to their simple cell division mechanism. And this is an interesting possibility when we think about early evolution of cells. The modern L-forms obviously are derived, and comparative genomics tells us that the last common ancestor of bacteria probably did have a cell wall. Wall-less forms might have been important in evolution of cells but at an even earlier stage. Suzan Mazur: Would you like to make a final point? Eugene Koonin: Yes. I would like to come back to this issue of the Modern Synthesis, population genetics theory and the like because it is true that population genetics theory is part of the Modern Synthesis. And that is great. That is part of the power of the concept and why it remains quite relevant in explanations of microevolution but also an important part of the new evolutionary biology. That's what I wanted to convey in the BMC paper, that population genetics theory (in its modernized form because it too has not remained static over 50 years) has to be systematically applied in evolutionary genomics, which is the new mainstream of evolutionary biology. Indeed, it's changed dramatically over the last 25 years, and as previously mentioned, has completely transformed the ability to investigate, assess and measure evolutionary processes. The modern version of population genetics theory (it too has not remained static over 50 years) has to be actively, constantly and systematically applied to our understanding of genome evolution. That is too often not the case. The whole of Mike Lynch's work on this, his talks, papers and books are of paramount importance, even if I sometimes disagree with Mike on specific issues. The foundation Mike Lynch laid for modern evolutionary.. from DIYS http://ift.tt/2jIbFq9