<?php
class B{
    public $a=0;
    public $b=0;
}
class A extends ArrayObject{
    public $genes;
    public $pairs;
    function __construct(){
        $this->pairs = array(new B, new B, new B);
        foreach($this->pairs as &$pair){
            $this->genes[] = &$pair->a;
            $this->genes[] = &$pair->b;
        }
    }
    function __clone() {
        $this->genes = array();
        foreach ($this->pairs as $i => $pair){
            $p = clone $pair;
            $this->pairs[$i] = $p;
            $this->genes[($i  )*2] = &$p->a;
            $this->genes[($i+1)*2] = &$p->b;
        }
    }
}

$a = new A;
$a->pairs[1]->a = 11;
$a->genes[3] = 22;
echo "print_r(\$a)\n";
print_r($a);

$b = clone $a;
echo "print_r(\$b)\n";
print_r($b);
$b->pairs[1]->a = 88;
$b->genes[3] = 44;
echo "print_r(\$b)\n";
print_r($b);
echo "print_r(\$a)\n";
print_r($a);